@article{berto_detection_2017,
	title = {Detection of potentially novel paramyxovirus and coronavirus viral {RNA} in bats and rats in the {Mekong} {Delta} region of southern {Viet} {Nam}.},
	copyright = {(c) 2017 The Authors. Zoonoses and Public Health Published by Blackwell Verlag GmbH.},
	issn = {1863-2378 1863-1959},
	doi = {10.1111/zph.12362},
	abstract = {Bats and rodents are being increasingly recognized as reservoirs of emerging zoonotic viruses. Various studies have investigated bat viruses in tropical regions, but to date there are no data regarding viruses with zoonotic potential  that circulate in bat and rat populations in Viet Nam. To address this paucity of data, we sampled three bat farms and three wet markets trading in rat meat in the Mekong Delta region of southern Viet Nam. Faecal and urine samples were screened  for the presence of RNA from paramyxoviruses, coronaviruses and filoviruses. Paramyxovirus RNA was detected in 4 of 248 (1\%) and 11 of 222 (4.9\%) bat faecal and urine samples, respectively. Coronavirus RNA was detected in 55 of 248 (22\%)  of bat faecal samples; filovirus RNA was not detected in any of the bat samples.  Further, coronavirus RNA was detected in 12 of 270 (4.4\%) of rat faecal samples;  all samples tested negative for paramyxovirus. Phylogenetic analysis revealed that the bat paramyxoviruses and bat and rat coronaviruses were related to viruses circulating in bat and rodent populations globally, but showed no cross-species mixing of viruses between bat and rat populations within Viet Nam.  Our study shows that potentially novel variants of paramyxoviruses and coronaviruses commonly circulate in bat and rat populations in Viet Nam. Further  characterization of the viruses and additional human and animal surveillance is required to evaluate the likelihood of viral spillover and to assess whether these viruses pose a risk to human health.},
	language = {eng},
	journal = {Zoonoses and public health},
	author = {Berto, A. and Anh, P. H. and Carrique-Mas, J. J. and Simmonds, P. and Van Cuong, N. and Tue, N. T. and Van Dung, N. and Woolhouse, M. E. and Smith, I. and Marsh, G. A. and Bryant, J. E. and Thwaites, G. E. and Baker, S. and Rabaa, M. A.},
	month = apr,
	year = {2017},
	pmid = {28418192},
	keywords = {Rats, Viet Nam, bats, coronavirus, paramyxovirus, zoonotic viruses},
}

Bats and rodents are being increasingly recognized as reservoirs of emerging zoonotic viruses. Various studies have investigated bat viruses in tropical regions, but to date there are no data regarding viruses with zoonotic potential that circulate in bat and rat populations in Viet Nam. To address this paucity of data, we sampled three bat farms and three wet markets trading in rat meat in the Mekong Delta region of southern Viet Nam. Faecal and urine samples were screened for the presence of RNA from paramyxoviruses, coronaviruses and filoviruses. Paramyxovirus RNA was detected in 4 of 248 (1%) and 11 of 222 (4.9%) bat faecal and urine samples, respectively. Coronavirus RNA was detected in 55 of 248 (22%) of bat faecal samples; filovirus RNA was not detected in any of the bat samples. Further, coronavirus RNA was detected in 12 of 270 (4.4%) of rat faecal samples; all samples tested negative for paramyxovirus. Phylogenetic analysis revealed that the bat paramyxoviruses and bat and rat coronaviruses were related to viruses circulating in bat and rodent populations globally, but showed no cross-species mixing of viruses between bat and rat populations within Viet Nam. Our study shows that potentially novel variants of paramyxoviruses and coronaviruses commonly circulate in bat and rat populations in Viet Nam. Further characterization of the viruses and additional human and animal surveillance is required to evaluate the likelihood of viral spillover and to assess whether these viruses pose a risk to human health.

@article{dung_universal_2017,
	title = {A universal genome sequencing method for rotavirus {A} from human fecal samples which identifies segment reassortment and multi-genotype mixed infection.},
	volume = {18},
	issn = {1471-2164 1471-2164},
	doi = {10.1186/s12864-017-3714-6},
	abstract = {BACKGROUND: Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS: To overcome these limitations, we developed a novel RoV capture and genome sequencing method combining commercial enzyme immunoassay plates and a set of routinely used reagents. RESULTS: Our approach had a 100\% success rate, producing {\textgreater}90\% genome coverage for diverse RoV present in fecal samples (Ct {\textless} 30). CONCLUSIONS: This method provides a novel, reproducible and comparatively simple approach for genomic RoV characterization and could be scaled-up for use in global RoV surveillance systems. TRIAL REGISTRATION (PROSPECTIVELY REGISTERED): Current Controlled Trials ISRCTN88101063 . Date of registration: 14/06/2012.},
	language = {eng},
	number = {1},
	journal = {BMC genomics},
	author = {Dung, Tran Thi Ngoc and Duy, Pham Thanh and Sessions, October M. and Sangumathi, Uma K. and Phat, Voong Vinh and Tam, Pham Thi Thanh and To, Nguyen Thi Nguyen and Phuc, Tran My and Hong Chau, Tran Thi and Chau, Nguyen Ngoc Minh and Minh, Ngoc Nguyen and Thwaites, Guy E. and Rabaa, Maia A. and Baker, Stephen},
	month = apr,
	year = {2017},
	pmid = {28438140},
	pmcid = {PMC5404283},
	keywords = {Antibody capture, Co-infection, Genome sequencing, Genomics, Phylogenetics, Reassortment, Rotavirus A},
	pages = {324},
}

BACKGROUND: Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS: To overcome these limitations, we developed a novel RoV capture and genome sequencing method combining commercial enzyme immunoassay plates and a set of routinely used reagents. RESULTS: Our approach had a 100% success rate, producing \textgreater90% genome coverage for diverse RoV present in fecal samples (Ct \textless 30). CONCLUSIONS: This method provides a novel, reproducible and comparatively simple approach for genomic RoV characterization and could be scaled-up for use in global RoV surveillance systems. TRIAL REGISTRATION (PROSPECTIVELY REGISTERED): Current Controlled Trials ISRCTN88101063 . Date of registration: 14/06/2012.

@article{phan_unbiased_2016,
	title = {Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection},
	copyright = {© 2016, Published by Cold Spring Harbor Laboratory Press. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	url = {http://www.biorxiv.org/content/early/2016/06/14/058875},
	doi = {10.1101/058875},
	abstract = {Coordinated and synchronous virological surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus is an important cause of viral gastroenteritis in humans and animals. We have documented the rotavirus diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of 60 human rotaviruses (all group A) and 31 porcine rotaviruses (13 group A, 7 group B, 6 group C and 5 group H). Phylogenetic analyses showed the co-circulation of multiple distinct rotavirus group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C and H, none of which have been previously reported in Vietnam. Furthermore the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event.},
	language = {en},
	urldate = {2017-07-06},
	journal = {bioRxiv},
	author = {Phan, My V. T. and Anh, Pham Hong and Cuong, Nguyen Van and Munnink, Bas B. Oude and Hoek, Lia van der and My, Phuc Tran and Tri, Tue Ngo and Bryant, Juliet E. and Baker, Stephen and Thwaites, Guy and Woolhouse, Mark and Kellam, Paul and Rabaa, Maia A. and Cotten, Matthew L.},
	month = jun,
	year = {2016},
	pages = {058875},
}

Coordinated and synchronous virological surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus is an important cause of viral gastroenteritis in humans and animals. We have documented the rotavirus diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of 60 human rotaviruses (all group A) and 31 porcine rotaviruses (13 group A, 7 group B, 6 group C and 5 group H). Phylogenetic analyses showed the co-circulation of multiple distinct rotavirus group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C and H, none of which have been previously reported in Vietnam. Furthermore the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event.

@article{holmes_evolution_2016,
	title = {The evolution of {Ebola} virus: {Insights} from the 2013-2016 epidemic.},
	volume = {538},
	issn = {1476-4687 0028-0836},
	doi = {10.1038/nature19790},
	abstract = {The 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude and changed our perspective on this lethal but sporadically emerging virus. This outbreak also marked the beginning of large-scale real-time molecular epidemiology. Here, we show how evolutionary analyses of Ebola virus genome sequences provided key insights into virus origins, evolution and spread during the epidemic. We provide basic scientists, epidemiologists, medical practitioners and other outbreak responders with an enhanced understanding of the utility and limitations of pathogen genomic sequencing. This will be crucially important in our attempts to track and control future infectious disease outbreaks.},
	language = {eng},
	number = {7624},
	journal = {Nature},
	author = {Holmes, Edward C. and Dudas, Gytis and Rambaut, Andrew and Andersen, Kristian G.},
	month = oct,
	year = {2016},
	pmid = {27734858},
	keywords = {*Evolution, Molecular, Animals, Ebolavirus/classification/*genetics, Genome, Viral/genetics, Hemorrhagic Fever, Ebola/*epidemiology/*virology, Humans, Molecular Epidemiology, Phenotype, Public Health},
	pages = {193--200},
}

The 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude and changed our perspective on this lethal but sporadically emerging virus. This outbreak also marked the beginning of large-scale real-time molecular epidemiology. Here, we show how evolutionary analyses of Ebola virus genome sequences provided key insights into virus origins, evolution and spread during the epidemic. We provide basic scientists, epidemiologists, medical practitioners and other outbreak responders with an enhanced understanding of the utility and limitations of pathogen genomic sequencing. This will be crucially important in our attempts to track and control future infectious disease outbreaks.

@article{huong_temporal_2016,
	title = {Temporal and spatial association of {Streptococcus} suis infection in humans and porcine reproductive and respiratory syndrome outbreaks in pigs in northern {Vietnam}.},
	volume = {144},
	issn = {1469-4409 0950-2688},
	doi = {10.1017/S0950268815000990},
	abstract = {Porcine reproductive and respiratory syndrome (PRRS) outbreaks in pigs are associated with increased susceptibility of pigs to secondary bacterial infections, including Streptococcus suis - an important zoonotic pathogen causing bacterial meningitis in humans. This case-control study examined the association  between human S. suis infection and PRRS outbreaks in pigs in northern Vietnam. We included 90 S. suis case-patients and 183 non-S. suis sepsis controls from a referral hospital in Hanoi in 2010, a period of major PRRS epizootics in Vietnam. PRRS exposure was determined using data from the National Centre of Veterinary Diagnosis. By univariate analysis, significantly more S. suis patients were reported residing in or adjacent to a PRRS district compared to controls [odds ratio (OR) 2.82, 95\% confidence interval (CI) 1.35-5.89 and OR 3.15, 95\% CI 1.62-6.15, respectively]. Only residency in adjacent districts remained significantly associated with risk of S. suis infection after adjusting for sex,  occupation, and eating practices. SaTScan analysis showed a possible cluster of S. suis infection in humans around PRRS confirmed locations during the March-August period. The findings indicate an epidemiological association between PRRS in pigs and S. suis infections in humans. Effective strategies to strengthen control of PRRS in pigs may help reduce transmission of S. suis infection to humans.},
	language = {eng},
	number = {1},
	journal = {Epidemiology and infection},
	author = {Huong, V. T. L. and Thanh, L. V. and Phu, V. D. and Trinh, D. T. and Inui, K. and Tung, N. and Oanh, N. T. K. and Trung, N. V. and Hoa, N. T. and Bryant, J. E. and Horby, P. W. and Kinh, N. V. and Wertheim, H. F. L.},
	month = jan,
	year = {2016},
	pmid = {25997360},
	pmcid = {PMC4697300},
	keywords = {Animals, Case-control, Disease Outbreaks/*veterinary, Humans, Porcine Reproductive and Respiratory Syndrome/*epidemiology/virology, Porcine respiratory and reproductive syndrome virus/*physiology, Risk Factors, Streptococcal Infections/*epidemiology/microbiology, Streptococcus suis, Streptococcus suis/*physiology, Swine, Vietnam, Vietnam/epidemiology, pigs, porcine reproductive and respiratory syndrome, secondary infection, zoonosis},
	pages = {35--44},
}

Porcine reproductive and respiratory syndrome (PRRS) outbreaks in pigs are associated with increased susceptibility of pigs to secondary bacterial infections, including Streptococcus suis - an important zoonotic pathogen causing bacterial meningitis in humans. This case-control study examined the association between human S. suis infection and PRRS outbreaks in pigs in northern Vietnam. We included 90 S. suis case-patients and 183 non-S. suis sepsis controls from a referral hospital in Hanoi in 2010, a period of major PRRS epizootics in Vietnam. PRRS exposure was determined using data from the National Centre of Veterinary Diagnosis. By univariate analysis, significantly more S. suis patients were reported residing in or adjacent to a PRRS district compared to controls [odds ratio (OR) 2.82, 95% confidence interval (CI) 1.35-5.89 and OR 3.15, 95% CI 1.62-6.15, respectively]. Only residency in adjacent districts remained significantly associated with risk of S. suis infection after adjusting for sex, occupation, and eating practices. SaTScan analysis showed a possible cluster of S. suis infection in humans around PRRS confirmed locations during the March-August period. The findings indicate an epidemiological association between PRRS in pigs and S. suis infections in humans. Effective strategies to strengthen control of PRRS in pigs may help reduce transmission of S. suis infection to humans.

@article{noauthor_role_2016,
	title = {Role for migratory wild birds in the global spread of avian influenza {H5N8}.},
	volume = {354},
	copyright = {Copyright (c) 2016, American Association for the Advancement of Science.},
	issn = {1095-9203 0036-8075},
	doi = {10.1126/science.aaf8852},
	abstract = {Avian influenza viruses affect both poultry production and public health. A subtype H5N8 (clade 2.3.4.4) virus, following an outbreak in poultry in South Korea in January 2014, rapidly spread worldwide in 2014-2015. Our analysis of H5N8 viral sequences, epidemiological investigations, waterfowl migration, and poultry trade showed that long-distance migratory birds can play a major role in  the global spread of avian influenza viruses. Further, we found that the hemagglutinin of clade 2.3.4.4 virus was remarkably promiscuous, creating reassortants with multiple neuraminidase subtypes. Improving our understanding of the circumpolar circulation of avian influenza viruses in migratory waterfowl will help to provide early warning of threats from avian influenza to poultry, and potentially human, health.},
	language = {eng},
	number = {6309},
	journal = {Science (New York, N.Y.)},
	month = oct,
	year = {2016},
	pmid = {27738169},
	keywords = {*Animal Migration, *Disease Outbreaks, Animals, Birds, Europe/epidemiology, Hemagglutinins/genetics, Humans, Influenza A Virus, H5N8 Subtype/*classification/genetics/isolation \& purification, Influenza in Birds/*epidemiology/virology, Influenza, Human/*epidemiology/virology, Japan, Neuraminidase/genetics, North America/epidemiology, Phylogeography, Poultry, Reassortant Viruses/*classification/genetics/isolation \& purification, Republic of Korea/epidemiology},
	pages = {213--217},
}

Avian influenza viruses affect both poultry production and public health. A subtype H5N8 (clade 2.3.4.4) virus, following an outbreak in poultry in South Korea in January 2014, rapidly spread worldwide in 2014-2015. Our analysis of H5N8 viral sequences, epidemiological investigations, waterfowl migration, and poultry trade showed that long-distance migratory birds can play a major role in the global spread of avian influenza viruses. Further, we found that the hemagglutinin of clade 2.3.4.4 virus was remarkably promiscuous, creating reassortants with multiple neuraminidase subtypes. Improving our understanding of the circumpolar circulation of avian influenza viruses in migratory waterfowl will help to provide early warning of threats from avian influenza to poultry, and potentially human, health.

@article{arias_rapid_2016,
	title = {Rapid outbreak sequencing of {Ebola} virus in {Sierra} {Leone} identifies transmission chains linked to sporadic cases},
	volume = {2},
	url = {https://academic.oup.com/ve/article/2/1/vew016/1753554/Rapid-outbreak-sequencing-of-Ebola-virus-in-Sierra},
	doi = {10.1093/ve/vew016},
	number = {1},
	urldate = {2017-07-06},
	journal = {Virus Evolution},
	author = {Arias, Armando and Watson, Simon J. and Asogun, Danny and Tobin, Ekaete Alice and Lu, Jia and Phan, My V. T. and Jah, Umaru and Wadoum, Raoul Emeric Guetiya and Meredith, Luke and Thorne, Lucy and Caddy, Sarah and Tarawalie, Alimamy and Langat, Pinky and Dudas, Gytis and Faria, Nuno R. and Dellicour, Simon and Kamara, Abdul and Kargbo, Brima and Kamara, Brima Osaio and Gevao, Sahr and Cooper, Daniel and Newport, Matthew and Horby, Peter and Dunning, Jake and Sahr, Foday and Brooks, Tim and Simpson, Andrew J. H. and Groppelli, Elisabetta and Liu, Guoying and Mulakken, Nisha and Rhodes, Kate and Akpablie, James and Yoti, Zabulon and Lamunu, Margaret and Vitto, Esther and Otim, Patrick and Owilli, Collins and Boateng, Isaac and Okoror, Lawrence and Omomoh, Emmanuel and Oyakhilome, Jennifer and Omiunu, Racheal and Yemisis, Ighodalo and Adomeh, Donatus and Ehikhiametalor, Solomon and Akhilomen, Patience and Aire, Chris and Kurth, Andreas and Cook, Nicola and Baumann, Jan and Gabriel, Martin and Wölfel, Roman and Di Caro, Antonino and Carroll, Miles W. and Günther, Stephan and Redd, John and Naidoo, Dhamari and Pybus, Oliver G. and Rambaut, Andrew and Kellam, Paul and Goodfellow, Ian and Cotten, Matthew},
	month = jan,
	year = {2016},
}

@article{nickbakhsh_modelling_2016,
	title = {Modelling the impact of co-circulating low pathogenic avian influenza viruses on  epidemics of highly pathogenic avian influenza in poultry.},
	volume = {17},
	copyright = {Copyright (c) 2016 The Authors. Published by Elsevier B.V. All rights reserved.},
	issn = {1878-0067 1878-0067},
	doi = {10.1016/j.epidem.2016.10.005},
	abstract = {It is well known that highly pathogenic avian influenza (HPAI) viruses emerge through mutation of precursor low pathogenic avian influenza (LPAI) viruses in domestic poultry populations. The potential for immunological cross-protection between these pathogenic variants is recognised but the epidemiological impact during co-circulation is not well understood. Here we use mathematical models to  investigate whether altered flock infection parameters consequent to primary LPAI infections can impact on the spread of HPAI at the population level. First we used mechanistic models reflecting the co-circulatory dynamics of LPAI and HPAI within a single commercial poultry flock. We found that primary infections with LPAI led to HPAI prevalence being maximised under a scenario of high but partial  cross-protection. We then tested the population impact in spatially-explicit simulations motivated by a major avian influenza A(H7N1) epidemic that afflicted  the Italian poultry industry in 1999-2001. We found that partial cross-protection can lead to a prolongation of HPAI epidemic duration. Our findings have implications for the control of HPAI in poultry particularly for settings in which LPAI and HPAI frequently co-circulate.},
	language = {eng},
	journal = {Epidemics},
	author = {Nickbakhsh, Sema and Hall, Matthew D. and Dorigatti, Ilaria and Lycett, Samantha J. and Mulatti, Paolo and Monne, Isabella and Fusaro, Alice and Woolhouse, Mark E. J. and Rambaut, Andrew and Kao, Rowland R.},
	month = dec,
	year = {2016},
	pmid = {27788412},
	keywords = {Cross-protection, Epidemiology, Interference, Mathematical models, Poultry},
	pages = {27--34},
}

It is well known that highly pathogenic avian influenza (HPAI) viruses emerge through mutation of precursor low pathogenic avian influenza (LPAI) viruses in domestic poultry populations. The potential for immunological cross-protection between these pathogenic variants is recognised but the epidemiological impact during co-circulation is not well understood. Here we use mathematical models to investigate whether altered flock infection parameters consequent to primary LPAI infections can impact on the spread of HPAI at the population level. First we used mechanistic models reflecting the co-circulatory dynamics of LPAI and HPAI within a single commercial poultry flock. We found that primary infections with LPAI led to HPAI prevalence being maximised under a scenario of high but partial cross-protection. We then tested the population impact in spatially-explicit simulations motivated by a major avian influenza A(H7N1) epidemic that afflicted the Italian poultry industry in 1999-2001. We found that partial cross-protection can lead to a prolongation of HPAI epidemic duration. Our findings have implications for the control of HPAI in poultry particularly for settings in which LPAI and HPAI frequently co-circulate.

@article{van_dung_large-scale_2016,
	title = {Large-scale screening and characterization of enteroviruses and kobuviruses infecting pigs in {Vietnam}.},
	volume = {97},
	issn = {1465-2099 0022-1317},
	doi = {10.1099/jgv.0.000366},
	abstract = {A recent survey of pigs in Dong Thap province, Vietnam identified a high frequency of enterovirus species G (EV-G) infection (144/198; 72.7\%). Amongst these was a plethora of EV-G types (EV-G1, EV-G6 and four new types},
	language = {eng},
	number = {2},
	journal = {The Journal of general virology},
	author = {Van Dung, Nguyen and Anh, Pham Hong and Van Cuong, Nguyen and Hoa, Ngo Thi and Carrique-Mas, Juan and Hien, Vo Be and Sharp, C. and Rabaa, M. and Berto, A. and Campbell, James and Baker, Stephen and Farrar, Jeremy and Woolhouse, Mark E. and Bryant, Juliet E. and Simmonds, Peter},
	month = feb,
	year = {2016},
	pmid = {26653281},
	pmcid = {PMC5115164},
	keywords = {Animals, Diarrhea/epidemiology/veterinary/virology, Enterovirus Infections/epidemiology/*veterinary/virology, Enterovirus/classification/genetics/*isolation \& purification, Feces/*virology, Genetic Variation, Kobuvirus/classification/genetics/*isolation \& purification, Mass Screening, Picornaviridae Infections/epidemiology/*veterinary/virology, Prevalence, Sus scrofa, Swine, Swine Diseases/*epidemiology/*virology, Vietnam/epidemiology, Viral Load},
	pages = {378--388},
}

A recent survey of pigs in Dong Thap province, Vietnam identified a high frequency of enterovirus species G (EV-G) infection (144/198; 72.7%). Amongst these was a plethora of EV-G types (EV-G1, EV-G6 and four new types

@article{phu_huong_lan_invasive_2016,
	title = {Invasive {Non}-typhoidal {Salmonella} {Infections} in {Asia}: {Clinical} {Observations}, {Disease} {Outcome} and {Dominant} {Serovars} from an {Infectious} {Disease} {Hospital} in {Vietnam}.},
	volume = {10},
	issn = {1935-2735 1935-2727},
	doi = {10.1371/journal.pntd.0004857},
	abstract = {Invasive non-typhoidal Salmonella (iNTS) infections are now a well-described cause of morbidity and mortality in children and HIV-infected adults in sub-Saharan Africa. In contrast, the epidemiology and clinical manifestations of  iNTS disease in Asia are not well documented. We retrospectively identified {\textgreater}100  cases of iNTS infections in an infectious disease hospital in Southern Vietnam between 2008 and 2013. Clinical records were accessed to evaluate demographic and clinical factors associated with iNTS infection and to identify risk factors associated with death. Multi-locus sequence typing and antimicrobial susceptibility testing was performed on all organisms. Of 102 iNTS patients, 71\%  were HIV-infected, {\textgreater}90\% were adults, 71\% were male and 33\% reported intravenous drug use. Twenty-six/92 (28\%) patients with a known outcome died; HIV infection was significantly associated with death (p = 0.039). S. Enteritidis (Sequence Types (ST)11) (48\%, 43/89) and S. Typhimurium (ST19, 34 and 1544) (26\%, 23/89) were the most commonly identified serovars; S. Typhimurium was significantly more common in HIV-infected individuals (p = 0.003). Isolates from HIV-infected patients were more likely to exhibit reduced susceptibility against trimethoprim-sulfamethoxazole than HIV-negative patients (p = 0.037). We conclude that iNTS disease is a severe infection in Vietnam with a high mortality rate. As in sub-Saharan Africa, HIV infection was a risk factor for death, with the majority of the burden in this population found in HIV-infected adult men.},
	language = {eng},
	number = {8},
	journal = {PLoS neglected tropical diseases},
	author = {Phu Huong Lan, Nguyen and Le Thi Phuong, Tu and Nguyen Huu, Hien and Thuy, Le and Mather, Alison E. and Park, Se Eun and Marks, Florian and Thwaites, Guy E. and Van Vinh Chau, Nguyen and Thompson, Corinne N. and Baker, Stephen},
	month = aug,
	year = {2016},
	pmid = {27513951},
	pmcid = {PMC4981332},
	keywords = {Adult, Aged, Anti-Infective Agents/therapeutic use, Ceftriaxone/therapeutic use, Drug Therapy, Combination, Female, Fluoroquinolones/therapeutic use, HIV Infections/epidemiology/*microbiology, Hospitals, Humans, Logistic Models, Male, Middle Aged, Multilocus Sequence Typing, Multivariate Analysis, Retrospective Studies, Salmonella Infections/drug therapy/*epidemiology/*mortality, Salmonella enterica/classification/isolation \& purification, Serogroup, Sex Factors, Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use, Typhoid Fever, Vietnam/epidemiology},
	pages = {e0004857},
}

Invasive non-typhoidal Salmonella (iNTS) infections are now a well-described cause of morbidity and mortality in children and HIV-infected adults in sub-Saharan Africa. In contrast, the epidemiology and clinical manifestations of iNTS disease in Asia are not well documented. We retrospectively identified \textgreater100 cases of iNTS infections in an infectious disease hospital in Southern Vietnam between 2008 and 2013. Clinical records were accessed to evaluate demographic and clinical factors associated with iNTS infection and to identify risk factors associated with death. Multi-locus sequence typing and antimicrobial susceptibility testing was performed on all organisms. Of 102 iNTS patients, 71% were HIV-infected, \textgreater90% were adults, 71% were male and 33% reported intravenous drug use. Twenty-six/92 (28%) patients with a known outcome died; HIV infection was significantly associated with death (p = 0.039). S. Enteritidis (Sequence Types (ST)11) (48%, 43/89) and S. Typhimurium (ST19, 34 and 1544) (26%, 23/89) were the most commonly identified serovars; S. Typhimurium was significantly more common in HIV-infected individuals (p = 0.003). Isolates from HIV-infected patients were more likely to exhibit reduced susceptibility against trimethoprim-sulfamethoxazole than HIV-negative patients (p = 0.037). We conclude that iNTS disease is a severe infection in Vietnam with a high mortality rate. As in sub-Saharan Africa, HIV infection was a risk factor for death, with the majority of the burden in this population found in HIV-infected adult men.

@article{agoti_human_2016,
	title = {Human {Rhinovirus} {B} and {C} {Genomes} from {Rural} {Coastal} {Kenya}.},
	volume = {4},
	copyright = {Copyright (c) 2016 Agoti et al.},
	issn = {2169-8287},
	doi = {10.1128/genomeA.00751-16},
	abstract = {Primer-independent agnostic deep sequencing was used to generate three human rhinovirus (HRV) B genomes and one HRV C genome from samples collected in a household respiratory survey in rural coastal Kenya. The study provides the first rhinovirus genomes from Kenya and will help improve the sensitivity of local molecular diagnostics.},
	language = {eng},
	number = {4},
	journal = {Genome announcements},
	author = {Agoti, Charles N. and Kiyuka, Patience K. and Kamau, Everlyn and Munywoki, Patrick K. and Bett, Anne and van der Hoek, Lia and Kellam, Paul and Nokes, D. James and Cotten, Matthew},
	month = jul,
	year = {2016},
	pmid = {27469941},
	pmcid = {PMC4966474},
}

Primer-independent agnostic deep sequencing was used to generate three human rhinovirus (HRV) B genomes and one HRV C genome from samples collected in a household respiratory survey in rural coastal Kenya. The study provides the first rhinovirus genomes from Kenya and will help improve the sensitivity of local molecular diagnostics.

@article{woolhouse_global_2016,
	title = {Global disease burden due to antibiotic resistance - state of the evidence.},
	volume = {6},
	issn = {2047-2986 2047-2978},
	doi = {10.7189/jogh.06.010306},
	language = {eng},
	number = {1},
	journal = {Journal of global health},
	author = {Woolhouse, Mark and Waugh, Catriona and Perry, Meghan Rose and Nair, Harish},
	month = jun,
	year = {2016},
	pmid = {27350872},
	pmcid = {PMC4920009},
	pages = {010306},
}

@article{oude_munnink_genome_2016,
	title = {Genome {Sequences} of a {Novel} {Vietnamese} {Bat} {Bunyavirus}.},
	volume = {4},
	copyright = {Copyright (c) 2016 Oude Munnink et al.},
	issn = {2169-8287},
	doi = {10.1128/genomeA.01366-16},
	abstract = {To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.},
	language = {eng},
	number = {6},
	journal = {Genome announcements},
	author = {Oude Munnink, Bas B. and Phan, My V. T. and van der Hoek, Lia and Kellam, Paul and Cotten, Matthew},
	month = dec,
	year = {2016},
	pmid = {28007850},
	pmcid = {PMC5180378},
}

To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.

@article{lu_evolution_2016,
	title = {Evolution and phylogeographic dissemination of endemic porcine picornaviruses in  {Vietnam}.},
	volume = {2},
	issn = {2057-1577 2057-1577},
	doi = {10.1093/ve/vew001},
	abstract = {Members of the Picornaviridae are important and often zoonotic viruses responsible for a variety of human and animal diseases. However, the evolution and spatial dissemination of different picornaviruses circulating in domestic animals are not well studied. We examined the rate of evolution and time of origin of porcine enterovirus G (EV-G) and porcine kobuvirus species C lineages (PKV-C) circulating in pig farms in Vietnam and from other countries. We further  explored the spatiotemporal spread of EV-G and PKV-C in Southwest Vietnam using phylogeographic models. Multiple types of EV-G are co-circulating in Vietnam. The two dominant EV-G types among isolates from Vietnam (G1 and G6) showed strong phylogenetic clustering. Three clades of PKV-C (PKV-C1-3) represent more recent introductions into Vietnam; PKV-C2 is closely related to PKV-C from Southwest China, indicating possible cross-border dissemination. In addition, high virus lineage migration rates were estimated within four districts in Dong Thap province in Vietnam for both EV-G types (G1, G6) and all PKV-C (C1-3) clades. We  found that Chau Thanh district is a primary source of both EV-G and PKV-C clades, consistent with extensive pig trading in and out of the district. Understanding the evolution and spatial dissemination of endemic picornaviruses in pigs may inform future strategies for the surveillance and control of picornaviruses.},
	language = {eng},
	number = {1},
	journal = {Virus evolution},
	author = {Lu, Lu and Van Dung, Nguyen and Bryant, Juliet E. and Carrique-Mas, Juan and Van Cuong, Nguyen and Anh, Pham Honh and Rabaa, Maia A. and Baker, Stephen and Simmonds, Peter and Woolhouse, Mark E.},
	month = jan,
	year = {2016},
	pmid = {27774295},
	pmcid = {PMC4989877},
	keywords = {Evolution, Phylogeography, enterovirus, kobuvirus, porcine picornavirus},
	pages = {vew001},
}

Members of the Picornaviridae are important and often zoonotic viruses responsible for a variety of human and animal diseases. However, the evolution and spatial dissemination of different picornaviruses circulating in domestic animals are not well studied. We examined the rate of evolution and time of origin of porcine enterovirus G (EV-G) and porcine kobuvirus species C lineages (PKV-C) circulating in pig farms in Vietnam and from other countries. We further explored the spatiotemporal spread of EV-G and PKV-C in Southwest Vietnam using phylogeographic models. Multiple types of EV-G are co-circulating in Vietnam. The two dominant EV-G types among isolates from Vietnam (G1 and G6) showed strong phylogenetic clustering. Three clades of PKV-C (PKV-C1-3) represent more recent introductions into Vietnam; PKV-C2 is closely related to PKV-C from Southwest China, indicating possible cross-border dissemination. In addition, high virus lineage migration rates were estimated within four districts in Dong Thap province in Vietnam for both EV-G types (G1, G6) and all PKV-C (C1-3) clades. We found that Chau Thanh district is a primary source of both EV-G and PKV-C clades, consistent with extensive pig trading in and out of the district. Understanding the evolution and spatial dissemination of endemic picornaviruses in pigs may inform future strategies for the surveillance and control of picornaviruses.

@article{duong_evaluation_2016,
	title = {Evaluation of {Luminex} {xTAG} {Gastrointestinal} {Pathogen} {Panel} {Assay} for {Detection} of {Multiple} {Diarrheal} {Pathogens} in {Fecal} {Samples} in {Vietnam}.},
	volume = {54},
	copyright = {Copyright (c) 2016 Duong et al.},
	issn = {1098-660X 0095-1137},
	doi = {10.1128/JCM.03321-15},
	abstract = {Diarrheal disease is a complex syndrome that remains a leading cause of global childhood morbidity and mortality. The diagnosis of enteric pathogens in a timely and precise manner is important for making treatment decisions and informing public health policy, but accurate diagnosis is a major challenge in industrializing countries. Multiplex molecular diagnostic techniques may represent a significant improvement over classical approaches. We evaluated the Luminex xTAG gastrointestinal pathogen panel (GPP) assay for the detection of common enteric bacterial and viral pathogens in Vietnam. Microbiological culture  and real-time PCR were used as gold standards. The tests were performed on 479 stool samples collected from people admitted to the hospital for diarrheal disease throughout Vietnam. Sensitivity and specificity were calculated for the xTAG GPP for the seven principal diarrheal etiologies. The sensitivity and specificity for the xTAG GPP were {\textgreater}88\% for Shigellaspp.,Campylobacterspp., rotavirus, norovirus genotype 1/2 (GI/GII), and adenovirus compared to those of microbiological culture and/or real-time PCR. However, the specificity was low (  approximately 60\%) for Salmonella species. Additionally, a number of important pathogens that are not identified in routine hospital procedures in this setting, such as Cryptosporidiumspp. and Clostridium difficile, were detected with the GPP. The use of the Luminex xTAG GPP for the detection of enteric pathogens in settings, like Vietnam, would dramatically improve the diagnostic accuracy and capacity of hospital laboratories, allowing for timely and appropriate therapy decisions and a wider understanding of the epidemiology of pathogens associated with severe diarrheal disease in low-resource settings.},
	language = {eng},
	number = {4},
	journal = {Journal of clinical microbiology},
	author = {Duong, Vu Thuy and Phat, Voong Vinh and Tuyen, Ha Thanh and Dung, Tran Thi Ngoc and Trung, Pham Duc and Minh, Pham Van and Tu, Le Thi Phuong and Campbell, James I. and Le Phuc, Hoang and Ha, Ton Thi Thanh and Ngoc, Nguyen Minh and Huong, Nguyen Thi Thanh and Tam, Pham Thi Thanh and Huong, Dang Thao and Xang, Nguyen Van and Dong, Nguyen and Phuong, Le Thi and Hung, Nguyen Van and Phu, Bui Duc and Phuc, Tran My and Thwaites, Guy E. and Vi, Lu Lan and Rabaa, Maia A. and Thompson, Corinne N. and Baker, Stephen},
	month = apr,
	year = {2016},
	pmid = {26865681},
	pmcid = {PMC4809950},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Bacteria/classification/*isolation \& purification, Child, Child, Preschool, Diarrhea/*diagnosis, Feces/*microbiology/*virology, Female, Humans, Immunoassay/*methods, Infant, Infant, Newborn, Male, Middle Aged, Sensitivity and Specificity, Vietnam, Viruses/classification/*isolation \& purification, Young Adult},
	pages = {1094--1100},
}

Diarrheal disease is a complex syndrome that remains a leading cause of global childhood morbidity and mortality. The diagnosis of enteric pathogens in a timely and precise manner is important for making treatment decisions and informing public health policy, but accurate diagnosis is a major challenge in industrializing countries. Multiplex molecular diagnostic techniques may represent a significant improvement over classical approaches. We evaluated the Luminex xTAG gastrointestinal pathogen panel (GPP) assay for the detection of common enteric bacterial and viral pathogens in Vietnam. Microbiological culture and real-time PCR were used as gold standards. The tests were performed on 479 stool samples collected from people admitted to the hospital for diarrheal disease throughout Vietnam. Sensitivity and specificity were calculated for the xTAG GPP for the seven principal diarrheal etiologies. The sensitivity and specificity for the xTAG GPP were \textgreater88% for Shigellaspp.,Campylobacterspp., rotavirus, norovirus genotype 1/2 (GI/GII), and adenovirus compared to those of microbiological culture and/or real-time PCR. However, the specificity was low ( approximately 60%) for Salmonella species. Additionally, a number of important pathogens that are not identified in routine hospital procedures in this setting, such as Cryptosporidiumspp. and Clostridium difficile, were detected with the GPP. The use of the Luminex xTAG GPP for the detection of enteric pathogens in settings, like Vietnam, would dramatically improve the diagnostic accuracy and capacity of hospital laboratories, allowing for timely and appropriate therapy decisions and a wider understanding of the epidemiology of pathogens associated with severe diarrheal disease in low-resource settings.

@article{oude_munnink_complete_2016,
	title = {Complete {Genome} {Characterization} of {Two} {Wild}-{Type} {Measles} {Viruses} from {Vietnamese} {Infants} during the 2014 {Outbreak}.},
	volume = {4},
	copyright = {Copyright (c) 2016 Oude Munnink et al.},
	issn = {2169-8287},
	doi = {10.1128/genomeA.00250-16},
	abstract = {A large measles virus outbreak occurred across Vietnam in 2014. We identified and obtained complete measles virus genomes in stool samples collected from two diarrheal pediatric patients in Dong Thap Province. These are the first complete  genome sequences of circulating measles viruses in Vietnam during the 2014 measles outbreak.},
	language = {eng},
	number = {2},
	journal = {Genome announcements},
	author = {Oude Munnink, Bas B. and Phan, My V. T. and Kellam, Paul and Cotten, Matthew},
	month = apr,
	year = {2016},
	pmid = {27081130},
	pmcid = {PMC4832158},
}

A large measles virus outbreak occurred across Vietnam in 2014. We identified and obtained complete measles virus genomes in stool samples collected from two diarrheal pediatric patients in Dong Thap Province. These are the first complete genome sequences of circulating measles viruses in Vietnam during the 2014 measles outbreak.

@article{woolhouse_assessing_2016,
	title = {Assessing the {Epidemic} {Potential} of {RNA} and {DNA} {Viruses}.},
	volume = {22},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid2212.160123},
	abstract = {Many new and emerging RNA and DNA viruses are zoonotic or have zoonotic origins in an animal reservoir that is usually mammalian and sometimes avian. Not all zoonotic viruses are transmissible (directly or by an arthropod vector) between human hosts. Virus genome sequence data provide the best evidence of transmission. Of human transmissible virus, 37 species have so far been restricted to self-limiting outbreaks. These viruses are priorities for surveillance because relatively minor changes in their epidemiologies can potentially lead to major changes in the threat they pose to public health. On the basis of comparisons across all recognized human viruses, we consider the characteristics of these priority viruses and assess the likelihood that they will further emerge in human populations. We also assess the likelihood that a virus that can infect humans but is not capable of transmission (directly or by a vector) between human hosts can acquire that capability.},
	language = {eng},
	number = {12},
	journal = {Emerging infectious diseases},
	author = {Woolhouse, Mark E. J. and Brierley, Liam and McCaffery, Chris and Lycett, Sam},
	month = dec,
	year = {2016},
	pmid = {27869592},
	pmcid = {PMC5189130},
	keywords = {DNA viruses, RNA viruses, emerging viruses, epidemic potential, outbreaks, transmission, viruses, zoonoses},
	pages = {2037--2044},
}

Many new and emerging RNA and DNA viruses are zoonotic or have zoonotic origins in an animal reservoir that is usually mammalian and sometimes avian. Not all zoonotic viruses are transmissible (directly or by an arthropod vector) between human hosts. Virus genome sequence data provide the best evidence of transmission. Of human transmissible virus, 37 species have so far been restricted to self-limiting outbreaks. These viruses are priorities for surveillance because relatively minor changes in their epidemiologies can potentially lead to major changes in the threat they pose to public health. On the basis of comparisons across all recognized human viruses, we consider the characteristics of these priority viruses and assess the likelihood that they will further emerge in human populations. We also assess the likelihood that a virus that can infect humans but is not capable of transmission (directly or by a vector) between human hosts can acquire that capability.

@article{van_vinh_chau_clinical_2016,
	title = {A {Clinical} and {Epidemiological} {Investigation} of the {First} {Reported} {Human} {Infection} {With} the {Zoonotic} {Parasite} {Trypanosoma} evansi in {Southeast} {Asia}.},
	volume = {62},
	copyright = {(c) The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America.},
	issn = {1537-6591 1058-4838},
	doi = {10.1093/cid/ciw052},
	abstract = {BACKGROUND: Trypanosomais a genus of unicellular parasitic flagellate protozoa.Trypanosoma bruceispecies and Trypanosoma cruziare the major agents of human trypanosomiasis; other Trypanosomaspecies can cause human disease, but are  rare. In March 2015, a 38-year-old woman presented to a healthcare facility in southern Vietnam with fever, headache, and arthralgia. Microscopic examination of blood revealed infection with Trypanosoma METHODS: Microscopic observation, polymerase chain reaction (PCR) amplification of blood samples, and serological testing were performed to identify the infecting species. The patient's blood was screened for the trypanocidal protein apolipoprotein L1 (APOL1), and a field investigation was performed to identify the zoonotic source. RESULTS: PCR amplification and serological testing identified the infecting species as Trypanosoma evansi.Despite relapsing 6 weeks after completing amphotericin B therapy, the patient made a complete recovery after 5 weeks of suramin. The patient was found to have 2 wild-type APOL1 alleles and a normal serum APOL1 concentration. After responsive animal sampling in the presumed location of exposure, cattle and/or buffalo were determined to be the most likely source of the infection, with 14 of 30 (47\%) animal blood samples testing PCR positive forT. evansi. CONCLUSIONS: We report the first laboratory-confirmed case ofT. evansiin a previously healthy individual without APOL1 deficiency, potentially contracted via a wound while butchering raw beef, and successfully treated with suramin. A linked epidemiological investigation revealed widespread and previously unidentified burden ofT. evansiin local cattle, highlighting the need  for surveillance of this infection in animals and the possibility of further human cases.},
	language = {eng},
	number = {8},
	journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
	author = {Van Vinh Chau, Nguyen and Buu Chau, Le and Desquesnes, Marc and Herder, Stephane and Phu Huong Lan, Nguyen and Campbell, James I. and Van Cuong, Nguyen and Yimming, Benjarat and Chalermwong, Piangjai and Jittapalapong, Sathaporn and Ramon Franco, Jose and Tri Tue, Ngo and Rabaa, Maia A. and Carrique-Mas, Juan and Pham Thi Thanh, Tam and Tran Vu Thieu, Nga and Berto, Alessandra and Thi Hoa, Ngo and Van Minh Hoang, Nguyen and Canh Tu, Nguyen and Khac Chuyen, Nguyen and Wills, Bridget and Tinh Hien, Tran and Thwaites, Guy E. and Yacoub, Sophie and Baker, Stephen},
	month = apr,
	year = {2016},
	pmid = {26908809},
	pmcid = {PMC4803109},
	keywords = {Adult, Animals, Apolipoproteins/blood/genetics, Asia, Southeastern/epidemiology, Blood/parasitology, Buffaloes/parasitology, Cattle, Communicable Diseases, Emerging/diagnosis/epidemiology/parasitology/transmission, DNA, Protozoan/analysis, Female, Humans, Lipoproteins, HDL/blood/genetics, Microscopy, Polymerase Chain Reaction, Trypanocidal Agents/therapeutic use, Trypanosoma evansi, Trypanosoma/classification/*isolation \& purification/ultrastructure, Trypanosomiasis/*diagnosis/drug therapy/*parasitology/transmission, Vietnam, Vietnam/epidemiology, Zoonoses/*diagnosis/epidemiology/transmission, case investigation, emerging infections, zoonosis},
	pages = {1002--1008},
}

BACKGROUND: Trypanosomais a genus of unicellular parasitic flagellate protozoa.Trypanosoma bruceispecies and Trypanosoma cruziare the major agents of human trypanosomiasis; other Trypanosomaspecies can cause human disease, but are rare. In March 2015, a 38-year-old woman presented to a healthcare facility in southern Vietnam with fever, headache, and arthralgia. Microscopic examination of blood revealed infection with Trypanosoma METHODS: Microscopic observation, polymerase chain reaction (PCR) amplification of blood samples, and serological testing were performed to identify the infecting species. The patient's blood was screened for the trypanocidal protein apolipoprotein L1 (APOL1), and a field investigation was performed to identify the zoonotic source. RESULTS: PCR amplification and serological testing identified the infecting species as Trypanosoma evansi.Despite relapsing 6 weeks after completing amphotericin B therapy, the patient made a complete recovery after 5 weeks of suramin. The patient was found to have 2 wild-type APOL1 alleles and a normal serum APOL1 concentration. After responsive animal sampling in the presumed location of exposure, cattle and/or buffalo were determined to be the most likely source of the infection, with 14 of 30 (47%) animal blood samples testing PCR positive forT. evansi. CONCLUSIONS: We report the first laboratory-confirmed case ofT. evansiin a previously healthy individual without APOL1 deficiency, potentially contracted via a wound while butchering raw beef, and successfully treated with suramin. A linked epidemiological investigation revealed widespread and previously unidentified burden ofT. evansiin local cattle, highlighting the need for surveillance of this infection in animals and the possibility of further human cases.

@article{rabaa_vietnam_2015,
	title = {The {Vietnam} {Initiative} on {Zoonotic} {Infections} ({VIZIONS}): {A} {Strategic} {Approach} to  {Studying} {Emerging} {Zoonotic} {Infectious} {Diseases}.},
	volume = {12},
	issn = {1612-9210 1612-9202},
	doi = {10.1007/s10393-015-1061-0},
	abstract = {The effect of newly emerging or re-emerging infectious diseases of zoonotic origin in human populations can be potentially catastrophic, and large-scale investigations of such diseases are highly challenging. The monitoring of emergence events is subject to ascertainment bias, whether at the level of species discovery, emerging disease events, or disease outbreaks in human populations. Disease surveillance is generally performed post hoc, driven by a response to recent events and by the availability of detection and identification technologies. Additionally, the inventory of pathogens that exist in mammalian and other reservoirs is incomplete, and identifying those with the potential to cause disease in humans is rarely possible in advance. A major step in understanding the burden and diversity of zoonotic infections, the local behavioral and demographic risks of infection, and the risk of emergence of these pathogens in human populations is to establish surveillance networks in populations that maintain regular contact with diverse animal populations, and to simultaneously characterize pathogen diversity in human and animal populations. Vietnam has been an epicenter of disease emergence over the last decade, and practices at the human/animal interface may facilitate the likelihood of spillover of zoonotic pathogens into humans. To tackle the scientific issues surrounding the origins and emergence of zoonotic infections in Vietnam, we have  established The Vietnam Initiative on Zoonotic Infections (VIZIONS). This countrywide project, in which several international institutions collaborate with Vietnamese organizations, is combining clinical data, epidemiology, high-throughput sequencing, and social sciences to address relevant one-health questions. Here, we describe the primary aims of the project, the infrastructure  established to address our scientific questions, and the current status of the project. Our principal objective is to develop an integrated approach to the surveillance of pathogens circulating in both human and animal populations and assess how frequently they are exchanged. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence.},
	language = {eng},
	number = {4},
	journal = {EcoHealth},
	author = {Rabaa, Maia A. and Tue, Ngo Tri and Phuc, Tran My and Carrique-Mas, Juan and Saylors, Karen and Cotten, Matthew and Bryant, Juliet E. and Nghia, Ho Dang Trung and Cuong, Nguyen Van and Pham, Hong Anh and Berto, Alessandra and Phat, Voong Vinh and Dung, Tran Thi Ngoc and Bao, Long Hoang and Hoa, Ngo Thi and Wertheim, Heiman and Nadjm, Behzad and Monagin, Corina and van Doorn, H. Rogier and Rahman, Motiur and Tra, My Phan Vu and Campbell, James I. and Boni, Maciej F. and Tam, Pham Thi Thanh and van der Hoek, Lia and Simmonds, Peter and Rambaut, Andrew and Toan, Tran Khanh and Van Vinh Chau, Nguyen and Hien, Tran Tinh and Wolfe, Nathan and Farrar, Jeremy J. and Thwaites, Guy and Kellam, Paul and Woolhouse, Mark E. J. and Baker, Stephen},
	month = dec,
	year = {2015},
	pmid = {26403795},
	pmcid = {PMC4700077},
	keywords = {*Animals, Wild, Animals, Communicable Diseases, Emerging/epidemiology/*prevention \& control/*transmission, Disease Outbreaks/*prevention \& control, Disease Reservoirs, Genomics, Humans, International Cooperation, United States, Vietnam, Vietnam/epidemiology, Zoonoses/epidemiology/*prevention \& control/*transmission, diagnostics, disease surveillance, diseases of unknown origin, high-risk cohort, social science, ultra-deep sequencing, zoonotic infection},
	pages = {726--735},
}

The effect of newly emerging or re-emerging infectious diseases of zoonotic origin in human populations can be potentially catastrophic, and large-scale investigations of such diseases are highly challenging. The monitoring of emergence events is subject to ascertainment bias, whether at the level of species discovery, emerging disease events, or disease outbreaks in human populations. Disease surveillance is generally performed post hoc, driven by a response to recent events and by the availability of detection and identification technologies. Additionally, the inventory of pathogens that exist in mammalian and other reservoirs is incomplete, and identifying those with the potential to cause disease in humans is rarely possible in advance. A major step in understanding the burden and diversity of zoonotic infections, the local behavioral and demographic risks of infection, and the risk of emergence of these pathogens in human populations is to establish surveillance networks in populations that maintain regular contact with diverse animal populations, and to simultaneously characterize pathogen diversity in human and animal populations. Vietnam has been an epicenter of disease emergence over the last decade, and practices at the human/animal interface may facilitate the likelihood of spillover of zoonotic pathogens into humans. To tackle the scientific issues surrounding the origins and emergence of zoonotic infections in Vietnam, we have established The Vietnam Initiative on Zoonotic Infections (VIZIONS). This countrywide project, in which several international institutions collaborate with Vietnamese organizations, is combining clinical data, epidemiology, high-throughput sequencing, and social sciences to address relevant one-health questions. Here, we describe the primary aims of the project, the infrastructure established to address our scientific questions, and the current status of the project. Our principal objective is to develop an integrated approach to the surveillance of pathogens circulating in both human and animal populations and assess how frequently they are exchanged. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence.

@article{thompson_impact_2015,
	title = {The impact of environmental and climatic variation on the spatiotemporal trends of hospitalized pediatric diarrhea in {Ho} {Chi} {Minh} {City}, {Vietnam}.},
	volume = {35},
	copyright = {Copyright (c) 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.},
	issn = {1873-2054 1353-8292},
	doi = {10.1016/j.healthplace.2015.08.001},
	abstract = {It is predicted that the integration of climate-based early warning systems into  existing action plans will facilitate the timely provision of interventions to diarrheal disease epidemics in resource-poor settings. Diarrhea remains a considerable public health problem in Ho Chi Minh City (HCMC), Vietnam and we aimed to quantify variation in the impact of environmental conditions on diarrheal disease risk across the city. Using all inpatient diarrheal admissions  data from three large hospitals within HCMC, we developed a mixed effects regression model to differentiate district-level variation in risk due to environmental conditions from the overarching seasonality of diarrheal disease hospitalization in HCMC. We identified considerable spatial heterogeneity in the  risk of all-cause diarrhea across districts of HCMC with low elevation and differential responses to flooding, air temperature, and humidity driving further spatial heterogeneity in diarrheal disease risk. The incorporation of these results into predictive forecasting algorithms will provide a powerful resource to aid diarrheal disease prevention and control practices in HCMC and other similar settings.},
	language = {eng},
	journal = {Health \& place},
	author = {Thompson, Corinne N. and Zelner, Jonathan L. and Nhu, Tran Do Hoang and Phan, My Vt and Hoang Le, Phuc and Nguyen Thanh, Hung and Vu Thuy, Duong and Minh Nguyen, Ngoc and Ha Manh, Tuan and Van Hoang Minh, Tu and Lu Lan, Vi and Nguyen Van Vinh, Chau and Tran Tinh, Hien and von Clemm, Emmiliese and Storch, Harry and Thwaites, Guy and Grenfell, Bryan T. and Baker, Stephen},
	month = sep,
	year = {2015},
	pmid = {26402922},
	pmcid = {PMC4664115},
	keywords = {*Environment, *Seasons, Child, Climate change, Diarrhea/*epidemiology, Environment, Female, Hospitals, Pediatric, Humans, Male, Mixed effects, Spatial risk, Vietnam/epidemiology, diarrhea},
	pages = {147--154},
}

It is predicted that the integration of climate-based early warning systems into existing action plans will facilitate the timely provision of interventions to diarrheal disease epidemics in resource-poor settings. Diarrhea remains a considerable public health problem in Ho Chi Minh City (HCMC), Vietnam and we aimed to quantify variation in the impact of environmental conditions on diarrheal disease risk across the city. Using all inpatient diarrheal admissions data from three large hospitals within HCMC, we developed a mixed effects regression model to differentiate district-level variation in risk due to environmental conditions from the overarching seasonality of diarrheal disease hospitalization in HCMC. We identified considerable spatial heterogeneity in the risk of all-cause diarrhea across districts of HCMC with low elevation and differential responses to flooding, air temperature, and humidity driving further spatial heterogeneity in diarrheal disease risk. The incorporation of these results into predictive forecasting algorithms will provide a powerful resource to aid diarrheal disease prevention and control practices in HCMC and other similar settings.

@article{carrique-mas_baseline_2015,
	title = {The baseline characteristics and interim analyses of the high-risk sentinel cohort of the {Vietnam} {Initiative} on {Zoonotic} {InfectiONS} ({VIZIONS}).},
	volume = {5},
	issn = {2045-2322 2045-2322},
	doi = {10.1038/srep17965},
	abstract = {The Vietnam Initiative for Zoonotic Infections (VIZIONS) includes community-based 'high-risk sentinel cohort' (HRSC) studies investigating individuals at risk of zoonotic infection due to occupational or residential exposure to animals. A total of 852 HRSC members were recruited between March 2013 and August 2014 from  three provinces (Ha Noi, Dak Lak, and Dong Thap). The most numerous group (72.8\%) corresponded to individuals living on farms, followed by slaughterers (16.3\%) and animal health workers (8.5\%). Nasal/pharyngeal and rectal swabs were collected from HRSC members at recruitment and after notifying illness. Exposure to exotic  animals (including wild pigs, porcupine, monkey, civet, bamboo rat and bat) was highest for the Dak Lak cohort (53.7\%), followed by Ha Noi (13.7\%) and Dong Thap  (4.0\%). A total of 26.8\% of individuals reported consumption of raw blood over the previous year; 33.6\% slaughterers reported no use of protective equipment at  work. Over 686 person-years of observation, 213 episodes of suspect infectious disease were notified, equivalent of 0.35 reports per person-year. Responsive samples were collected from animals in the farm cohort. There was noticeable time and space clustering of disease episodes suggesting that the VIZIONS set up is also suitable for the formal epidemiological investigation of disease outbreaks.},
	language = {eng},
	journal = {Scientific reports},
	author = {Carrique-Mas, Juan J. and Tue, Ngo T. and Bryant, Juliet E. and Saylors, Karen and Cuong, Nguyen V. and Hoa, Ngo T. and An, Nguyen N. and Hien, Vo B. and Lao, Pham V. and Tu, Nguyen C. and Chuyen, Nguyen K. and Chuc, Nguyen T. K. and Tan, Dinh V. and Duong, Hoang Van V. and Toan, Tran K. and Chi, Nguyen T. Y. and Campbell, James and Rabaa, Maia A. and Nadjm, Behzad and Woolhouse, Mark and Wertheim, Heiman and Thwaites, Guy and Baker, Stephen},
	month = dec,
	year = {2015},
	pmid = {26659094},
	pmcid = {PMC4674710},
	keywords = {*Sentinel Surveillance, Agriculture, Animals, Cluster Analysis, Cohort Studies, Communicable Diseases, Emerging/*epidemiology, Farmers, Geography, Medical, Humans, Meat Products/adverse effects, Occupational Exposure, Risk, Vietnam/epidemiology, Zoonoses/*epidemiology},
	pages = {17965},
}

The Vietnam Initiative for Zoonotic Infections (VIZIONS) includes community-based 'high-risk sentinel cohort' (HRSC) studies investigating individuals at risk of zoonotic infection due to occupational or residential exposure to animals. A total of 852 HRSC members were recruited between March 2013 and August 2014 from three provinces (Ha Noi, Dak Lak, and Dong Thap). The most numerous group (72.8%) corresponded to individuals living on farms, followed by slaughterers (16.3%) and animal health workers (8.5%). Nasal/pharyngeal and rectal swabs were collected from HRSC members at recruitment and after notifying illness. Exposure to exotic animals (including wild pigs, porcupine, monkey, civet, bamboo rat and bat) was highest for the Dak Lak cohort (53.7%), followed by Ha Noi (13.7%) and Dong Thap (4.0%). A total of 26.8% of individuals reported consumption of raw blood over the previous year; 33.6% slaughterers reported no use of protective equipment at work. Over 686 person-years of observation, 213 episodes of suspect infectious disease were notified, equivalent of 0.35 reports per person-year. Responsive samples were collected from animals in the farm cohort. There was noticeable time and space clustering of disease episodes suggesting that the VIZIONS set up is also suitable for the formal epidemiological investigation of disease outbreaks.

@article{van_cuong_rodents_2015,
	title = {Rodents and risk in the {Mekong} {Delta} of {Vietnam}: seroprevalence of selected zoonotic viruses in rodents and humans.},
	volume = {15},
	issn = {1557-7759 1530-3667},
	doi = {10.1089/vbz.2014.1603},
	abstract = {In the Mekong Delta in southern Vietnam, rats are commonly traded in wet markets  and sold live for food consumption. We investigated seroprevalence to selected groups of rodent-borne viruses among human populations with high levels of animal exposure and among co-located rodent populations. The indirect fluorescence antibody test (IFAT) was used to determine seropositivity to representative reference strains of hantaviruses (Dobrava virus [DOBV], Seoul virus [SEOV]), cowpox virus, arenaviruses (lymphocytic choriomeningitis virus [LCMV]), flaviviruses (tick-borne encephalitis virus [TBEV]), and rodent parechoviruses (Ljungan virus), using sera from 245 humans living in Dong Thap Province and 275  rodents representing the five common rodent species sold in wet markets and present in peridomestic and farm settings. Combined seropositivity to DOBV and SEOV among the rodents and humans was 6.9\% (19/275) and 3.7\% (9/245), respectively; 1.1\% (3/275) and 4.5\% (11/245) to cowpox virus; 5.4\% (15/275) and 47.3\% (116/245) for TBEV; and exposure to Ljungan virus was 18.8\% (46/245) in humans, but 0\% in rodents. Very little seroreactivity was observed to LCMV in either rodents (1/275, 0.4\%) or humans (2/245, 0.8\%). Molecular screening of rodent liver tissues using consensus primers for flaviviruses did not yield any amplicons, whereas molecular screening of rodent lung tissues for hantavirus yielded one hantavirus sequence (SEOV). In summary, these results indicate low to moderate levels of endemic hantavirus circulation, possible circulation of a flavivirus in rodent reservoirs, and the first available data on human exposures  to parechoviruses in Vietnam. Although the current evidence suggests only limited exposure of humans to known rodent-borne diseases, further research is warranted  to assess public health implications of the rodent trade.},
	language = {eng},
	number = {1},
	journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
	author = {Van Cuong, Nguyen and Carrique-Mas, Juan and Vo Be, Hien and An, Nguyen Ngoc and Tue, Ngo Tri and Anh, Nguyet Lam and Anh, Pham Hong and Phuc, Nguyen The and Baker, Stephen and Voutilainen, Liina and Jaaskelainen, Anne and Huhtamo, Eili and Utriainen, Mira and Sironen, Tarja and Vaheri, Antti and Henttonen, Heikki and Vapalahti, Olli and Chaval, Yannick and Morand, Serge and Bryant, Juliet E.},
	month = jan,
	year = {2015},
	pmid = {25629782},
	pmcid = {PMC4676424},
	keywords = {*Disease Vectors, *Seroepidemiologic Studies, Animals, Arenavirus/immunology/isolation \& purification, Cowpox virus-Arenavirus, Cowpox virus/immunology/isolation \& purification, Flavivirus, Flavivirus/immunology/isolation \& purification, Hantavirus, Hantavirus/immunology/isolation \& purification, Humans, Ljungan virus, Meat/*virology, Parechovirus/immunology/isolation \& purification, Rodentia/immunology/*virology, Rodents, Vietnam, Vietnam/epidemiology, zoonoses},
	pages = {65--72},
}

In the Mekong Delta in southern Vietnam, rats are commonly traded in wet markets and sold live for food consumption. We investigated seroprevalence to selected groups of rodent-borne viruses among human populations with high levels of animal exposure and among co-located rodent populations. The indirect fluorescence antibody test (IFAT) was used to determine seropositivity to representative reference strains of hantaviruses (Dobrava virus [DOBV], Seoul virus [SEOV]), cowpox virus, arenaviruses (lymphocytic choriomeningitis virus [LCMV]), flaviviruses (tick-borne encephalitis virus [TBEV]), and rodent parechoviruses (Ljungan virus), using sera from 245 humans living in Dong Thap Province and 275 rodents representing the five common rodent species sold in wet markets and present in peridomestic and farm settings. Combined seropositivity to DOBV and SEOV among the rodents and humans was 6.9% (19/275) and 3.7% (9/245), respectively; 1.1% (3/275) and 4.5% (11/245) to cowpox virus; 5.4% (15/275) and 47.3% (116/245) for TBEV; and exposure to Ljungan virus was 18.8% (46/245) in humans, but 0% in rodents. Very little seroreactivity was observed to LCMV in either rodents (1/275, 0.4%) or humans (2/245, 0.8%). Molecular screening of rodent liver tissues using consensus primers for flaviviruses did not yield any amplicons, whereas molecular screening of rodent lung tissues for hantavirus yielded one hantavirus sequence (SEOV). In summary, these results indicate low to moderate levels of endemic hantavirus circulation, possible circulation of a flavivirus in rodent reservoirs, and the first available data on human exposures to parechoviruses in Vietnam. Although the current evidence suggests only limited exposure of humans to known rodent-borne diseases, further research is warranted to assess public health implications of the rodent trade.

@article{hoa_population_2015,
	title = {Population susceptibility to a variant swine-origin influenza virus {A}({H3N2}) in {Vietnam}, 2011-2012.},
	volume = {143},
	issn = {1469-4409 0950-2688},
	doi = {10.1017/S0950268815000187},
	abstract = {A reassortant swine-origin A(H3N2) virus (A/swine/BinhDuong/03-9/2010) was detected through swine surveillance programmes in southern Vietnam in 2010. This  virus contains haemagglutinin and neuraminidase genes from a human A(H3N2) virus  circulating around 2004-2006, and the internal genes from triple-reassortant swine influenza A viruses (IAVs). To assess population susceptibility to this virus we measured haemagglutination inhibiting (HI) titres to A/swine/BinhDuong/03-9/2010 and to seasonal A/Perth/16/2009 for 947 sera collected from urban and rural Vietnamese people during 2011-2012. Seroprevalence (HI 40) was high and similar for both viruses, with 62.6\% [95\% confidence interval (CI) 59.4-65.7] against A/Perth/16/2009 and 54.6\% (95\% CI 51.4-57.8\%) against A/swine/BinhDuong/03-9/2010, and no significant differences between urban and rural participants. Children aged {\textless}5 years lacked antibodies to the swine origin H3 virus despite high seroprevalence for A/Perth/16/2009. These results reveal vulnerability to infection to this contemporary swine IAV in children aged {\textless}5 years; however, cross-reactive immunity in adults would likely limit epidemic  emergence potential.},
	language = {eng},
	number = {14},
	journal = {Epidemiology and infection},
	author = {Hoa, L. N. M. and Bryant, J. E. and Choisy, M. and Nguyet, L. A. and Bao, N. T. and Trang, N. H. and Chuc, N. T. K. and Toan, T. K. and Saito, T. and Takemae, N. and Horby, P. and Wertheim, H. and Fox, A.},
	month = oct,
	year = {2015},
	pmid = {25761949},
	pmcid = {PMC4595856},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Animals, Antibodies, Viral/*blood, Child, Child, Preschool, Female, Hemagglutination Inhibition Tests, Humans, Infant, Infant, Newborn, Influenza A, Influenza A Virus, H3N2 Subtype/*immunology/isolation \& purification, Influenza, Human/epidemiology/*immunology, Male, Middle Aged, Orthomyxoviridae Infections/virology, Reassortant Viruses/*immunology/isolation \& purification, Seroepidemiologic Studies, Sus scrofa/virology, Swine, Swine Diseases/virology, Vietnam/epidemiology, Young Adult, virology (human) and epidemiology, zoonoses},
	pages = {2959--2964},
}

A reassortant swine-origin A(H3N2) virus (A/swine/BinhDuong/03-9/2010) was detected through swine surveillance programmes in southern Vietnam in 2010. This virus contains haemagglutinin and neuraminidase genes from a human A(H3N2) virus circulating around 2004-2006, and the internal genes from triple-reassortant swine influenza A viruses (IAVs). To assess population susceptibility to this virus we measured haemagglutination inhibiting (HI) titres to A/swine/BinhDuong/03-9/2010 and to seasonal A/Perth/16/2009 for 947 sera collected from urban and rural Vietnamese people during 2011-2012. Seroprevalence (HI 40) was high and similar for both viruses, with 62.6% [95% confidence interval (CI) 59.4-65.7] against A/Perth/16/2009 and 54.6% (95% CI 51.4-57.8%) against A/swine/BinhDuong/03-9/2010, and no significant differences between urban and rural participants. Children aged \textless5 years lacked antibodies to the swine origin H3 virus despite high seroprevalence for A/Perth/16/2009. These results reveal vulnerability to infection to this contemporary swine IAV in children aged \textless5 years; however, cross-reactive immunity in adults would likely limit epidemic emergence potential.

@article{saylors_mobilising_2015,
	title = {Mobilising community-based research on zoonotic infections: {A} case study of longitudinal cohorts in {Vietnam}},
	volume = {8},
	copyright = {Copyright (c) 2015 Karen Saylors, Tue Ngo Tri, Toan Tran Khanh, Kiet Bach Tuan, Heiman FL Wertheim, Stephen Baker, Hoa Ngo Thi, Juliet E Bryant},
	issn = {1836-3393},
	shorttitle = {Mobilising community-based research on zoonotic infections},
	url = {http://epress.lib.uts.edu.au/journals/index.php/ijcre/article/view/3922},
	doi = {10.5130/ijcre.v8i1.3922},
	abstract = {We initiated the Vietnam Initiative on Zoonotic Infections (VIZIONS) research program to better understand the epidemiology of disease transmission at the human–animal interface in Vietnamese rural communities and to integrate One Health approaches to disease surveillance. We established a longitudinal community cohort study of individuals with occupational exposure to animals, which involves concurrent targeted sampling from domestic livestock species and follow-up monitoring of human clinical cases. The project was implemented by government agencies at the provincial and district levels of the public health and animal health sectors in Vietnam. Engaging with rural communities builds response capacity at the grassroots level, and has improved dialogue between local stakeholders responsible for monitoring human and animal health. Here we describe the process of initiating participatory research and cohort field implementation over the first year in two study sites in Vietnam.Keywords: Vietnam, participatory research, zoonoses, field epidemiology},
	language = {en},
	number = {1},
	urldate = {2017-07-06},
	journal = {Gateways: International Journal of Community Research and Engagement},
	author = {Saylors, Karen and Tri, Tue Ngo and Khanh, Toan Tran and Tuan, Kiet Bach and Wertheim, Heiman FL and Baker, Stephen and Thi, Hoa Ngo and Bryant, Juliet E.},
	month = sep,
	year = {2015},
	pages = {23--42},
}

We initiated the Vietnam Initiative on Zoonotic Infections (VIZIONS) research program to better understand the epidemiology of disease transmission at the human–animal interface in Vietnamese rural communities and to integrate One Health approaches to disease surveillance. We established a longitudinal community cohort study of individuals with occupational exposure to animals, which involves concurrent targeted sampling from domestic livestock species and follow-up monitoring of human clinical cases. The project was implemented by government agencies at the provincial and district levels of the public health and animal health sectors in Vietnam. Engaging with rural communities builds response capacity at the grassroots level, and has improved dialogue between local stakeholders responsible for monitoring human and animal health. Here we describe the process of initiating participatory research and cohort field implementation over the first year in two study sites in Vietnam.Keywords: Vietnam, participatory research, zoonoses, field epidemiology

@article{woolhouse_lessons_2015,
	title = {Lessons from {Ebola}: {Improving} infectious disease surveillance to inform outbreak  management.},
	volume = {7},
	copyright = {Copyright (c) 2015, American Association for the Advancement of Science.},
	issn = {1946-6242 1946-6234},
	doi = {10.1126/scitranslmed.aab0191},
	abstract = {The current Ebola virus disease outbreak in West Africa has revealed serious shortcomings in national and international capacity to detect, monitor, and respond to infectious disease outbreaks as they occur. Recent advances in diagnostics, risk mapping, mathematical modeling, pathogen genome sequencing, phylogenetics, and phylogeography have the potential to improve substantially the quantity and quality of information available to guide the public health response to outbreaks of all kinds.},
	language = {eng},
	number = {307},
	journal = {Science translational medicine},
	author = {Woolhouse, Mark E. J. and Rambaut, Andrew and Kellam, Paul},
	month = sep,
	year = {2015},
	pmid = {26424572},
	keywords = {*Population Surveillance, Communicable Diseases/*epidemiology, Disease Outbreaks/*prevention \& control, Ebolavirus/*physiology, Humans, Models, Biological, Sequence Analysis, DNA},
	pages = {307rv5},
}

The current Ebola virus disease outbreak in West Africa has revealed serious shortcomings in national and international capacity to detect, monitor, and respond to infectious disease outbreaks as they occur. Recent advances in diagnostics, risk mapping, mathematical modeling, pathogen genome sequencing, phylogenetics, and phylogeography have the potential to improve substantially the quantity and quality of information available to guide the public health response to outbreaks of all kinds.

@article{nhung_induction_2015,
	title = {Induction of {Antimicrobial} {Resistance} in {Escherichia} coli and {Non}-{Typhoidal} {Salmonella} {Strains} after {Adaptation} to {Disinfectant} {Commonly} {Used} on {Farms} in {Vietnam}.},
	volume = {4},
	issn = {2079-6382 2079-6382},
	doi = {10.3390/antibiotics4040480},
	abstract = {In Vietnam, commercial disinfectants containing quaternary ammonium compounds (QACs) are commonly used in pig and poultry farms to maintain hygiene during production. We hypothesized that sustained exposure to sub-bactericidal concentrations of QAC-based disinfectants may result in increased levels of antimicrobial resistance (AMR) among Enterobacteriacea due to the increase of efflux pump expression. To test this hypothesis we exposed six antimicrobial-susceptible Escherichia coli (E. coli) and six antimicrobial-susceptible non-typhoidal Salmonella (NTS) isolates to increasing concentrations of a commonly used commercial disinfectant containing a mix of benzalkonium chloride and glutaraldehyde. Over the 12-day experiment, strains exhibited a significant change in their minimum inhibitory concentration (MIC) of the disinfectant product (mean increase of 31\% (SD +/- 40)) (p = 0.02, paired Wilcoxon test). Increases in MIC for the disinfectant product were strongly correlated with increases in MIC (or decreases in inhibition zone) for all antimicrobials (Pearson's correlation coefficient 0.71-0.83, all p {\textless} 0.01). The greatest increases in MIC (or decreases in inhibition zone) were observed for ampicillin, tetracycline, ciprofloxacin, and chloramphenicol, and the smallest for gentamicin, trimethoprim/sulphamethoxazole. The treatment of 155 representative E. coli isolates from farmed and wild animals in the Mekong Delta  (Vietnam) with phenyl-arginine beta-naphthylamide (PAbetaN), a generic efflux pump inhibitor, resulted in reductions in the prevalence of AMR ranging from 0.7\% to 3.3\% in these organisms, indicating a small contribution of efflux pumps on the observed prevalence of AMR on farms. These results suggest that the mass usage of commercial disinfectants, many of which contain QACs, is potentially a contributing factor on the generation and maintenance of AMR in animal production in Vietnam.},
	language = {eng},
	number = {4},
	journal = {Antibiotics (Basel, Switzerland)},
	author = {Nhung, Nguyen T. and Thuy, Cao T. and Trung, Nguyen V. and Campbell, James and Baker, Stephen and Thwaites, Guy and Hoa, Ngo T. and Carrique-Mas, Juan},
	month = oct,
	year = {2015},
	pmid = {27025637},
	pmcid = {PMC4790309},
	keywords = {adaptation, antimicrobials, disinfectant, efflux pumps},
	pages = {480--494},
}

In Vietnam, commercial disinfectants containing quaternary ammonium compounds (QACs) are commonly used in pig and poultry farms to maintain hygiene during production. We hypothesized that sustained exposure to sub-bactericidal concentrations of QAC-based disinfectants may result in increased levels of antimicrobial resistance (AMR) among Enterobacteriacea due to the increase of efflux pump expression. To test this hypothesis we exposed six antimicrobial-susceptible Escherichia coli (E. coli) and six antimicrobial-susceptible non-typhoidal Salmonella (NTS) isolates to increasing concentrations of a commonly used commercial disinfectant containing a mix of benzalkonium chloride and glutaraldehyde. Over the 12-day experiment, strains exhibited a significant change in their minimum inhibitory concentration (MIC) of the disinfectant product (mean increase of 31% (SD +/- 40)) (p = 0.02, paired Wilcoxon test). Increases in MIC for the disinfectant product were strongly correlated with increases in MIC (or decreases in inhibition zone) for all antimicrobials (Pearson's correlation coefficient 0.71-0.83, all p \textless 0.01). The greatest increases in MIC (or decreases in inhibition zone) were observed for ampicillin, tetracycline, ciprofloxacin, and chloramphenicol, and the smallest for gentamicin, trimethoprim/sulphamethoxazole. The treatment of 155 representative E. coli isolates from farmed and wild animals in the Mekong Delta (Vietnam) with phenyl-arginine beta-naphthylamide (PAbetaN), a generic efflux pump inhibitor, resulted in reductions in the prevalence of AMR ranging from 0.7% to 3.3% in these organisms, indicating a small contribution of efflux pumps on the observed prevalence of AMR on farms. These results suggest that the mass usage of commercial disinfectants, many of which contain QACs, is potentially a contributing factor on the generation and maintenance of AMR in animal production in Vietnam.

@article{le_minh_vitro_2015,
	title = {In vitro activity of colistin in antimicrobial combination against carbapenem-resistant {Acinetobacter} baumannii isolated from patients with ventilator-associated pneumonia in {Vietnam}.},
	volume = {64},
	issn = {1473-5644 0022-2615},
	doi = {10.1099/jmm.0.000137},
	abstract = {Acinetobacter baumannii has become one of the major infection threats in intensive care units (ICUs) globally. Since 2008, A. baumannii has been the leading cause of ventilator-associated pneumonia (VAP) in our ICU at an infectious disease hospital in southern Vietnam. The emergence of this pathogen in our setting is consistent with the persistence of a specific clone exhibiting  resistance to carbapenems. Antimicrobial combinations may be a strategy to treat  infections caused by these carbapenem-resistant A. baumannii. Therefore, we assessed potential antimicrobial combinations against local carbapenem-resistant  A. baumannii by measuring in vitro interactions of colistin with four antimicrobials that are locally certified for treating VAP. We first performed antimicrobial susceptibility testing and multilocus variable number tandem repeat analysis (MLVA) genotyping on 74 A. baumannii isolated from quantitative tracheal aspirates from patients with VAP over an 18-month period. These 74 isolates could be subdivided into 21 main clusters by MLVA and {\textgreater}80 \% were resistant to carbapenems. We selected 56 representative isolates for in vitro combination synergy testing. Synergy was observed in four (7 \%), seven (13 \%), 20 (36 \%) and  38 (68 \%) isolates with combinations of colistin with ceftazidime, ceftriaxone, imipenem and meropenem, respectively. Notably, more carbapenem-resistant A. baumannii isolates (36/43; 84 \%) exhibited synergistic activity with a combination of colistin and meropenem than carbapenem-susceptible A. baumannii isolates (2/13; 15 \%) (P = 0.023; Fisher's exact test). Our findings suggest that combinations of colistin and meropenem should be considered when treating carbapenem-resistant A. baumannii infections in Vietnam, and we advocate clinical trials investigating combination therapy for VAP.},
	language = {eng},
	number = {10},
	journal = {Journal of medical microbiology},
	author = {Le Minh, Vien and Thi Khanh Nhu, Nguyen and Vinh Phat, Voong and Thompson, Corinne and Huong Lan, Nguyen Phu and Thieu Nga, Tran Vu and Thanh Tam, Pham Thi and Tuyen, Ha Thanh and Hoang Nhu, Tran Do and Van Hao, Nguyen and Thi Loan, Huynh and Minh Yen, Lam and Parry, Christopher M. and Trung Nghia, Ho Dang and Campbell, James I. and Hien, Tran Tinh and Thwaites, Louise and Thwaites, Guy and Van Vinh Chau, Nguyen and Baker, Stephen},
	month = oct,
	year = {2015},
	pmid = {26297024},
	pmcid = {PMC4755130},
	keywords = {*Drug Synergism, Acinetobacter baumannii/classification/*drug effects/genetics/isolation \& purification, Anti-Bacterial Agents/*pharmacology, Carbapenems/*pharmacology, Cluster Analysis, Colistin/*pharmacology, Genotype, Hospitals, Humans, Microbial Sensitivity Tests, Multilocus Sequence Typing, Pneumonia, Ventilator-Associated/epidemiology/*microbiology, Vietnam/epidemiology, beta-Lactam Resistance},
	pages = {1162--1169},
}

Acinetobacter baumannii has become one of the major infection threats in intensive care units (ICUs) globally. Since 2008, A. baumannii has been the leading cause of ventilator-associated pneumonia (VAP) in our ICU at an infectious disease hospital in southern Vietnam. The emergence of this pathogen in our setting is consistent with the persistence of a specific clone exhibiting resistance to carbapenems. Antimicrobial combinations may be a strategy to treat infections caused by these carbapenem-resistant A. baumannii. Therefore, we assessed potential antimicrobial combinations against local carbapenem-resistant A. baumannii by measuring in vitro interactions of colistin with four antimicrobials that are locally certified for treating VAP. We first performed antimicrobial susceptibility testing and multilocus variable number tandem repeat analysis (MLVA) genotyping on 74 A. baumannii isolated from quantitative tracheal aspirates from patients with VAP over an 18-month period. These 74 isolates could be subdivided into 21 main clusters by MLVA and \textgreater80 % were resistant to carbapenems. We selected 56 representative isolates for in vitro combination synergy testing. Synergy was observed in four (7 %), seven (13 %), 20 (36 %) and 38 (68 %) isolates with combinations of colistin with ceftazidime, ceftriaxone, imipenem and meropenem, respectively. Notably, more carbapenem-resistant A. baumannii isolates (36/43; 84 %) exhibited synergistic activity with a combination of colistin and meropenem than carbapenem-susceptible A. baumannii isolates (2/13; 15 %) (P = 0.023; Fisher's exact test). Our findings suggest that combinations of colistin and meropenem should be considered when treating carbapenem-resistant A. baumannii infections in Vietnam, and we advocate clinical trials investigating combination therapy for VAP.

@article{loan_how_2015,
	title = {How important are rats as vectors of leptospirosis in the {Mekong} {Delta} of {Vietnam}?},
	volume = {15},
	issn = {1557-7759 1530-3667},
	doi = {10.1089/vbz.2014.1613},
	abstract = {Leptospirosis is a zoonosis known to be endemic in the Mekong Delta of Vietnam, even though clinical reports are uncommon. We investigated leptospira infection in rats purchased in food markets during the rainy season (October) (n=150), as well as those trapped during the dry season (February-March) (n=125) in the region using RT-PCR for the lipL32 gene, confirmed by 16S rRNA, as well as by the microscopic agglutination test (MAT). Results were compared with the serovar distribution of human cases referred from Ho Chi Minh City hospitals (2004-2012)  confirmed by MAT (n=45). The MAT seroprevalence among rats was 18.3\%. The highest MAT seroprevalence corresponded, in decreasing order, to: Rattus norvegicus (33.0\%), Bandicota indica (26.5\%), Rattus tanezumi (24.6\%), Rattus exulans (14.3\%), and Rattus argentiventer (7.1\%). The most prevalent serovars were, in descending order: Javanica (4.6\% rats), Lousiana (4.2\%), Copenageni (4.2\%), Cynopterie (3.7\%), Pomona (2.9\%), and Icterohaemorrhagiae (2.5\%). A total of 16 rats (5.8\%) tested positive by RT-PCR. Overall, larger rats tended to have a higher prevalence of detection. There was considerable agreement between MAT and  PCR (kappa=0.28 [0.07-0.49]), although significantly more rats were positive by MAT (McNemar 29.9 (p{\textless}0.001). MAT prevalence was higher among rats during the rainy season compared with rats in the dry season. There are no current available data on leptospira serovars in humans in the Mekong Delta, although existing studies suggest limited overlapping between human and rat serovars. Further studies should take into account a wider range of potential reservoirs (i.e., dogs, pigs) as well as perform geographically linked co-sampling of humans and animals to establish the main sources of leptospirosis in the region.},
	language = {eng},
	number = {1},
	journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
	author = {Loan, Hoang Kim and Van Cuong, Nguyen and Takhampunya, Ratree and Kiet, Bach Tuan and Campbell, James and Them, Lac Ngoc and Bryant, Juliet E. and Tippayachai, Bousaraporn and Van Hoang, Nguyen and Morand, Serge and Hien, Vo Be and Carrique-Mas, Juan J.},
	month = jan,
	year = {2015},
	pmid = {25629781},
	pmcid = {PMC4307199},
	keywords = {*Disease Vectors, Agglutination Tests, Animals, Humans, Leptospira/classification, Leptospirosis, Leptospirosis/*epidemiology/*transmission, Meat/microbiology, Mekong Delta, Vietnam, Prevalence, RNA, Ribosomal, 16S, Rats, Real-Time Polymerase Chain Reaction, Rodent Diseases/epidemiology, Seasons, Seroepidemiologic Studies, Vietnam/epidemiology, Zoonoses/microbiology},
	pages = {56--64},
}

Leptospirosis is a zoonosis known to be endemic in the Mekong Delta of Vietnam, even though clinical reports are uncommon. We investigated leptospira infection in rats purchased in food markets during the rainy season (October) (n=150), as well as those trapped during the dry season (February-March) (n=125) in the region using RT-PCR for the lipL32 gene, confirmed by 16S rRNA, as well as by the microscopic agglutination test (MAT). Results were compared with the serovar distribution of human cases referred from Ho Chi Minh City hospitals (2004-2012) confirmed by MAT (n=45). The MAT seroprevalence among rats was 18.3%. The highest MAT seroprevalence corresponded, in decreasing order, to: Rattus norvegicus (33.0%), Bandicota indica (26.5%), Rattus tanezumi (24.6%), Rattus exulans (14.3%), and Rattus argentiventer (7.1%). The most prevalent serovars were, in descending order: Javanica (4.6% rats), Lousiana (4.2%), Copenageni (4.2%), Cynopterie (3.7%), Pomona (2.9%), and Icterohaemorrhagiae (2.5%). A total of 16 rats (5.8%) tested positive by RT-PCR. Overall, larger rats tended to have a higher prevalence of detection. There was considerable agreement between MAT and PCR (kappa=0.28 [0.07-0.49]), although significantly more rats were positive by MAT (McNemar 29.9 (p\textless0.001). MAT prevalence was higher among rats during the rainy season compared with rats in the dry season. There are no current available data on leptospira serovars in humans in the Mekong Delta, although existing studies suggest limited overlapping between human and rat serovars. Further studies should take into account a wider range of potential reservoirs (i.e., dogs, pigs) as well as perform geographically linked co-sampling of humans and animals to establish the main sources of leptospirosis in the region.

@article{tu_high_2015,
	title = {High levels of contamination and antimicrobial-resistant non-typhoidal {Salmonella} serovars on pig and poultry farms in the {Mekong} {Delta} of {Vietnam}.},
	volume = {143},
	issn = {1469-4409 0950-2688},
	doi = {10.1017/S0950268815000102},
	abstract = {We investigated the prevalence, diversity, and antimicrobial resistance (AMR) profiles of non-typhoidal Salmonella (NTS) and associated risk factors on 341 pig, chicken, and duck farms in Dong Thap province (Mekong Delta, Vietnam). Sampling was stratified by species, district (four categories), and farm size (three categories). Pooled faeces, collected using boot swabs, were tested using  ISO 6575: 2002 (Annex D). Isolates were serogrouped; group B isolates were tested by polymerase chain reaction to detect S. Typhimurium and (monophasic) serovar 4,[5],12:i:- variants. The farm-level adjusted NTS prevalence was 64.7\%, 94.3\% and 91.3\% for chicken, duck and pig farms, respectively. Factors independently associated with NTS were duck farms [odds ratio (OR) 21.2], farm with {\textgreater}50 pigs (OR 11.9), pig farm with 5-50 pigs (OR 4.88) (vs. chickens), and frequent rodent  sightings (OR 2.3). Both S. Typhimurium and monophasic S. Typhimurium were more common in duck farms. Isolates had a high prevalence of resistance (77.6\%) against tetracycline, moderate resistance (20-30\%) against chloramphenicol, sulfamethoxazole-trimethoprim, ampicillin and nalidixic acid, and low resistance  ({\textless}5\%) against ciprofloxacin and third-generation cephalosporins. Multidrug resistance (resistance against 3 classes of antimicrobial) was independently associated with monophasic S. Typhimurium and other group B isolates (excluding S. Typhimurium) and pig farms. The unusually high prevalence of NTS on Mekong Delta farms poses formidable challenges for control.},
	language = {eng},
	number = {14},
	journal = {Epidemiology and infection},
	author = {Tu, L. T. P. and Hoang, N. V. M. and Cuong, N. V. and Campbell, J. and Bryant, J. E. and Hoa, N. T. and Kiet, B. T. and Thompson, C. and Duy, D. T. and Phat, V. V. and Hien, V. B. and Thwaites, G. and Baker, S. and Carrique-Mas, J. J.},
	month = oct,
	year = {2015},
	pmid = {25778282},
	pmcid = {PMC4595858},
	keywords = {*Animal Husbandry, *Drug Resistance, Bacterial, *Environmental Pollution, *Poultry, *Swine, Animals, Epidemiology, Feces/microbiology, Prevalence, Salmonella, Salmonella Infections, Animal/*epidemiology/microbiology, Salmonella/drug effects/*isolation \& purification, Serotyping, Vietnam, zoonoses},
	pages = {3074--3086},
}

We investigated the prevalence, diversity, and antimicrobial resistance (AMR) profiles of non-typhoidal Salmonella (NTS) and associated risk factors on 341 pig, chicken, and duck farms in Dong Thap province (Mekong Delta, Vietnam). Sampling was stratified by species, district (four categories), and farm size (three categories). Pooled faeces, collected using boot swabs, were tested using ISO 6575: 2002 (Annex D). Isolates were serogrouped; group B isolates were tested by polymerase chain reaction to detect S. Typhimurium and (monophasic) serovar 4,[5],12:i:- variants. The farm-level adjusted NTS prevalence was 64.7%, 94.3% and 91.3% for chicken, duck and pig farms, respectively. Factors independently associated with NTS were duck farms [odds ratio (OR) 21.2], farm with \textgreater50 pigs (OR 11.9), pig farm with 5-50 pigs (OR 4.88) (vs. chickens), and frequent rodent sightings (OR 2.3). Both S. Typhimurium and monophasic S. Typhimurium were more common in duck farms. Isolates had a high prevalence of resistance (77.6%) against tetracycline, moderate resistance (20-30%) against chloramphenicol, sulfamethoxazole-trimethoprim, ampicillin and nalidixic acid, and low resistance (\textless5%) against ciprofloxacin and third-generation cephalosporins. Multidrug resistance (resistance against 3 classes of antimicrobial) was independently associated with monophasic S. Typhimurium and other group B isolates (excluding S. Typhimurium) and pig farms. The unusually high prevalence of NTS on Mekong Delta farms poses formidable challenges for control.

@article{nhung_high_2015,
	title = {High levels of antimicrobial resistance among escherichia coli isolates from livestock farms and synanthropic rats and shrews in the {Mekong} {Delta} of {Vietnam}.},
	volume = {81},
	copyright = {Copyright (c) 2015, American Society for Microbiology. All Rights Reserved.},
	issn = {1098-5336 0099-2240},
	doi = {10.1128/AEM.03366-14},
	abstract = {In Mekong Delta farms (Vietnam), antimicrobials are extensively used, but limited data are available on levels of antimicrobial resistance (AMR) among Escherichia  coli isolates. We performed a structured survey of AMR in E. coli isolates (n = 434) from 90 pig, chicken, and duck farms. The results were compared with AMR among E. coli isolates (n = 234) from 66 small wild animals (rats and shrews) trapped on farms and in forests and rice fields. The isolates were susceptibility tested against eight antimicrobials. E. coli isolates from farmed animals were resistant to a median of 4 (interquartile range [IQR], 3 to 6) antimicrobials versus 1 (IQR, 1 to 2) among wild mammal isolates (P {\textless} 0.001). The prevalences of AMR among farmed species isolates (versus wild animals) were as follows: tetracycline, 84.7\% (versus 25.6\%); ampicillin, 78.9\% (versus 85.9\%); trimethoprim-sulfamethoxazole, 52.1\% (versus 18.8\%); chloramphenicol, 39.9\% (versus 22.5\%); amoxicillin-clavulanic acid, 36.6\% (versus 34.5\%); and ciprofloxacin, 24.9\% (versus 7.3\%). The prevalence of multidrug resistance (MDR)  (resistance against three or more antimicrobial classes) among pig isolates was 86.7\% compared to 66.9 to 72.7\% among poultry isolates. After adjusting for host  species, MDR was approximately 8 times greater among isolates from wild mammals trapped on farms than among those trapped in forests/rice fields (P {\textless} 0.001). Isolates were assigned to unique profiles representing their combinations of susceptibility results. Multivariable analysis of variance indicated that AMR profiles from wild mammals trapped on farms and those from domestic animals were  more alike (R(2) range, 0.14 to 0.30) than E. coli isolates from domestic animals and mammals trapped in the wild (R(2) range, 0.25 to 0.45). The results strongly  suggest that AMR on farms is a key driver of environmental AMR in the Mekong Delta.},
	language = {eng},
	number = {3},
	journal = {Applied and environmental microbiology},
	author = {Nhung, N. T. and Cuong, N. V. and Campbell, J. and Hoa, N. T. and Bryant, J. E. and Truc, V. N. T. and Kiet, B. T. and Jombart, T. and Trung, N. V. and Hien, V. B. and Thwaites, G. and Baker, S. and Carrique-Mas, J.},
	month = feb,
	year = {2015},
	pmid = {25398864},
	pmcid = {PMC4292488},
	keywords = {*Drug Resistance, Bacterial, Animals, Animals, Domestic/*microbiology, Animals, Wild/*microbiology, Anti-Bacterial Agents/*pharmacology, Chickens, Ducks, Escherichia coli Infections/microbiology/*veterinary, Escherichia coli/*drug effects/isolation \& purification, Microbial Sensitivity Tests, Rats, Shrews/microbiology, Swine, Vietnam},
	pages = {812--820},
}

In Mekong Delta farms (Vietnam), antimicrobials are extensively used, but limited data are available on levels of antimicrobial resistance (AMR) among Escherichia coli isolates. We performed a structured survey of AMR in E. coli isolates (n = 434) from 90 pig, chicken, and duck farms. The results were compared with AMR among E. coli isolates (n = 234) from 66 small wild animals (rats and shrews) trapped on farms and in forests and rice fields. The isolates were susceptibility tested against eight antimicrobials. E. coli isolates from farmed animals were resistant to a median of 4 (interquartile range [IQR], 3 to 6) antimicrobials versus 1 (IQR, 1 to 2) among wild mammal isolates (P \textless 0.001). The prevalences of AMR among farmed species isolates (versus wild animals) were as follows: tetracycline, 84.7% (versus 25.6%); ampicillin, 78.9% (versus 85.9%); trimethoprim-sulfamethoxazole, 52.1% (versus 18.8%); chloramphenicol, 39.9% (versus 22.5%); amoxicillin-clavulanic acid, 36.6% (versus 34.5%); and ciprofloxacin, 24.9% (versus 7.3%). The prevalence of multidrug resistance (MDR) (resistance against three or more antimicrobial classes) among pig isolates was 86.7% compared to 66.9 to 72.7% among poultry isolates. After adjusting for host species, MDR was approximately 8 times greater among isolates from wild mammals trapped on farms than among those trapped in forests/rice fields (P \textless 0.001). Isolates were assigned to unique profiles representing their combinations of susceptibility results. Multivariable analysis of variance indicated that AMR profiles from wild mammals trapped on farms and those from domestic animals were more alike (R(2) range, 0.14 to 0.30) than E. coli isolates from domestic animals and mammals trapped in the wild (R(2) range, 0.25 to 0.45). The results strongly suggest that AMR on farms is a key driver of environmental AMR in the Mekong Delta.

@article{weinert_genomic_2015,
	title = {Genomic signatures of human and animal disease in the zoonotic pathogen {Streptococcus} suis.},
	volume = {6},
	issn = {2041-1723 2041-1723},
	doi = {10.1038/ncomms7740},
	abstract = {Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates with detailed clinical phenotypes from pigs and humans from the United Kingdom and Vietnam. Here, we show that isolates associated with disease contain substantially fewer genes than non-clinical isolates, but are more likely to encode virulence factors. Human disease isolates are limited to a single-virulent population, originating in the 1920, s when pig production was intensified, but no consistent genomic differences between pig and human isolates are observed. There is little geographical clustering of different S. suis subpopulations, and  the bacterium undergoes high rates of recombination, implying that an increase in virulence anywhere in the world could have a global impact over a short timescale.},
	language = {eng},
	journal = {Nature communications},
	author = {Weinert, Lucy A. and Chaudhuri, Roy R. and Wang, Jinhong and Peters, Sarah E. and Corander, Jukka and Jombart, Thibaut and Baig, Abiyad and Howell, Kate J. and Vehkala, Minna and Valimaki, Niko and Harris, David and Chieu, Tran Thi Bich and Van Vinh Chau, Nguyen and Campbell, James and Schultsz, Constance and Parkhill, Julian and Bentley, Stephen D. and Langford, Paul R. and Rycroft, Andrew N. and Wren, Brendan W. and Farrar, Jeremy and Baker, Stephen and Hoa, Ngo Thi and Holden, Matthew T. G. and Tucker, Alexander W. and Maskell, Duncan J.},
	month = mar,
	year = {2015},
	pmid = {25824154},
	pmcid = {PMC4389249},
	keywords = {Animals, Genetic Variation, Genomics, Humans, Streptococcal Infections/microbiology/*veterinary, Streptococcus suis/*genetics/pathogenicity, Sus scrofa, Swine Diseases/*microbiology, Swine/microbiology, United Kingdom, Vietnam, Virulence Factors/genetics},
	pages = {6740},
}

Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates with detailed clinical phenotypes from pigs and humans from the United Kingdom and Vietnam. Here, we show that isolates associated with disease contain substantially fewer genes than non-clinical isolates, but are more likely to encode virulence factors. Human disease isolates are limited to a single-virulent population, originating in the 1920, s when pig production was intensified, but no consistent genomic differences between pig and human isolates are observed. There is little geographical clustering of different S. suis subpopulations, and the bacterium undergoes high rates of recombination, implying that an increase in virulence anywhere in the world could have a global impact over a short timescale.

@article{anh_diversity_2015,
	title = {Diversity of {Bartonella} spp. in {Bats}, {Southern} {Vietnam}.},
	volume = {21},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid2107.141760},
	language = {eng},
	number = {7},
	journal = {Emerging infectious diseases},
	author = {Anh, Pham Hong and Van Cuong, Nguyen and Son, Nguyen Truong and Tue, Ngo Tri and Kosoy, Michael and Woolhouse, Mark E. J. and Baker, Stephen and Bryant, Juliet E. and Thwaites, Guy and Carrique-Mas, Juan J. and Rabaa, Maia A.},
	month = jul,
	year = {2015},
	pmid = {26079810},
	pmcid = {PMC4480386},
	keywords = {Animals, Bacterial Proteins/genetics, Bartonella, Bartonella Infections/microbiology/*veterinary, Bartonella/*genetics, Chiroptera/*microbiology, Citrate (si)-Synthase/genetics, Disease Reservoirs, Genes, Bacterial, Genetic Variation, Molecular Sequence Data, Molecular Typing, Vietnam, bacteria, bats, diversity, reservoir species, zoonoses},
	pages = {1266--1267},
}

@article{le_diagnosing_2015,
	title = {Diagnosing {Rhodococcus} equi infections in a setting where tuberculosis is highly  endemic: a double challenge.},
	volume = {53},
	copyright = {Copyright (c) 2015, Le et al.},
	issn = {1098-660X 0095-1137},
	doi = {10.1128/JCM.02284-14},
	abstract = {Rhodococcus equi infection is increasing in regions with high HIV prevalence worldwide. The microbiological features and clinical mimicry of tuberculosis infection pose diagnostic challenges in high-tuberculosis-incidence settings. We  present two HIV-associated cases of R. equi infection from Vietnam and discuss the unique diagnostic challenges in such settings.},
	language = {eng},
	number = {4},
	journal = {Journal of clinical microbiology},
	author = {Le, Thuy and Cash-Goldwasser, Shama and Tho, Phan Vinh and Lan, Nguyen Phu Huong and Campbell, James I. and van Doorn, H. Rogier and Lam, Nguyen Tien and Trung, Nguyen Vu and Trinh, Dao Tuyet and Van Kinh, Nguyen and Wertheim, Heiman F. L.},
	month = apr,
	year = {2015},
	pmid = {25631800},
	pmcid = {PMC4365230},
	keywords = {*Rhodococcus equi, Actinomycetales Infections/complications/*diagnosis/epidemiology/microbiology, Adult, Anti-Bacterial Agents/therapeutic use, Anti-HIV Agents/therapeutic use, Ascorbic Acid, Cholecalciferol, Dehydroepiandrosterone/analogs \& derivatives, HIV Infections/complications/drug therapy, Humans, Male, Nicotinic Acids, Plant Extracts, Tuberculosis, Pulmonary/complications/*diagnosis/epidemiology, Vietnam/epidemiology},
	pages = {1431--1433},
}

Rhodococcus equi infection is increasing in regions with high HIV prevalence worldwide. The microbiological features and clinical mimicry of tuberculosis infection pose diagnostic challenges in high-tuberculosis-incidence settings. We present two HIV-associated cases of R. equi infection from Vietnam and discuss the unique diagnostic challenges in such settings.

@article{loan_bartonella_2015,
	title = {Bartonella species and trombiculid mites of rats from the {Mekong} {Delta} of {Vietnam}.},
	volume = {15},
	issn = {1557-7759 1530-3667},
	doi = {10.1089/vbz.2014.1604},
	abstract = {A survey of Bartonella spp. from 275 rats purchased in food markets (n=150) and trapped in different ecosystems (rice field, forest, and animal farms) (n=125) was carried out during October, 2012-March, 2013, in the Mekong Delta of Vietnam. The overall Bartonella spp. prevalence detected by culture and PCR in blood was 14.9\% (10.7-19.1\%), the highest corresponding to Rattus tanezumi (49.2\%), followed by Rattus norvegicus (20.7\%). Trapped rats were also investigated for the presence and type of chiggers (larvae of trombiculid mites), and Bartonella spp. were investigated on chigger pools collected from each rat by RT-PCR. A total of five Bartonella spp. were identified in rats, three of which (B. elizabethae, B. rattimassiliensis, and B. tribocorum) are known zoonotic pathogens. Among trapped rats, factors independently associated with increased prevalence of Bartonella spp. included: (1) Rat species (R. tanezumi); (2) the number of Trombiculini-Blankaartia and Schoengastiini-Ascoschoengastia mites found on rats; and (3) the habitat of the rat (i.e., forest/fields vs. animal farms). The prevalence of Bartonella infection among chiggers from Bartonella spp.-positive R. tanezumi rats was 5/25 (25\%), compared with 1/27 (3.7\%) among Bartonella spp.-negative R. tanezumi rats (relative risk [RR]=5.4, 95\% confidence interval [CI] 0.68-43.09). The finding of Bartonella spp.-positive chiggers on Bartonella spp.-negative rats is strongly suggestive of a transovarial transmission cycle. Rats are ubiquitous in areas of human activity and farms in the Mekong Delta; in addition, trapping and trading of rats for food is common. To correctly assess the human risks due to rat trapping, marketing, and carcass dressing, further studies are needed to establish the routes of transmission and  cycle of infection. The widespread presence of these zoonotic pathogens in rats and the abundance of human-rat interactions suggest that surveillance efforts should be enhanced to detect any human cases of Bartonella infection that may arise.},
	language = {eng},
	number = {1},
	journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
	author = {Loan, Hoang Kim and Cuong, Nguyen Van and Takhampunya, Ratree and Klangthong, Kewalin and Osikowicz, Lynn and Kiet, Bach Tuan and Campbell, James and Bryant, Juliet and Promstaporn, Sommai and Kosoy, Michael and Hoang, Nguyen Van and Morand, Serge and Chaval, Yannick and Hien, Vo Be and Carrique-Mas, Juan},
	month = jan,
	year = {2015},
	pmid = {25629779},
	pmcid = {PMC4307099},
	keywords = {Animals, Bartonella, Bartonella Infections/transmission/veterinary, Bartonella/*physiology, Chiggers, Disease Reservoirs/microbiology, Disease Vectors, Human Activities, Humans, Meat/microbiology, Rats, Rattus, Real-Time Polymerase Chain Reaction, Rodent Diseases/*microbiology/transmission, Trombiculidae/*microbiology, Vietnam, Zoonoses/microbiology},
	pages = {40--47},
}

A survey of Bartonella spp. from 275 rats purchased in food markets (n=150) and trapped in different ecosystems (rice field, forest, and animal farms) (n=125) was carried out during October, 2012-March, 2013, in the Mekong Delta of Vietnam. The overall Bartonella spp. prevalence detected by culture and PCR in blood was 14.9% (10.7-19.1%), the highest corresponding to Rattus tanezumi (49.2%), followed by Rattus norvegicus (20.7%). Trapped rats were also investigated for the presence and type of chiggers (larvae of trombiculid mites), and Bartonella spp. were investigated on chigger pools collected from each rat by RT-PCR. A total of five Bartonella spp. were identified in rats, three of which (B. elizabethae, B. rattimassiliensis, and B. tribocorum) are known zoonotic pathogens. Among trapped rats, factors independently associated with increased prevalence of Bartonella spp. included: (1) Rat species (R. tanezumi); (2) the number of Trombiculini-Blankaartia and Schoengastiini-Ascoschoengastia mites found on rats; and (3) the habitat of the rat (i.e., forest/fields vs. animal farms). The prevalence of Bartonella infection among chiggers from Bartonella spp.-positive R. tanezumi rats was 5/25 (25%), compared with 1/27 (3.7%) among Bartonella spp.-negative R. tanezumi rats (relative risk [RR]=5.4, 95% confidence interval [CI] 0.68-43.09). The finding of Bartonella spp.-positive chiggers on Bartonella spp.-negative rats is strongly suggestive of a transovarial transmission cycle. Rats are ubiquitous in areas of human activity and farms in the Mekong Delta; in addition, trapping and trading of rats for food is common. To correctly assess the human risks due to rat trapping, marketing, and carcass dressing, further studies are needed to establish the routes of transmission and cycle of infection. The widespread presence of these zoonotic pathogens in rats and the abundance of human-rat interactions suggest that surveillance efforts should be enhanced to detect any human cases of Bartonella infection that may arise.

@article{thompson_prospective_2015,
	title = {A prospective multi-center observational study of children hospitalized with diarrhea in {Ho} {Chi} {Minh} {City}, {Vietnam}.},
	volume = {92},
	copyright = {(c) The American Society of Tropical Medicine and Hygiene.},
	issn = {1476-1645 0002-9637},
	doi = {10.4269/ajtmh.14-0655},
	abstract = {We performed a prospective multicenter study to address the lack of data on the etiology, clinical and demographic features of hospitalized pediatric diarrhea in Ho Chi Minh City (HCMC), Vietnam. Over 2,000 (1,419 symptomatic and 609 non-diarrheal control) children were enrolled in three hospitals over a 1-year period in 2009-2010. Aiming to detect a panel of pathogens, we identified a known diarrheal pathogen in stool samples from 1,067/1,419 (75.2\%) children with diarrhea and from 81/609 (13.3\%) children without diarrhea. Rotavirus predominated in the symptomatic children (664/1,419; 46.8\%), followed by norovirus (293/1,419; 20.6\%). The bacterial pathogens Salmonella, Campylobacter,  and Shigella were cumulatively isolated from 204/1,419 (14.4\%) diarrheal children and exhibited extensive antimicrobial resistance, most notably to fluoroquinolones and third-generation cephalosporins. We suggest renewed efforts  in generation and implementation of policies to control the sale and prescription of antimicrobials to curb bacterial resistance and advise consideration of a subsidized rotavirus vaccination policy to limit the morbidity due to diarrheal disease in Vietnam.},
	language = {eng},
	number = {5},
	journal = {The American journal of tropical medicine and hygiene},
	author = {Thompson, Corinne N. and Phan, My V. T. and Hoang, Nguyen Van Minh and Minh, Pham Van and Vinh, Nguyen Thanh and Thuy, Cao Thu and Nga, Tran Thi Thu and Rabaa, Maia A. and Duy, Pham Thanh and Dung, Tran Thi Ngoc and Phat, Voong Vinh and Nga, Tran Vu Thieu and Tu, Le Thi Phuong and Tuyen, Ha Thanh and Yoshihara, Keisuke and Jenkins, Claire and Duong, Vu Thuy and Phuc, Hoang Le and Tuyet, Pham Thi Ngoc and Ngoc, Nguyen Minh and Vinh, Ha and Chinh, Nguyen Tran and Thuong, Tang Chi and Tuan, Ha Manh and Hien, Tran Tinh and Campbell, James I. and Chau, Nguyen Van Vinh and Thwaites, Guy and Baker, Stephen},
	month = may,
	year = {2015},
	pmid = {25802437},
	pmcid = {PMC4426562},
	keywords = {Anti-Infective Agents/pharmacology, Bacteria/drug effects, Bacterial Infections/complications/*epidemiology/microbiology, Caliciviridae Infections/complications/*epidemiology/microbiology, Child, Preschool, Cross-Sectional Studies, Demography, Diarrhea/*complications/epidemiology/microbiology, Female, Hospitalization, Humans, Infant, Male, Microbial Sensitivity Tests, Norovirus/drug effects/*isolation \& purification, Prospective Studies, Rotavirus Infections/complications/*epidemiology/microbiology, Rotavirus/drug effects/isolation \& purification, Seasons, Vietnam/epidemiology},
	pages = {1045--1052},
}

We performed a prospective multicenter study to address the lack of data on the etiology, clinical and demographic features of hospitalized pediatric diarrhea in Ho Chi Minh City (HCMC), Vietnam. Over 2,000 (1,419 symptomatic and 609 non-diarrheal control) children were enrolled in three hospitals over a 1-year period in 2009-2010. Aiming to detect a panel of pathogens, we identified a known diarrheal pathogen in stool samples from 1,067/1,419 (75.2%) children with diarrhea and from 81/609 (13.3%) children without diarrhea. Rotavirus predominated in the symptomatic children (664/1,419; 46.8%), followed by norovirus (293/1,419; 20.6%). The bacterial pathogens Salmonella, Campylobacter, and Shigella were cumulatively isolated from 204/1,419 (14.4%) diarrheal children and exhibited extensive antimicrobial resistance, most notably to fluoroquinolones and third-generation cephalosporins. We suggest renewed efforts in generation and implementation of policies to control the sale and prescription of antimicrobials to curb bacterial resistance and advise consideration of a subsidized rotavirus vaccination policy to limit the morbidity due to diarrheal disease in Vietnam.

@article{tan_viral_2014,
	title = {Viral aetiology of central nervous system infections in adults admitted to a tertiary referral hospital in southern {Vietnam} over 12 years.},
	volume = {8},
	issn = {1935-2735 1935-2727},
	doi = {10.1371/journal.pntd.0003127},
	abstract = {BACKGROUND: Central nervous system (CNS) infections are important diseases in both children and adults worldwide. The spectrum of infections is broad, encompassing bacterial/aseptic meningitis and encephalitis. Viruses are regarded  as the most common causes of encephalitis and aseptic meningitis. Better understanding of the viral causes of the diseases is of public health importance, in order to better inform immunization policy, and may influence clinical management. METHODOLOGY/PRINCIPAL FINDINGS: Study was conducted at the Hospital for Tropical Diseases in Ho Chi Minh City, a primary, secondary, and tertiary referral hospital for all southern provinces of Vietnam. Between December 1996 and May 2008, patients with CNS infections of presumed viral origin were enrolled. Laboratory diagnostics consisted of molecular and serological tests targeted at 14 meningitis/encephalitis-associated viruses. Of 291 enrolled patients, fatal outcome and neurological sequelae were recorded in 10\% (28/291) and 27\% (78/291), respectively. Mortality was especially high (9/19, 47\%) amongst those with confirmed herpes simplex encephalitis which is attributed to the limited availability of intravenous acyclovir/valacyclovir. Japanese encephalitis virus, dengue virus, herpes simplex virus, and enteroviruses were the most common viruses detected, responsible for 36 (12\%), 19 (6.5\%), 19 (6.5\%) and 8 (2.7\%) respectively, followed by rubella virus (6, 2\%), varicella zoster virus (5, 1.7\%), mumps virus (2, 0.7\%), cytomegalovirus (1, 0.3\%), and rabies virus (1, 0.3\%). CONCLUSIONS/SIGNIFICANCE: Viral infections of the CNS in adults in Vietnam are associated with high morbidity and mortality. Despite extensive laboratory testing, 68\% of the patients remain undiagnosed. Together with our previous reports, the data confirm that Japanese encephalitis virus, dengue virus, herpes  simplex virus, and enteroviruses are the leading identified causes of CNS viral infections in Vietnam, suggest that the majority of morbidity/mortality amongst patients with a confirmed/probable diagnosis is preventable by adequate vaccination/treatment, and are therefore of public health significance.},
	language = {eng},
	number = {8},
	journal = {PLoS neglected tropical diseases},
	author = {Tan, Le Van and Thai, Le Hong and Phu, Nguyen Hoan and Nghia, Ho Dang Trung and Chuong, Ly Van and Sinh, Dinh Xuan and Phong, Nguyen Duy and Mai, Nguyen Thi Hoang and Man, Dinh Nguyen Huy and Hien, Vo Minh and Vinh, Nguyen Thanh and Day, Jeremy and Chau, Nguyen Van Vinh and Hien, Tran Tinh and Farrar, Jeremy and de Jong, Menno D. and Thwaites, Guy and van Doorn, H. Rogier and Chau, Tran Thi Hong},
	month = aug,
	year = {2014},
	pmid = {25165820},
	pmcid = {PMC4148224},
	keywords = {*Central Nervous System Infections/epidemiology/mortality/virology, Adolescent, Adult, Aged, Female, Humans, Male, Prospective Studies, Tertiary Care Centers/*statistics \& numerical data, Vietnam/epidemiology, Viruses/*isolation \& purification, Young Adult},
	pages = {e3127},
}

BACKGROUND: Central nervous system (CNS) infections are important diseases in both children and adults worldwide. The spectrum of infections is broad, encompassing bacterial/aseptic meningitis and encephalitis. Viruses are regarded as the most common causes of encephalitis and aseptic meningitis. Better understanding of the viral causes of the diseases is of public health importance, in order to better inform immunization policy, and may influence clinical management. METHODOLOGY/PRINCIPAL FINDINGS: Study was conducted at the Hospital for Tropical Diseases in Ho Chi Minh City, a primary, secondary, and tertiary referral hospital for all southern provinces of Vietnam. Between December 1996 and May 2008, patients with CNS infections of presumed viral origin were enrolled. Laboratory diagnostics consisted of molecular and serological tests targeted at 14 meningitis/encephalitis-associated viruses. Of 291 enrolled patients, fatal outcome and neurological sequelae were recorded in 10% (28/291) and 27% (78/291), respectively. Mortality was especially high (9/19, 47%) amongst those with confirmed herpes simplex encephalitis which is attributed to the limited availability of intravenous acyclovir/valacyclovir. Japanese encephalitis virus, dengue virus, herpes simplex virus, and enteroviruses were the most common viruses detected, responsible for 36 (12%), 19 (6.5%), 19 (6.5%) and 8 (2.7%) respectively, followed by rubella virus (6, 2%), varicella zoster virus (5, 1.7%), mumps virus (2, 0.7%), cytomegalovirus (1, 0.3%), and rabies virus (1, 0.3%). CONCLUSIONS/SIGNIFICANCE: Viral infections of the CNS in adults in Vietnam are associated with high morbidity and mortality. Despite extensive laboratory testing, 68% of the patients remain undiagnosed. Together with our previous reports, the data confirm that Japanese encephalitis virus, dengue virus, herpes simplex virus, and enteroviruses are the leading identified causes of CNS viral infections in Vietnam, suggest that the majority of morbidity/mortality amongst patients with a confirmed/probable diagnosis is preventable by adequate vaccination/treatment, and are therefore of public health significance.

@article{pham_prevalence_2014,
	title = {The prevalence and genetic diversity of group {A} rotaviruses on pig farms in the {Mekong} {Delta} region of {Vietnam}.},
	volume = {170},
	copyright = {Copyright (c) 2014 The Authors. Published by Elsevier B.V. All rights reserved.},
	issn = {1873-2542 0378-1135},
	doi = {10.1016/j.vetmic.2014.02.030},
	abstract = {Group A rotaviruses (ARoVs) are a common cause of severe diarrhea among children  worldwide and the cause of approximately 45\% of pediatric hospitalizations for acute diarrhea in Vietnam. ARoVs are known to cause significant economic losses to livestock producers by reducing growth performance and production efficiencies, however little is known about the implications of asymptomatic endemic circulation of ARoV. We aimed to determine the prevalence and predominant circulating genotypes of ARoVs on pig farms in a southern province of Vietnam. We found overall animal-level and farm-level prevalence of 32.7\% (239/730) and 74\% (77/104), respectively, and identified six different G types and 4 P types in various combinations (G2, G3, G4, G5, G9, G11 and P[6], P[13], P[23], and P[34]). There was no significant association between ARoV infection and clinical disease  in pigs, suggesting that endemic asymptomatic circulation of ARoV may complicate  rotavirus disease attribution during outbreaks of diarrhea in swine. Sequence analysis of the detected ARoVs suggested homology to recent human clinical cases  and extensive genetic diversity. The epidemiological relevance of these findings  for veterinary practitioners and to ongoing pediatric ARoV vaccine initiatives in Vietnam merits further study.},
	language = {eng},
	number = {3-4},
	journal = {Veterinary microbiology},
	author = {Pham, Hong Anh and Carrique-Mas, Juan J. and Nguyen, Van Cuong and Ngo, Thi Hoa and Nguyet, Lam Anh and Do, Tien Duy and Vo, Be Hien and Phan, Vu Tra My and Rabaa, Maia A. and Farrar, Jeremy and Baker, Stephen and Bryant, Juliet E.},
	month = jun,
	year = {2014},
	pmid = {24679960},
	pmcid = {PMC4003349},
	keywords = {*Genetic Variation, Animals, Animals, Newborn, Feces/virology, Genotype, Phylogeny, Prevalence, Regression Analysis, Risk Factors, Rotavirus Infections/*epidemiology/*virology, Rotavirus/classification/genetics/*physiology, Rotaviruses, Swine, Vietnam, Vietnam/epidemiology, pigs},
	pages = {258--265},
}

Group A rotaviruses (ARoVs) are a common cause of severe diarrhea among children worldwide and the cause of approximately 45% of pediatric hospitalizations for acute diarrhea in Vietnam. ARoVs are known to cause significant economic losses to livestock producers by reducing growth performance and production efficiencies, however little is known about the implications of asymptomatic endemic circulation of ARoV. We aimed to determine the prevalence and predominant circulating genotypes of ARoVs on pig farms in a southern province of Vietnam. We found overall animal-level and farm-level prevalence of 32.7% (239/730) and 74% (77/104), respectively, and identified six different G types and 4 P types in various combinations (G2, G3, G4, G5, G9, G11 and P[6], P[13], P[23], and P[34]). There was no significant association between ARoV infection and clinical disease in pigs, suggesting that endemic asymptomatic circulation of ARoV may complicate rotavirus disease attribution during outbreaks of diarrhea in swine. Sequence analysis of the detected ARoVs suggested homology to recent human clinical cases and extensive genetic diversity. The epidemiological relevance of these findings for veterinary practitioners and to ongoing pediatric ARoV vaccine initiatives in Vietnam merits further study.

@article{cuong_serological_2014,
	title = {Serological and virological surveillance for porcine reproductive and respiratory syndrome virus, porcine circovirus type 2, and influenza {A} viruses among smallholder swine farms of the {Mekong} {Delta}, {Vietnam}},
	volume = {22},
	issn = {1537-209X},
	url = {https://ora.ox.ac.uk/objects/uuid%3Abd78499a-7813-4854-a676-dc0f40053394},
	number = {5},
	urldate = {2017-07-06},
	journal = {JOURNAL OF SWINE HEALTH AND PRODUCTION},
	author = {Cuong, N. V. and Carrique-Mas, J. and Thu, H. T. V. and Hien, N. D. and Hoa, N. T. and Nguyet, L. A. and Anh, P. H. and Bryant, J. E.},
	year = {2014},
	pages = {224--231},
}

@article{huong_raw_2014,
	title = {Raw pig blood consumption and potential risk for {Streptococcus} suis infection, {Vietnam}.},
	volume = {20},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid2011.140915},
	abstract = {We assessed consumption of raw pig blood, which is a risk factor for Streptococcus suis infection in Vietnam, by using a mix-method design. Factors associated with consumption included rural residency, age, sex, occupation, income, and marital status. We identified risk groups and practices and perceptions that should be targeted by communication programs.},
	language = {eng},
	number = {11},
	journal = {Emerging infectious diseases},
	author = {Huong, Vu Thi Lan and Hoa, Ngo Thi and Horby, Peter and Bryant, Juliet E. and Van Kinh, Nguyen and Toan, Tran Khanh and Wertheim, Heiman F. L.},
	month = nov,
	year = {2014},
	pmid = {25340391},
	pmcid = {PMC4214319},
	keywords = {*Feeding Behavior, *Public Health Surveillance, *Streptococcus suis, Adolescent, Adult, Aged, Animals, Female, Humans, Male, Middle Aged, Odds Ratio, Risk, Streptococcal Infections/*epidemiology/*transmission, Vietnam/epidemiology, Young Adult},
	pages = {1895--1898},
}

We assessed consumption of raw pig blood, which is a risk factor for Streptococcus suis infection in Vietnam, by using a mix-method design. Factors associated with consumption included rural residency, age, sex, occupation, income, and marital status. We identified risk groups and practices and perceptions that should be targeted by communication programs.

@article{van_dung_prevalence_2014,
	title = {Prevalence, genetic diversity and recombination of species {G} enteroviruses infecting pigs in {Vietnam}.},
	volume = {95},
	issn = {1465-2099 0022-1317},
	doi = {10.1099/vir.0.061978-0},
	abstract = {Picornaviruses infecting pigs, described for many years as 'porcine enteroviruses', have recently been recognized as distinct viruses within three distinct genera (Teschovirus, Sapelovirus and Enterovirus). To better characterize the epidemiology and genetic diversity of members of the Enterovirus genus, faecal samples from pigs from four provinces in Vietnam were screened by PCR using conserved enterovirus (EV)-specific primers from the 5' untranslated region (5' UTR). High rates of infection were recorded in pigs on all farms, with detection frequencies of approximately 90\% in recently weaned pigs but declining  to 40\% in those aged over 1 year. No differences in EV detection rates were observed between pigs with and without diarrhoea [74\% (n = 70) compared with 72\%  (n = 128)]. Genetic analysis of consensus VP4/VP2 and VP1 sequences amplified from a subset of EV-infected pigs identified species G EVs in all samples. Among  these, VP1 sequence comparisons identified six type 1 and seven type 6 variants,  while four further VP1 sequences failed to group with any previously identified},
	language = {eng},
	number = {Pt 3},
	journal = {The Journal of general virology},
	author = {Van Dung, Nguyen and Anh, Pham Hong and Van Cuong, Nguyen and Hoa, Ngo Thi and Carrique-Mas, Juan and Hien, Vo Be and Campbell, James and Baker, Stephen and Farrar, Jeremy and Woolhouse, Mark E. and Bryant, Juliet E. and Simmonds, Peter},
	month = mar,
	year = {2014},
	pmid = {24323635},
	pmcid = {PMC4029279},
	keywords = {*Genetic Variation, *Recombination, Genetic, Animals, Enterovirus Infections/epidemiology/*veterinary/virology, Enteroviruses, Porcine/classification/*genetics/isolation \& purification, Molecular Sequence Data, Phylogeny, Prevalence, Sus scrofa, Swine, Swine Diseases/epidemiology/*virology, Vietnam/epidemiology, Viral Proteins/genetics},
	pages = {549--556},
}

Picornaviruses infecting pigs, described for many years as 'porcine enteroviruses', have recently been recognized as distinct viruses within three distinct genera (Teschovirus, Sapelovirus and Enterovirus). To better characterize the epidemiology and genetic diversity of members of the Enterovirus genus, faecal samples from pigs from four provinces in Vietnam were screened by PCR using conserved enterovirus (EV)-specific primers from the 5' untranslated region (5' UTR). High rates of infection were recorded in pigs on all farms, with detection frequencies of approximately 90% in recently weaned pigs but declining to 40% in those aged over 1 year. No differences in EV detection rates were observed between pigs with and without diarrhoea [74% (n = 70) compared with 72% (n = 128)]. Genetic analysis of consensus VP4/VP2 and VP1 sequences amplified from a subset of EV-infected pigs identified species G EVs in all samples. Among these, VP1 sequence comparisons identified six type 1 and seven type 6 variants, while four further VP1 sequences failed to group with any previously identified

@article{dunning_open_2014,
	title = {Open source clinical science for emerging infections.},
	volume = {14},
	issn = {1474-4457 1473-3099},
	doi = {10.1016/S1473-3099(13)70327-X},
	language = {eng},
	number = {1},
	journal = {The Lancet. Infectious diseases},
	author = {Dunning, Jake W. and Merson, Laura and Rohde, Gernot G. U. and Gao, Zhancheng and Semple, Malcolm G. and Tran, Dat and Gordon, Anthony and Olliaro, Piero L. and Khoo, Saye H. and Bruzzone, Roberto and Horby, Peter and Cobb, J. Perren and Longuere, Kajsa-Stina and Kellam, Paul and Nichol, Alistair and Brett, Stephen and Everett, Dean and Walsh, Timothy S. and Hien, Tran-Tinh and Yu, Hongjie and Zambon, Maria and Ruiz-Palacios, Guillermo and Lang, Trudie and Akhvlediani, Tamuna and Hayden, Frederick G. and Marshall, John and Webb, Steve and Angus, Derek C. and Shindo, Nahoko and van der Werf, Sylvie and Openshaw, Peter J. M. and Farrar, Jeremy and Carson, Gail and Baillie, J. Kenneth},
	month = jan,
	year = {2014},
	pmid = {24355025},
	keywords = {Clinical Medicine/*methods, Communicable Diseases, Emerging/*diagnosis/*epidemiology/prevention \& control/therapy, Global Health, Humans, Information Dissemination/*methods, Information Services/*instrumentation/*organization \& administration},
	pages = {8--9},
}

@article{my_novel_2014,
	title = {Novel porcine-like human {G26P}[19] rotavirus identified in hospitalized paediatric diarrhoea patients in {Ho} {Chi} {Minh} {City}, {Vietnam}.},
	volume = {95},
	copyright = {(c) 2014 The Authors.},
	issn = {1465-2099 0022-1317},
	doi = {10.1099/vir.0.068403-0},
	abstract = {During a hospital-based diarrhoeal disease study conducted in Ho Chi Minh City, Vietnam from 2009 to 2010, we identified four symptomatic children infected with  G26P[19] rotavirus (RV)--an atypical variant that has not previously been reported in human gastroenteritis. To determine the genetic structure and investigate the origin of this G26P[19] strain, the whole genome of a representative example was characterized, revealing a novel genome constellation:},
	language = {eng},
	number = {Pt 12},
	journal = {The Journal of general virology},
	author = {My, Phan Vu Tra and Rabaa, Maia A. and Donato, Celeste and Cowley, Daniel and Phat, Voong Vinh and Dung, Tran Thi Ngoc and Anh, Pham Hong and Vinh, Ha and Bryant, Juliet E. and Kellam, Paul and Thwaites, Guy and Woolhouse, Mark E. J. and Kirkwood, Carl D. and Baker, Stephen},
	month = dec,
	year = {2014},
	pmid = {25121549},
	pmcid = {PMC4233630},
	keywords = {Child, Preschool, Diarrhea/epidemiology/*virology, Genotype, Humans, Inpatients, Molecular Sequence Data, Phylogeny, Rotavirus Infections/epidemiology/*virology, Rotavirus/*classification/genetics/*isolation \& purification, Vietnam/epidemiology},
	pages = {2727--2733},
}

During a hospital-based diarrhoeal disease study conducted in Ho Chi Minh City, Vietnam from 2009 to 2010, we identified four symptomatic children infected with G26P[19] rotavirus (RV)–an atypical variant that has not previously been reported in human gastroenteritis. To determine the genetic structure and investigate the origin of this G26P[19] strain, the whole genome of a representative example was characterized, revealing a novel genome constellation:

@article{le_limited_2014,
	title = {Limited geographic distribution of the novel cyclovirus {CyCV}-{VN}.},
	volume = {4},
	issn = {2045-2322 2045-2322},
	doi = {10.1038/srep03967},
	abstract = {A novel cyclovirus, CyCV-VN, was recently identified in cerebrospinal fluid (CSF) from patients with central nervous system (CNS) infections in central and southern Vietnam. To explore the geographic distribution of this novel virus, more than 600 CSF specimens from patients with suspected CNS infections in northern Vietnam, Cambodia, Nepal and The Netherlands were screened for the presence of CyCV-VN but all were negative. Sequence comparison and phylogenetic analysis between CyCV-VN and another novel cyclovirus recently identified in CSF  from Malawian patients indicated that these represent distinct cycloviral species, albeit phylogenetically closely related. The data suggest that CyCV-VN has a limited geographic distribution within southern and central Vietnam. Further research is needed to determine the global distribution and diversity of  cycloviruses and importantly their possible association with human disease.},
	language = {eng},
	journal = {Scientific reports},
	author = {Le, Van Tan and de Jong, Menno D. and Nguyen, Van Kinh and Nguyen, Vu Trung and Taylor, Walter and Wertheim, Heiman F. L. and van der Ende, Arie and van der Hoek, Lia and Canuti, Marta and Crusat, Martin and Sona, Soeng and Nguyen, Hanh Uyen and Giri, Abhishek and Nguyen, Thi Thuy Chinh Bkrong and Ho, Dang Trung Nghia and Farrar, Jeremy and Bryant, Juliet E. and Tran, Tinh Hien and Nguyen, Van Vinh Chau and van Doorn, H. Rogier},
	month = feb,
	year = {2014},
	pmid = {24495921},
	pmcid = {PMC3913916},
	keywords = {Adult, Base Sequence, Central Nervous System Infections/cerebrospinal fluid/epidemiology/*virology, Child, Circoviridae Infections/cerebrospinal fluid/*epidemiology/virology, Circoviridae/classification/*genetics/isolation \& purification, DNA, Viral/genetics, Female, Genetic Variation, Genome, Viral, Geography, Humans, Malawi/epidemiology, Male, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, DNA, Vietnam/epidemiology},
	pages = {3967},
}

A novel cyclovirus, CyCV-VN, was recently identified in cerebrospinal fluid (CSF) from patients with central nervous system (CNS) infections in central and southern Vietnam. To explore the geographic distribution of this novel virus, more than 600 CSF specimens from patients with suspected CNS infections in northern Vietnam, Cambodia, Nepal and The Netherlands were screened for the presence of CyCV-VN but all were negative. Sequence comparison and phylogenetic analysis between CyCV-VN and another novel cyclovirus recently identified in CSF from Malawian patients indicated that these represent distinct cycloviral species, albeit phylogenetically closely related. The data suggest that CyCV-VN has a limited geographic distribution within southern and central Vietnam. Further research is needed to determine the global distribution and diversity of cycloviruses and importantly their possible association with human disease.

@article{van_nguyen_high_2014,
	title = {High rates of infection with novel enterovirus variants in wild populations of mandrills and other old world monkey species.},
	volume = {88},
	issn = {1098-5514 0022-538X},
	doi = {10.1128/JVI.00088-14},
	abstract = {UNLABELLED: Enteroviruses (EVs) are a genetically and antigenically diverse group of viruses infecting humans. A mostly distinct set of EV variants have additionally been documented to infect wild apes and several, primarily captive,  Old World monkey (OWM) species. To investigate the prevalence and genetic characteristics of EVs infecting OWMs in the wild, fecal samples from mandrills (Mandrillus sphinx) and other species collected in remote regions of southern Cameroon were screened for EV RNA. Remarkably high rates of EV positivity were detected in M. sphinx (100 of 102 screened), Cercocebus torquatus (7/7), and Cercopithecus cephus (2/4), with high viral loads indicative of active infection. Genetic characterization in VP4/VP2 and VP1 regions allowed EV variants to be assigned to simian species H (EV-H) and EV-J (including one or more new types), while seven matched simian EV-B variants, SA5 and EV110 (chimpanzee). Sequences from the remaining 70 formed a new genetic group distinct in VP4/2 and VP1 region from all currently recognized human or simian EV species. Complete genome sequences were obtained from three to determine their species assignment. In common with EV-J and the EV-A A13 isolate, new group sequences were chimeric, being most closely related to EV-A in capsid genes and to EV-B in the nonstructural gene region. Further recombination events created different groupings in 5' and 3' untranslated regions. While clearly a distinct EV group, the hybrid nature of new variants prevented their unambiguous classification as either members of a new species or as divergent members of EV-A using current International Committee on Taxonomy of Viruses (ICTV) assignment criteria. IMPORTANCE: This study is the first large-scale investigation of the frequency of infection and diversity of enteroviruses (EVs) infecting monkeys (primarily mandrills) in the wild. Our findings demonstrate extremely high frequencies of active infection (95\%) among mandrills and other Old World monkey species inhabiting remote regions of Cameroon without human contact. EV variants detected were distinct from those infecting human populations, comprising members of enterovirus species B, J, and H and a large novel group of viruses most closely related to species A in the P1 region. The viral sequences obtained contribute substantially to our growing understanding of the genetic diversity of EVs and the existence of interspecies chimerism that characterizes the novel variants in  the current study, as well as in previously characterized species A and J viruses infecting monkeys. The latter findings will contribute to future development of consensus criteria for species assignments in enteroviruses and other picornavirus genera.},
	language = {eng},
	number = {11},
	journal = {Journal of virology},
	author = {Van Nguyen, Dung and Harvala, Heli and Ngole, Eitel Mpoudi and Delaporte, Eric and Woolhouse, Mark E. J. and Peeters, Martine and Simmonds, Peter},
	month = jun,
	year = {2014},
	pmid = {24623420},
	pmcid = {PMC4093852},
	keywords = {*Mandrillus, Animals, Base Sequence, Cameroon/epidemiology, Cercocebus/virology, Cercopithecus/virology, Enterovirus Infections/epidemiology/*veterinary/virology, Enterovirus/classification/*genetics, Feces/virology, Molecular Sequence Data, Monkey Diseases/*epidemiology/*virology, Prevalence, Sequence Analysis, DNA, Species Specificity},
	pages = {5967--5976},
}

UNLABELLED: Enteroviruses (EVs) are a genetically and antigenically diverse group of viruses infecting humans. A mostly distinct set of EV variants have additionally been documented to infect wild apes and several, primarily captive, Old World monkey (OWM) species. To investigate the prevalence and genetic characteristics of EVs infecting OWMs in the wild, fecal samples from mandrills (Mandrillus sphinx) and other species collected in remote regions of southern Cameroon were screened for EV RNA. Remarkably high rates of EV positivity were detected in M. sphinx (100 of 102 screened), Cercocebus torquatus (7/7), and Cercopithecus cephus (2/4), with high viral loads indicative of active infection. Genetic characterization in VP4/VP2 and VP1 regions allowed EV variants to be assigned to simian species H (EV-H) and EV-J (including one or more new types), while seven matched simian EV-B variants, SA5 and EV110 (chimpanzee). Sequences from the remaining 70 formed a new genetic group distinct in VP4/2 and VP1 region from all currently recognized human or simian EV species. Complete genome sequences were obtained from three to determine their species assignment. In common with EV-J and the EV-A A13 isolate, new group sequences were chimeric, being most closely related to EV-A in capsid genes and to EV-B in the nonstructural gene region. Further recombination events created different groupings in 5' and 3' untranslated regions. While clearly a distinct EV group, the hybrid nature of new variants prevented their unambiguous classification as either members of a new species or as divergent members of EV-A using current International Committee on Taxonomy of Viruses (ICTV) assignment criteria. IMPORTANCE: This study is the first large-scale investigation of the frequency of infection and diversity of enteroviruses (EVs) infecting monkeys (primarily mandrills) in the wild. Our findings demonstrate extremely high frequencies of active infection (95%) among mandrills and other Old World monkey species inhabiting remote regions of Cameroon without human contact. EV variants detected were distinct from those infecting human populations, comprising members of enterovirus species B, J, and H and a large novel group of viruses most closely related to species A in the P1 region. The viral sequences obtained contribute substantially to our growing understanding of the genetic diversity of EVs and the existence of interspecies chimerism that characterizes the novel variants in the current study, as well as in previously characterized species A and J viruses infecting monkeys. The latter findings will contribute to future development of consensus criteria for species assignments in enteroviruses and other picornavirus genera.

@article{horby_for_2014,
	title = {For some groups traditionally considered to be 'high risk', the evidence of an increased risk of severe influenza-associated illness is poor quality.},
	volume = {19},
	issn = {1473-6810 1356-5524},
	doi = {10.1136/eb-2013-101572},
	language = {eng},
	number = {3},
	journal = {Evidence-based medicine},
	author = {Horby, Peter},
	month = jun,
	year = {2014},
	pmid = {24357401},
	keywords = {Female, Hospitalization/*statistics \& numerical data, Humans, Influenza A Virus, H1N1 Subtype/*immunology, Influenza Vaccines/*administration \& dosage, Influenza, Human/*epidemiology/*prevention \& control, Male, Pregnancy, Pregnancy Complications, Infectious/*virology, Public Health},
	pages = {110},
}

@article{huong_epidemiology_2014,
	title = {Epidemiology, clinical manifestations, and outcomes of {Streptococcus} suis infection in humans.},
	volume = {20},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid2007.131594},
	abstract = {Streptococcus suis, a bacterium that affects pigs, is a neglected pathogen that causes systemic disease in humans. We conducted a systematic review and meta-analysis to summarize global estimates of the epidemiology, clinical characteristics, and outcomes of this zoonosis. We searched main literature databases for all studies through December 2012 using the search term "streptococcus suis." The prevalence of S. suis infection is highest in Asia; the primary risk factors are occupational exposure and eating of contaminated food. The pooled proportions of case-patients with pig-related occupations and history  of eating high-risk food were 38.1\% and 37.3\%, respectively. The main clinical syndrome was meningitis (pooled rate 68.0\%), followed by sepsis, arthritis, endocarditis, and endophthalmitis. The pooled case-fatality rate was 12.8\%. Sequelae included hearing loss (39.1\%) and vestibular dysfunction (22.7\%). Our analysis identified gaps in the literature, particularly in assessing risk factors and sequelae of this infection.},
	language = {eng},
	number = {7},
	journal = {Emerging infectious diseases},
	author = {Huong, Vu Thi Lan and Ha, Ngo and Huy, Nguyen Tien and Horby, Peter and Nghia, Ho Dang Trung and Thiem, Vu Dinh and Zhu, Xiaotong and Hoa, Ngo Thi and Hien, Tran Tinh and Zamora, Javier and Schultsz, Constance and Wertheim, Heiman Frank Louis and Hirayama, Kenji},
	month = jul,
	year = {2014},
	pmid = {24959701},
	pmcid = {PMC4073838},
	keywords = {Adult, Animals, Case-Control Studies, Communicable Diseases/epidemiology, Cross-Sectional Studies/methods, Female, Humans, Male, Middle Aged, Occupations, Risk Factors, Streptococcal Infections/*epidemiology, Streptococcus suis, Sus scrofa/microbiology, Swine/microbiology, Zoonoses/*epidemiology, bacteria, bacterial meningitis, meta-analysis, systematic review, zoonoses},
	pages = {1105--1114},
}

Streptococcus suis, a bacterium that affects pigs, is a neglected pathogen that causes systemic disease in humans. We conducted a systematic review and meta-analysis to summarize global estimates of the epidemiology, clinical characteristics, and outcomes of this zoonosis. We searched main literature databases for all studies through December 2012 using the search term "streptococcus suis." The prevalence of S. suis infection is highest in Asia; the primary risk factors are occupational exposure and eating of contaminated food. The pooled proportions of case-patients with pig-related occupations and history of eating high-risk food were 38.1% and 37.3%, respectively. The main clinical syndrome was meningitis (pooled rate 68.0%), followed by sepsis, arthritis, endocarditis, and endophthalmitis. The pooled case-fatality rate was 12.8%. Sequelae included hearing loss (39.1%) and vestibular dysfunction (22.7%). Our analysis identified gaps in the literature, particularly in assessing risk factors and sequelae of this infection.

@article{nhu_emergence_2014,
	title = {Emergence of carbapenem-resistant {Acinetobacter} baumannii as the major cause of ventilator-associated pneumonia in intensive care unit patients at an infectious  disease hospital in southern {Vietnam}.},
	volume = {63},
	copyright = {(c) 2014 The Authors.},
	issn = {1473-5644 0022-2615},
	doi = {10.1099/jmm.0.076646-0},
	abstract = {Ventilator-associated pneumonia (VAP) is a serious healthcare-associated infection that affects up to 30 \% of intubated and mechanically ventilated patients in intensive care units (ICUs) worldwide. The bacterial aetiology and corresponding antimicrobial susceptibility of VAP is highly variable, and can differ between countries, national provinces and even between different wards in  the same hospital. We aimed to understand and document changes in the causative agents of VAP and their antimicrobial susceptibility profiles retrospectively over an 11 year period in a major infectious disease hospital in southern Vietnam. Our analysis outlined a significant shift from Pseudomonas aeruginosa to Acinetobacter spp. as the most prevalent bacteria isolated from quantitative tracheal aspirates in patients with VAP in this setting. Antimicrobial resistance was common across all bacterial species and we found a marked proportional annual increase in carbapenem-resistant Acinetobacter spp. over a 3 year period from 2008 (annual trend; odds ratio 1.656, P = 0.010). We further investigated the possible emergence of a carbapenem-resistant Acinetobacter baumannii clone by multiple-locus variable number tandem repeat analysis, finding a blaOXA-23-positive strain that was associated with an upsurge in the isolation of this pathogen. We additionally identified a single blaNDM-1-positive A. baumannii isolate. This work highlights the emergence of a carbapenem-resistant clone of A. baumannii and a worrying trend of antimicrobial resistance in the ICU of the Hospital for Tropical Diseases in Ho Chi Minh City, Vietnam.},
	language = {eng},
	number = {Pt 10},
	journal = {Journal of medical microbiology},
	author = {Nhu, Nguyen Thi Khanh and Lan, Nguyen Phu Huong and Campbell, James I. and Parry, Christopher M. and Thompson, Corinne and Tuyen, Ha Thanh and Hoang, Nguyen Van Minh and Tam, Pham Thi Thanh and Le, Vien Minh and Nga, Tran Vu Thieu and Nhu, Tran Do Hoang and Van Minh, Pham and Nga, Nguyen Thi Thu and Thuy, Cao Thu and Dung, Le Thi and Yen, Nguyen Thi Thu and Van Hao, Nguyen and Loan, Huynh Thi and Yen, Lam Minh and Nghia, Ho Dang Trung and Hien, Tran Tinh and Thwaites, Louise and Thwaites, Guy and Chau, Nguyen Van Vinh and Baker, Stephen},
	month = oct,
	year = {2014},
	pmid = {25038137},
	pmcid = {PMC4170484},
	keywords = {*beta-Lactam Resistance, Acinetobacter Infections/epidemiology/*microbiology, Acinetobacter baumannii/*drug effects/isolation \& purification, Adolescent, Adult, Aged, Aged, 80 and over, Carbapenems/*pharmacology, Child, Child, Preschool, DNA, Bacterial/chemistry/genetics, Female, Genotype, Hospitals, Humans, Intensive Care Units, Male, Middle Aged, Molecular Epidemiology, Multilocus Sequence Typing, Pneumonia, Ventilator-Associated/epidemiology/*microbiology, Prevalence, Retrospective Studies, Vietnam/epidemiology, Young Adult},
	pages = {1386--1394},
}

Ventilator-associated pneumonia (VAP) is a serious healthcare-associated infection that affects up to 30 % of intubated and mechanically ventilated patients in intensive care units (ICUs) worldwide. The bacterial aetiology and corresponding antimicrobial susceptibility of VAP is highly variable, and can differ between countries, national provinces and even between different wards in the same hospital. We aimed to understand and document changes in the causative agents of VAP and their antimicrobial susceptibility profiles retrospectively over an 11 year period in a major infectious disease hospital in southern Vietnam. Our analysis outlined a significant shift from Pseudomonas aeruginosa to Acinetobacter spp. as the most prevalent bacteria isolated from quantitative tracheal aspirates in patients with VAP in this setting. Antimicrobial resistance was common across all bacterial species and we found a marked proportional annual increase in carbapenem-resistant Acinetobacter spp. over a 3 year period from 2008 (annual trend; odds ratio 1.656, P = 0.010). We further investigated the possible emergence of a carbapenem-resistant Acinetobacter baumannii clone by multiple-locus variable number tandem repeat analysis, finding a blaOXA-23-positive strain that was associated with an upsurge in the isolation of this pathogen. We additionally identified a single blaNDM-1-positive A. baumannii isolate. This work highlights the emergence of a carbapenem-resistant clone of A. baumannii and a worrying trend of antimicrobial resistance in the ICU of the Hospital for Tropical Diseases in Ho Chi Minh City, Vietnam.

@article{cotten_deep_2014,
	title = {Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting.},
	volume = {88},
	copyright = {Copyright (c) 2014 Cotten et al.},
	issn = {1098-5514 0022-538X},
	doi = {10.1128/JVI.01333-14},
	abstract = {UNLABELLED: Norovirus is a highly transmissible infectious agent that causes epidemic gastroenteritis in susceptible children and adults. Norovirus infections can be severe and can be initiated from an exceptionally small number of viral particles. Detailed genome sequence data are useful for tracking norovirus transmission and evolution. To address this need, we have developed a whole-genome deep-sequencing method that generates entire genome sequences from small amounts of clinical specimens. This novel approach employs an algorithm for reverse transcription and PCR amplification primer design using all of the publically available norovirus sequence data. Deep sequencing and de novo assembly were used to generate norovirus genomes from a large set of diarrheal patients attending three hospitals in Ho Chi Minh City, Vietnam, over a 2.5-year  period. Positive-selection analysis and direct examination of protein changes in  the virus over time identified codons in the regions encoding proteins VP1, p48 (NS1-2), and p22 (NS4) under positive selection and expands the known targets of  norovirus evolutionary pressure. IMPORTANCE: The high transmissibility and rapid  evolutionary rate of norovirus, combined with a short-lived host immune responses, are thought to be the reasons why the virus causes the majority of pediatric viral diarrhea cases. The evolutionary patterns of this RNA virus have  been described in detail for only a portion of the virus genome and never for a virus from a detailed urban tropical setting. We provide a detailed sequence description of the noroviruses circulating in three Ho Chi Minh City hospitals over a 2.5-year period. This study identified patterns of virus change in known sites of host immune response and identified three additional regions of the virus genome under selection that were not previously recognized. In addition, the method described here provides a robust full-genome sequencing platform for community-based virus surveillance.},
	language = {eng},
	number = {19},
	journal = {Journal of virology},
	author = {Cotten, Matthew and Petrova, Velislava and Phan, My V. T. and Rabaa, Maia A. and Watson, Simon J. and Ong, Swee Hoe and Kellam, Paul and Baker, Stephen},
	month = oct,
	year = {2014},
	pmid = {25056894},
	pmcid = {PMC4178781},
	keywords = {*Genome, Viral, *Phylogeny, Biological Evolution, Caliciviridae Infections/virology, Child, Child, Preschool, Cities, Codon, Diarrhea/virology, Gastroenteritis/virology, Gene Expression, High-Throughput Nucleotide Sequencing/*methods, Humans, Infant, Norovirus/classification/*genetics/isolation \& purification, RNA, Viral/*genetics, Vietnam, Viral Nonstructural Proteins/genetics},
	pages = {11056--11069},
}

UNLABELLED: Norovirus is a highly transmissible infectious agent that causes epidemic gastroenteritis in susceptible children and adults. Norovirus infections can be severe and can be initiated from an exceptionally small number of viral particles. Detailed genome sequence data are useful for tracking norovirus transmission and evolution. To address this need, we have developed a whole-genome deep-sequencing method that generates entire genome sequences from small amounts of clinical specimens. This novel approach employs an algorithm for reverse transcription and PCR amplification primer design using all of the publically available norovirus sequence data. Deep sequencing and de novo assembly were used to generate norovirus genomes from a large set of diarrheal patients attending three hospitals in Ho Chi Minh City, Vietnam, over a 2.5-year period. Positive-selection analysis and direct examination of protein changes in the virus over time identified codons in the regions encoding proteins VP1, p48 (NS1-2), and p22 (NS4) under positive selection and expands the known targets of norovirus evolutionary pressure. IMPORTANCE: The high transmissibility and rapid evolutionary rate of norovirus, combined with a short-lived host immune responses, are thought to be the reasons why the virus causes the majority of pediatric viral diarrhea cases. The evolutionary patterns of this RNA virus have been described in detail for only a portion of the virus genome and never for a virus from a detailed urban tropical setting. We provide a detailed sequence description of the noroviruses circulating in three Ho Chi Minh City hospitals over a 2.5-year period. This study identified patterns of virus change in known sites of host immune response and identified three additional regions of the virus genome under selection that were not previously recognized. In addition, the method described here provides a robust full-genome sequencing platform for community-based virus surveillance.

@article{carrique-mas_epidemiological_2014,
	title = {An epidemiological investigation of {Campylobacter} in pig and poultry farms in the {Mekong} delta of {Vietnam}.},
	volume = {142},
	issn = {1469-4409 0950-2688},
	doi = {10.1017/S0950268813002410},
	abstract = {Campylobacter are zoonotic pathogens commonly associated with gastroenteritis. To assess the relevance of Campylobacter in Vietnam, an economically transitioning country in SE Asia, we conducted a survey of 343 pig and poultry farms in the Mekong delta, a region characterized by mixed species farming with limited biosecurity. The animal-level prevalence of Campylobacter was 31.9\%, 23.9\% and 53.7\% for chickens, ducks and pigs, respectively. C. jejuni was predominant in all three host species, with the highest prevalence in pigs in high-density production areas. Campylobacter isolates demonstrated high levels of antimicrobial resistance (21\% and 100\% resistance against ciprofloxacin and erythromycin, respectively). Multilocus sequence type genotyping showed a high level of genetic diversity within C. jejuni, and predicted C. coli inter-species  transmission. We suggest that on-going intensification of animal production systems, limited biosecurity, and increased urbanization in Vietnam is likely to  result in Campylobacter becoming an increasingly significant cause of human diarrhoeal infections in coming years.},
	language = {eng},
	number = {7},
	journal = {Epidemiology and infection},
	author = {Carrique-Mas, J. J. and Bryant, J. E. and Cuong, N. V. and Hoang, N. V. M. and Campbell, J. and Hoang, N. V. and Dung, T. T. N. and Duy, D. T. and Hoa, N. T. and Thompson, C. and Hien, V. V. and Phat, V. V. and Farrar, J. and Baker, S.},
	month = jul,
	year = {2014},
	pmid = {24067502},
	pmcid = {PMC4045178},
	keywords = {Animals, Anti-Bacterial Agents/pharmacology, Campylobacter Infections/epidemiology/microbiology/*veterinary, Campylobacter/classification/drug effects/genetics/isolation \& purification, Cross-Sectional Studies, Drug Resistance, Bacterial, Feces/microbiology, Microbial Sensitivity Tests, Multilocus Sequence Typing, Poultry, Poultry Diseases/*epidemiology/microbiology, Prevalence, Risk Factors, Swine, Swine Diseases/*epidemiology/microbiology, Vietnam/epidemiology},
	pages = {1425--1436},
}

Campylobacter are zoonotic pathogens commonly associated with gastroenteritis. To assess the relevance of Campylobacter in Vietnam, an economically transitioning country in SE Asia, we conducted a survey of 343 pig and poultry farms in the Mekong delta, a region characterized by mixed species farming with limited biosecurity. The animal-level prevalence of Campylobacter was 31.9%, 23.9% and 53.7% for chickens, ducks and pigs, respectively. C. jejuni was predominant in all three host species, with the highest prevalence in pigs in high-density production areas. Campylobacter isolates demonstrated high levels of antimicrobial resistance (21% and 100% resistance against ciprofloxacin and erythromycin, respectively). Multilocus sequence type genotyping showed a high level of genetic diversity within C. jejuni, and predicted C. coli inter-species transmission. We suggest that on-going intensification of animal production systems, limited biosecurity, and increased urbanization in Vietnam is likely to result in Campylobacter becoming an increasingly significant cause of human diarrhoeal infections in coming years.

@article{liverani_understanding_2013,
	title = {Understanding and managing zoonotic risk in the new livestock industries.},
	volume = {121},
	issn = {1552-9924 0091-6765},
	doi = {10.1289/ehp.1206001},
	abstract = {BACKGROUND: In many parts of the world, livestock production is undergoing a process of rapid intensification. The health implications of this development are uncertain. Intensification creates cheaper products, allowing more people to access animal-based foods. However, some practices associated with intensification may contribute to zoonotic disease emergence and spread: for example, the sustained use of antibiotics, concentration of animals in confined units, and long distances and frequent movement of livestock. OBJECTIVES: Here we present the diverse range of ecological, biological, and socioeconomic factors likely to enhance or reduce zoonotic risk, and identify ways in which a comprehensive risk analysis may be conducted by using an interdisciplinary approach. We also offer a conceptual framework to guide systematic research on this problem. DISCUSSION: We recommend that interdisciplinary work on zoonotic risk should take into account the complexity of risk environments, rather than limiting studies to simple linear causal relations between risk drivers and disease emergence and/or spread. In addition, interdisciplinary integration is needed at different levels of analysis, from the study of risk environments to the identification of policy options for risk management. CONCLUSION: Given rapid changes in livestock production systems and their potential health implications at the local and global level, the problem we analyze here is of great importance for environmental health and development. Although we offer a systematic interdisciplinary approach to understand and address these implications, we recognize that further research is needed to clarify methodological and practical questions arising from the integration of the natural and social sciences.},
	language = {eng},
	number = {8},
	journal = {Environmental health perspectives},
	author = {Liverani, Marco and Waage, Jeff and Barnett, Tony and Pfeiffer, Dirk U. and Rushton, Jonathan and Rudge, James W. and Loevinsohn, Michael E. and Scoones, Ian and Smith, Richard D. and Cooper, Ben S. and White, Lisa J. and Goh, Shan and Horby, Peter and Wren, Brendan and Gundogdu, Ozan and Woods, Abigail and Coker, Richard J.},
	month = aug,
	year = {2013},
	pmid = {23665854},
	pmcid = {PMC3734490},
	keywords = {*Livestock/physiology, Animal Husbandry/economics/*methods, Animal Nutritional Physiological Phenomena, Animals, Humans, Risk Assessment, Zoonoses/*epidemiology/etiology/*prevention \& control},
	pages = {873--877},
}

BACKGROUND: In many parts of the world, livestock production is undergoing a process of rapid intensification. The health implications of this development are uncertain. Intensification creates cheaper products, allowing more people to access animal-based foods. However, some practices associated with intensification may contribute to zoonotic disease emergence and spread: for example, the sustained use of antibiotics, concentration of animals in confined units, and long distances and frequent movement of livestock. OBJECTIVES: Here we present the diverse range of ecological, biological, and socioeconomic factors likely to enhance or reduce zoonotic risk, and identify ways in which a comprehensive risk analysis may be conducted by using an interdisciplinary approach. We also offer a conceptual framework to guide systematic research on this problem. DISCUSSION: We recommend that interdisciplinary work on zoonotic risk should take into account the complexity of risk environments, rather than limiting studies to simple linear causal relations between risk drivers and disease emergence and/or spread. In addition, interdisciplinary integration is needed at different levels of analysis, from the study of risk environments to the identification of policy options for risk management. CONCLUSION: Given rapid changes in livestock production systems and their potential health implications at the local and global level, the problem we analyze here is of great importance for environmental health and development. Although we offer a systematic interdisciplinary approach to understand and address these implications, we recognize that further research is needed to clarify methodological and practical questions arising from the integration of the natural and social sciences.

@article{cotten_transmission_2013,
	title = {Transmission and evolution of the {Middle} {East} respiratory syndrome coronavirus in {Saudi} {Arabia}: a descriptive genomic study.},
	volume = {382},
	copyright = {Copyright (c) 2013 Cotten et al. Open Access article distributed under the terms  of CC BY-NC-ND. Published by Elsevier Ltd. All rights reserved.},
	issn = {1474-547X 0140-6736},
	doi = {10.1016/S0140-6736(13)61887-5},
	abstract = {BACKGROUND: Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has, worldwide, caused 104 infections in people including 49 deaths, with 82 cases and 41 deaths reported from Saudi Arabia. In addition to confirming diagnosis, we generated the MERS-CoV genomic sequences obtained directly from patient samples to provide important information on MERS-CoV transmission, evolution, and origin. METHODS: Full genome deep sequencing was done on nucleic acid extracted directly from PCR-confirmed clinical samples. Viral genomes were obtained from 21 MERS cases of which 13 had 100\%, four 85-95\%, and four 30-50\% genome coverage. Phylogenetic analysis of the 21 sequences, combined with nine published MERS-CoV genomes, was done. FINDINGS: Three distinct MERS-CoV genotypes were identified in Riyadh. Phylogeographic analyses suggest the MERS-CoV zoonotic reservoir is geographically disperse. Selection analysis of the MERS-CoV genomes  reveals the expected accumulation of genetic diversity including changes in the S protein. The genetic diversity in the Al-Hasa cluster suggests that the hospital  outbreak might have had more than one virus introduction. INTERPRETATION: We present the largest number of MERS-CoV genomes (21) described so far. MERS-CoV full genome sequences provide greater detail in tracking transmission. Multiple introductions of MERS-CoV are identified and suggest lower R0 values. Transmission within Saudi Arabia is consistent with either movement of an animal  reservoir, animal products, or movement of infected people. Further definition of the exposures responsible for the sporadic introductions of MERS-CoV into human populations is urgently needed. FUNDING: Saudi Arabian Ministry of Health, Wellcome Trust, European Community, and National Institute of Health Research University College London Hospitals Biomedical Research Centre.},
	language = {eng},
	number = {9909},
	journal = {Lancet (London, England)},
	author = {Cotten, Matthew and Watson, Simon J. and Kellam, Paul and Al-Rabeeah, Abdullah A. and Makhdoom, Hatem Q. and Assiri, Abdullah and Al-Tawfiq, Jaffar A. and Alhakeem, Rafat F. and Madani, Hossam and AlRabiah, Fahad A. and Al Hajjar, Sami and Al-nassir, Wafa N. and Albarrak, Ali and Flemban, Hesham and Balkhy, Hanan H. and Alsubaie, Sarah and Palser, Anne L. and Gall, Astrid and Bashford-Rogers, Rachael and Rambaut, Andrew and Zumla, Alimuddin I. and Memish, Ziad A.},
	month = dec,
	year = {2013},
	pmid = {24055451},
	pmcid = {PMC3898949},
	keywords = {*Disease Outbreaks, *Evolution, Molecular, *Genome, Viral, Base Sequence, Coronavirus Infections/epidemiology/*genetics/transmission, Coronavirus/*genetics, Gene Amplification, Humans, Respiratory Tract Infections/epidemiology/*genetics/transmission, Saudi Arabia/epidemiology, Syndrome},
	pages = {1993--2002},
}

BACKGROUND: Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has, worldwide, caused 104 infections in people including 49 deaths, with 82 cases and 41 deaths reported from Saudi Arabia. In addition to confirming diagnosis, we generated the MERS-CoV genomic sequences obtained directly from patient samples to provide important information on MERS-CoV transmission, evolution, and origin. METHODS: Full genome deep sequencing was done on nucleic acid extracted directly from PCR-confirmed clinical samples. Viral genomes were obtained from 21 MERS cases of which 13 had 100%, four 85-95%, and four 30-50% genome coverage. Phylogenetic analysis of the 21 sequences, combined with nine published MERS-CoV genomes, was done. FINDINGS: Three distinct MERS-CoV genotypes were identified in Riyadh. Phylogeographic analyses suggest the MERS-CoV zoonotic reservoir is geographically disperse. Selection analysis of the MERS-CoV genomes reveals the expected accumulation of genetic diversity including changes in the S protein. The genetic diversity in the Al-Hasa cluster suggests that the hospital outbreak might have had more than one virus introduction. INTERPRETATION: We present the largest number of MERS-CoV genomes (21) described so far. MERS-CoV full genome sequences provide greater detail in tracking transmission. Multiple introductions of MERS-CoV are identified and suggest lower R0 values. Transmission within Saudi Arabia is consistent with either movement of an animal reservoir, animal products, or movement of infected people. Further definition of the exposures responsible for the sporadic introductions of MERS-CoV into human populations is urgently needed. FUNDING: Saudi Arabian Ministry of Health, Wellcome Trust, European Community, and National Institute of Health Research University College London Hospitals Biomedical Research Centre.

@article{holt_tracking_2013,
	title = {Tracking the establishment of local endemic populations of an emergent enteric pathogen.},
	volume = {110},
	issn = {1091-6490 0027-8424},
	doi = {10.1073/pnas.1308632110},
	abstract = {Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling.  This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.},
	language = {eng},
	number = {43},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Holt, Kathryn E. and Thieu Nga, Tran Vu and Thanh, Duy Pham and Vinh, Ha and Kim, Dong Wook and Vu Tra, My Phan and Campbell, James I. and Hoang, Nguyen Van Minh and Vinh, Nguyen Thanh and Minh, Pham Van and Thuy, Cao Thu and Nga, Tran Thi Thu and Thompson, Corinne and Dung, Tran Thi Ngoc and Nhu, Nguyen Thi Khanh and Vinh, Phat Voong and Tuyet, Pham Thi Ngoc and Phuc, Hoang Le and Lien, Nguyen Thi Nam and Phu, Bui Duc and Ai, Nguyen Thi Thuy and Tien, Nguyen Manh and Dong, Nguyen and Parry, Christopher M. and Hien, Tran Tinh and Farrar, Jeremy J. and Parkhill, Julian and Dougan, Gordon and Thomson, Nicholas R. and Baker, Stephen},
	month = oct,
	year = {2013},
	pmid = {24082120},
	pmcid = {PMC3808646},
	keywords = {*Endemic Diseases, *Genetic Variation, Anti-Bacterial Agents/therapeutic use, Child, Child, Preschool, Chromosomes, Bacterial/genetics, Ciprofloxacin/therapeutic use, Dysentery, Bacillary/drug therapy/*epidemiology/microbiology, Evolution, Molecular, Fluoroquinolones/therapeutic use, Genome, Bacterial/genetics, Genomics, Genomics/methods, Geography, Humans, Infant, Molecular Sequence Data, Mutation Rate, Phylogeny, Phylogeography, Sequence Analysis, DNA, Shigella sonnei/classification/*genetics/physiology, Vietnam/epidemiology, drug resistance, enteric disease},
	pages = {17522--17527},
}

Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.

@article{dung_validation_2013,
	title = {The validation and utility of a quantitative one-step multiplex {RT} real-time {PCR}  targeting rotavirus {A} and norovirus.},
	volume = {187},
	copyright = {Copyright (c) 2012 Elsevier B.V. All rights reserved.},
	issn = {1879-0984 0166-0934},
	doi = {10.1016/j.jviromet.2012.09.021},
	abstract = {Rotavirus (RoV) and Norovirus (NoV) are the main causes of viral gastroenteritis. Currently, there is no validated multiplex real-time PCR that can detect and quantify RoV and NoV simultaneously. The aim of the study was to develop, validate, and internally control a multiplex one-step RT real-time PCR to detect  and quantify RoV and NoV in stool samples. PCR sensitivity was assessed by comparing amplification against the current gold standard, enzyme immunoassay (EIA), on stool samples from 94 individuals with diarrhea and 94 individuals without diarrhea. PCR detected 10\% more RoV positive samples than EIA in stools samples from patients with diarrhea. PCR detected 23\% more NoV genogroup II positive samples from individuals with diarrhea and 9\% more from individuals without diarrhea than EIA, respectively. Genotyping of the PCR positive/EIA negative samples suggested the higher rate of PCR positivity, in comparison to EIA, was due to increased sensitivity, rather than nonspecific hybridization. Quantitation demonstrated that the viral loads of RoV and NoV in the stools of diarrheal patients were an order of magnitude greater than in individuals without diarrhea. This internally controlled real-time PCR method is robust, exhibits a high degree of reproducibility, and may have a greater utility and sensitivity than commercial EIA kits.},
	language = {eng},
	number = {1},
	journal = {Journal of virological methods},
	author = {Dung, Tran Thi Ngoc and Phat, Voong Vinh and Nga, Tran Vu Thieu and My, Phan Vu Tra and Duy, Pham Thanh and Campbell, James I. and Thuy, Cao Thu and Hoang, Nguyen Van Minh and Van Minh, Pham and Le Phuc, Hoang and Tuyet, Pham Thi Ngoc and Vinh, Ha and Kien, Duong Thi Hue and Huy, Huynh Le Anh and Vinh, Nguyen Thanh and Nga, Tran Thi Thu and Hau, Nguyen Thi Thu and Chinh, Nguyen Tran and Thuong, Tang Chi and Tuan, Ha Manh and Simmons, Cameron and Farrar, Jeremy J. and Baker, Stephen},
	month = jan,
	year = {2013},
	pmid = {23046990},
	pmcid = {PMC3528950},
	keywords = {*Multiplex Polymerase Chain Reaction, *Real-Time Polymerase Chain Reaction, Caliciviridae Infections/*diagnosis/virology, Child, Preschool, Diarrhea/diagnosis/virology, Feces/virology, Gastroenteritis/diagnosis/genetics, Genotype, Humans, Infant, Infant, Newborn, Norovirus/genetics/*isolation \& purification, RNA, Viral/analysis, Reproducibility of Results, Reverse Transcriptase Polymerase Chain Reaction, Rotavirus Infections/*diagnosis/virology, Rotavirus/genetics/*isolation \& purification},
	pages = {138--143},
}

Rotavirus (RoV) and Norovirus (NoV) are the main causes of viral gastroenteritis. Currently, there is no validated multiplex real-time PCR that can detect and quantify RoV and NoV simultaneously. The aim of the study was to develop, validate, and internally control a multiplex one-step RT real-time PCR to detect and quantify RoV and NoV in stool samples. PCR sensitivity was assessed by comparing amplification against the current gold standard, enzyme immunoassay (EIA), on stool samples from 94 individuals with diarrhea and 94 individuals without diarrhea. PCR detected 10% more RoV positive samples than EIA in stools samples from patients with diarrhea. PCR detected 23% more NoV genogroup II positive samples from individuals with diarrhea and 9% more from individuals without diarrhea than EIA, respectively. Genotyping of the PCR positive/EIA negative samples suggested the higher rate of PCR positivity, in comparison to EIA, was due to increased sensitivity, rather than nonspecific hybridization. Quantitation demonstrated that the viral loads of RoV and NoV in the stools of diarrheal patients were an order of magnitude greater than in individuals without diarrhea. This internally controlled real-time PCR method is robust, exhibits a high degree of reproducibility, and may have a greater utility and sensitivity than commercial EIA kits.

@article{shieh_policy_2013,
	title = {The policy of free healthcare for children under the age of 6 years in {Vietnam}: assessment of the uptake for children hospitalised with acute diarrhoea in {Ho} {Chi} {Minh} {City}.},
	volume = {18},
	copyright = {(c) 2013 John Wiley \& Sons Ltd.},
	issn = {1365-3156 1360-2276},
	doi = {10.1111/tmi.12208},
	abstract = {OBJECTIVE: To assess the proportion of, and reasons for, households not utilising the policy of free healthcare for children under 6 years of age (FCCU6) for hospitalisation with diarrhoea, and assess the risk of catastrophic expenditure for households that forgo FCCU6 and pay out of pocket. METHODS: Invoices detailing insurance information and charges incurred from 472 hospitalised diarrhoeal cases in one paediatric hospital in Ho Chi Minh City were retrieved. Hospital charges and the utilisation of elective services were analysed for patients utilising and not utilising FCCU6. Associations between socio-economic factors with non-utilisation of FCCU6 were evaluated. RESULTS: Overall, 29\% of patients were FCCU6 non-users. The FCCU6 non-users paid a median hospital charge  of \$29.13 (interquartile range, IQR: \$18.57-46.24), consuming no more than 1.4\% of a medium-income household's annual income. Seventy per cent of low-income FCCU6 non-users utilised less-expensive elective services, whereas only 43\% of medium income patients and 21\% of high-income patients did (P = 0.036). Patients  from larger households and those with a parent working in government were more likely to use FCCU6. CONCLUSIONS: The rate of FCCU6 non-usage in this study population was 29\%. A significant proportion of those that did not use FCCU6 was  from lower income households and may perceive a justifiable cost-benefit ratio when forgoing FCCU6. Although a single diarrhoeal hospitalisation is unlikely to  induce a catastrophic expenditure, FCCU6 non-usage may disproportionately increase the risk of catastrophic expenditure for lower income households over multiple illnesses.},
	language = {eng},
	number = {12},
	journal = {Tropical medicine \& international health : TM \& IH},
	author = {Shieh, Mae and Thompson, Corinne and Phan, Vu Tra My and Van, Thi Thuy Linh and Tediosi, Fabrizio and Merson, Laura and Farrar, Jeremy J. and Ha, Manh Tuan and Ho, Lu Viet and Pham, Thi Ngoc Tuyet and Baker, Stephen},
	month = dec,
	year = {2013},
	pmid = {24134427},
	pmcid = {PMC3992841},
	keywords = {Age Factors, Child, Preschool, Diarrhea/economics/*epidemiology/therapy, Female, Financing, Personal/statistics \& numerical data, Health Care Costs/statistics \& numerical data, Health Policy, Hospitalization/*statistics \& numerical data, Hospitals, Pediatric/statistics \& numerical data, Humans, Income/statistics \& numerical data, Infant, Male, Tertiary Care Centers/economics/utilization, Universal Coverage/organization \& administration/statistics \& numerical data/*utilization, Vietnam, Vietnam/epidemiology, acute diarrhoea, child health, health insurance utilisation, hospital charges, out-of-pocket expenditures, social health insurance},
	pages = {1444--1451},
}

OBJECTIVE: To assess the proportion of, and reasons for, households not utilising the policy of free healthcare for children under 6 years of age (FCCU6) for hospitalisation with diarrhoea, and assess the risk of catastrophic expenditure for households that forgo FCCU6 and pay out of pocket. METHODS: Invoices detailing insurance information and charges incurred from 472 hospitalised diarrhoeal cases in one paediatric hospital in Ho Chi Minh City were retrieved. Hospital charges and the utilisation of elective services were analysed for patients utilising and not utilising FCCU6. Associations between socio-economic factors with non-utilisation of FCCU6 were evaluated. RESULTS: Overall, 29% of patients were FCCU6 non-users. The FCCU6 non-users paid a median hospital charge of $29.13 (interquartile range, IQR: $18.57-46.24), consuming no more than 1.4% of a medium-income household's annual income. Seventy per cent of low-income FCCU6 non-users utilised less-expensive elective services, whereas only 43% of medium income patients and 21% of high-income patients did (P = 0.036). Patients from larger households and those with a parent working in government were more likely to use FCCU6. CONCLUSIONS: The rate of FCCU6 non-usage in this study population was 29%. A significant proportion of those that did not use FCCU6 was from lower income households and may perceive a justifiable cost-benefit ratio when forgoing FCCU6. Although a single diarrhoeal hospitalisation is unlikely to induce a catastrophic expenditure, FCCU6 non-usage may disproportionately increase the risk of catastrophic expenditure for lower income households over multiple illnesses.

@article{tra_my_dynamics_2013,
	title = {The dynamics of {GII}.4 {Norovirus} in {Ho} {Chi} {Minh} {City}, {Vietnam}.},
	volume = {18},
	copyright = {Copyright (c) 2013 The Authors. Published by Elsevier B.V. All rights reserved.},
	issn = {1567-7257 1567-1348},
	doi = {10.1016/j.meegid.2013.04.014},
	abstract = {Norovirus (NoV) is a major cause of epidemic gastroenteritis in industrialized countries, yet the epidemiological significance of NoV in industrializing countries remains poorly understood. The spatiotemporal distribution of NoV genotypes identified in 2054 enrolled children was investigated between May 2009  and December 2010, in Ho Chi Minh City (HCMC), Vietnam. A total of 315 NoV extracted from stool samples were genotyped and GPS mapped to their source. Genogroup II NoV, particularly GII.4, were predominant, and the GII.4 strains could be subgrouped into GII.4-2006b (Minerva) and GII.4-2010 (New Orleans) variants. There was no spatiotemporal structure among the endemic GII strains; yet a significant spatiotemporal signal corresponding with the novel introduction of GII.4-2010 variant was detected. These data show that NoV GII.4 variants are highly endemic in HCMC and describe a scenario of rapid NoV strain replacement occurring in HCMC in early 2010.},
	language = {eng},
	journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
	author = {Tra My, Phan Vu and Lam, Ha Minh and Thompson, Corinne N. and Phuc, Hoang Le and Tuyet, Pham Thi Ngoc and Vinh, Ha and Hoang, Nguyen Van Minh and Minh, Phamvan and Vinh, Nguyen Thanh and Thuy, Cao Thu and Nga, Tran Thi Thu and Hau, Nguyen Thi Thu and Chinh, Nguyen Tran and Thuong, Tang Chi and Tuan, Ha Manh and Campbell, James I. and Clements, Archie C. A. and Farrar, Jeremy and Boni, Maciej F. and Baker, Stephen},
	month = aug,
	year = {2013},
	pmid = {23612321},
	pmcid = {PMC4047827},
	keywords = {Caliciviridae Infections/*virology, Child, Preschool, Cluster, Cluster Analysis, Feces/virology, GII.4, Gastroenteritis/*virology, Genotype, Geographic Information Systems, Humans, Infant, Infant, Newborn, Norovirus/*classification/genetics/isolation \& purification, Phylogenetic, Phylogeography, Spatial, Spatio-Temporal Analysis, Temporal, Vietnam, norovirus},
	pages = {335--343},
}

Norovirus (NoV) is a major cause of epidemic gastroenteritis in industrialized countries, yet the epidemiological significance of NoV in industrializing countries remains poorly understood. The spatiotemporal distribution of NoV genotypes identified in 2054 enrolled children was investigated between May 2009 and December 2010, in Ho Chi Minh City (HCMC), Vietnam. A total of 315 NoV extracted from stool samples were genotyped and GPS mapped to their source. Genogroup II NoV, particularly GII.4, were predominant, and the GII.4 strains could be subgrouped into GII.4-2006b (Minerva) and GII.4-2010 (New Orleans) variants. There was no spatiotemporal structure among the endemic GII strains; yet a significant spatiotemporal signal corresponding with the novel introduction of GII.4-2010 variant was detected. These data show that NoV GII.4 variants are highly endemic in HCMC and describe a scenario of rapid NoV strain replacement occurring in HCMC in early 2010.

@article{trang_characterization_2013,
	title = {The characterization of {ESBL} genes in {Escherichia} coli and {Klebsiella} pneumoniae  causing nosocomial infections in {Vietnam}.},
	volume = {7},
	issn = {1972-2680 1972-2680},
	abstract = {BACKGROUND: Extended-spectrum beta-lactamases (ESBLs) are enzymes capable of hydrolyzing oxyimino-beta-lactams and inducing resistance to third generation cephalosporins. The genes encoding ESBLs are widespread and generally located on  highly transmissible resistance plasmids. We aimed to investigate the complement  of ESBL genes in E. coli and Klebsiella pneumoniae causing nosocomial infections  in hospitals in Ho Chi Minh City, Vietnam. METHODOLOGY: Thirty-two non-duplicate  isolates of E. coli and Klebsiella pneumoniae causing nosocomial infections, isolated between March and June 2010, were subjected to antimicrobial susceptibility testing. All isolates were PCR-amplified to detect the blaSHV, blaTEM and blaCTX-M ESBL genes and subjected to plasmid analysis. RESULTS: We found that co-resistance to multiple antimicrobials was highly prevalent, and we  report the predominance of the blaCTX-M-15 and blaCTX-M-27 genes, located on highly transmissible plasmids ranging from 50 to 170 kb in size. CONCLUSIONS: Our study represents a snap shot of ESBL-producing enteric bacteria causing nosocomial infections in this setting. We suggest that antimicrobial resistance in nosocomial E. coli and Klebsiella pneumoniae is rampant in Vietnam and ESBL organisms are widespread. In view of these data and the dramatic levels of antimicrobial resistance reported in Vietnam we advocate an urgent review of antimicrobial use in the Vietnamese healthcare system.},
	language = {eng},
	number = {12},
	journal = {Journal of infection in developing countries},
	author = {Trang, Nguyen Hoang Thu and Nga, Tran Vu Thieu and Campbell, James I. and Hiep, Nguyen Trong and Farrar, Jeremy and Baker, Stephen and Duy, Pham Thanh},
	month = dec,
	year = {2013},
	pmid = {24334938},
	keywords = {Anti-Bacterial Agents/pharmacology, Cross Infection/*microbiology, DNA, Bacterial/genetics, Escherichia coli Infections/*microbiology, Escherichia coli/*enzymology/genetics/isolation \& purification, Genes, Bacterial, Humans, Klebsiella Infections/*microbiology, Klebsiella pneumoniae/*enzymology/genetics/isolation \& purification, Microbial Sensitivity Tests, Plasmids/analysis, Polymerase Chain Reaction, Vietnam, beta-Lactam Resistance, beta-Lactamases/*genetics},
	pages = {922--928},
}

BACKGROUND: Extended-spectrum beta-lactamases (ESBLs) are enzymes capable of hydrolyzing oxyimino-beta-lactams and inducing resistance to third generation cephalosporins. The genes encoding ESBLs are widespread and generally located on highly transmissible resistance plasmids. We aimed to investigate the complement of ESBL genes in E. coli and Klebsiella pneumoniae causing nosocomial infections in hospitals in Ho Chi Minh City, Vietnam. METHODOLOGY: Thirty-two non-duplicate isolates of E. coli and Klebsiella pneumoniae causing nosocomial infections, isolated between March and June 2010, were subjected to antimicrobial susceptibility testing. All isolates were PCR-amplified to detect the blaSHV, blaTEM and blaCTX-M ESBL genes and subjected to plasmid analysis. RESULTS: We found that co-resistance to multiple antimicrobials was highly prevalent, and we report the predominance of the blaCTX-M-15 and blaCTX-M-27 genes, located on highly transmissible plasmids ranging from 50 to 170 kb in size. CONCLUSIONS: Our study represents a snap shot of ESBL-producing enteric bacteria causing nosocomial infections in this setting. We suggest that antimicrobial resistance in nosocomial E. coli and Klebsiella pneumoniae is rampant in Vietnam and ESBL organisms are widespread. In view of these data and the dramatic levels of antimicrobial resistance reported in Vietnam we advocate an urgent review of antimicrobial use in the Vietnamese healthcare system.

@article{le_subclinical_2013,
	title = {Subclinical avian influenza {A}({H5N1}) virus infection in human, {Vietnam}.},
	volume = {19},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid1910.130730},
	abstract = {Laboratory-confirmed cases of subclinical infection with avian influenza A(H5N1)  virus in humans are rare, and the true number of these cases is unknown. We describe the identification of a laboratory-confirmed subclinical case in a woman during an influenza A(H5N1) contact investigation in northern Vietnam.},
	language = {eng},
	number = {10},
	journal = {Emerging infectious diseases},
	author = {Le, Mai Quynh and Horby, Peter and Fox, Annette and Nguyen, Hien Tran and Le Nguyen, Hang Khanh and Hoang, Phuong Mai Vu and Nguyen, Khanh Cong and de Jong, Menno D. and Jeeninga, Rienk E. and Rogier van Doorn, H. and Farrar, Jeremy and Wertheim, Heiman F. L.},
	month = oct,
	year = {2013},
	pmid = {24047510},
	pmcid = {PMC3810763},
	keywords = {Adolescent, Adult, Amino Acid Substitution, Animals, Asymptomatic Infections, Chickens/virology, Contact Tracing, Dogs, Fatal Outcome, Female, H5N1, Humans, Infant, Influenza A Virus, H5N1 Subtype/*genetics, Influenza in Birds/transmission/*virology, Influenza, Human/*diagnosis/transmission/virology, Madin Darby Canine Kidney Cells, Male, Middle Aged, Molecular Diagnostic Techniques, Phylogeny, Polymerase Chain Reaction, Poultry, Vietnam, asymptomatic, avian influenza, avian influenza A(H5N1), clades, human, influenza, subclinical, viruses, zoonoses},
	pages = {1674--1677},
}

Laboratory-confirmed cases of subclinical infection with avian influenza A(H5N1) virus in humans are rare, and the true number of these cases is unknown. We describe the identification of a laboratory-confirmed subclinical case in a woman during an influenza A(H5N1) contact investigation in northern Vietnam.

@article{hoa_streptococcus_2013,
	title = {Streptococcus suis and porcine reproductive and respiratory syndrome, {Vietnam}.},
	volume = {19},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid1902.120470},
	language = {eng},
	number = {2},
	journal = {Emerging infectious diseases},
	author = {Hoa, Ngo Thi and Chieu, Tran Thi Bich and Do Dung, Sam and Long, Ngo Thanh and Hieu, Thai Quoc and Luc, Nguyen Tien and Nhuong, Pham Thanh and Huong, Vu Thi Lan and Trinh, Dao Tuyet and Wertheim, Heiman F. L. and Van Kinh, Nguyen and Campbell, James I. and Farrar, Jeremy and Chau, Nguyen Van Vinh and Baker, Stephen and Bryant, Juliet E.},
	month = feb,
	year = {2013},
	pmid = {23343623},
	pmcid = {PMC3559037},
	keywords = {*Disease Outbreaks, Animals, Anti-Bacterial Agents/pharmacology, Coinfection/diagnosis/epidemiology/*veterinary, Disk Diffusion Antimicrobial Tests, Humans, Molecular Diagnostic Techniques, Polymerase Chain Reaction, Porcine Reproductive and Respiratory Syndrome/diagnosis/*epidemiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Streptococcal Infections/diagnosis/epidemiology/*veterinary, Streptococcus suis/drug effects/*genetics/isolation \& purification, Sus scrofa, Swine, Vietnam/epidemiology},
	pages = {331--333},
}

@article{woolhouse_microbiology._2013,
	title = {Microbiology. {Sources} of antimicrobial resistance.},
	volume = {341},
	issn = {1095-9203 0036-8075},
	doi = {10.1126/science.1243444},
	language = {eng},
	number = {6153},
	journal = {Science (New York, N.Y.)},
	author = {Woolhouse, Mark E. J. and Ward, Melissa J.},
	month = sep,
	year = {2013},
	pmid = {24030495},
	keywords = {*Host-Pathogen Interactions, Animals, Drug Resistance, Multiple, Bacterial/*genetics, Humans, Salmonella Infections, Animal/*microbiology, Salmonella Infections/*microbiology, Salmonella typhimurium/*classification, Zoonoses/*microbiology},
	pages = {1460--1461},
}

@article{horby_prospects_2013,
	title = {Prospects for emerging infections in {East} and southeast {Asia} 10 years after severe acute respiratory syndrome.},
	volume = {19},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid1906.121783},
	abstract = {It is 10 years since severe acute respiratory syndrome (SARS) emerged, and East and Southeast Asia retain a reputation as a hot spot of emerging infectious diseases. The region is certainly a hot spot of socioeconomic and environmental change, and although some changes (e.g., urbanization and agricultural intensification) may reduce the probability of emerging infectious diseases, the  effect of any individual emergence event may be increased by the greater concentration and connectivity of livestock, persons, and products. The region is now better able to detect and respond to emerging infectious diseases than it was a decade ago, but the tools and methods to produce sufficiently refined assessments of the risks of disease emergence are still lacking. Given the continued scale and pace of change in East and Southeast Asia, it is vital that capabilities for predicting, identifying, and controlling biologic threats do not stagnate as the memory of SARS fades.},
	language = {eng},
	number = {6},
	journal = {Emerging infectious diseases},
	author = {Horby, Peter W. and Pfeiffer, Dirk and Oshitani, Hitoshi},
	month = jun,
	year = {2013},
	pmid = {23738977},
	pmcid = {PMC3713834},
	keywords = {Agriculture, Animals, Asia, Southeastern/epidemiology, Commerce, Communicable Diseases, Emerging/*epidemiology/history, East Asia, Ecosystem, Epidemiological Monitoring, Global Health, History, 21st Century, Humans, Livestock, SARS, Severe Acute Respiratory Syndrome/*epidemiology/history, Southeast Asia, Travel, Urbanization, animal health, bacteria, emerging infections, influenza, influenza A(H5N1), respiratory infections, severe acute respiratory syndrome, viruses},
	pages = {853--860},
}

It is 10 years since severe acute respiratory syndrome (SARS) emerged, and East and Southeast Asia retain a reputation as a hot spot of emerging infectious diseases. The region is certainly a hot spot of socioeconomic and environmental change, and although some changes (e.g., urbanization and agricultural intensification) may reduce the probability of emerging infectious diseases, the effect of any individual emergence event may be increased by the greater concentration and connectivity of livestock, persons, and products. The region is now better able to detect and respond to emerging infectious diseases than it was a decade ago, but the tools and methods to produce sufficiently refined assessments of the risks of disease emergence are still lacking. Given the continued scale and pace of change in East and Southeast Asia, it is vital that capabilities for predicting, identifying, and controlling biologic threats do not stagnate as the memory of SARS fades.

@article{alkhamis_modeling_2013,
	title = {Modeling the association of space, time, and host species with variation of the {HA}, {NA}, and {NS} genes of {H5N1} highly pathogenic avian influenza viruses isolated from birds in {Romania} in 2005-2007.},
	volume = {57},
	issn = {0005-2086 0005-2086},
	doi = {10.1637/10494-011713-Reg.1},
	abstract = {Molecular characterization studies of a diverse collection of avian influenza viruses (AIVs) have demonstrated that AIVs' greatest genetic variability lies in  the HA, NA, and NS genes. The objective here was to quantify the association between geographical locations, periods of time, and host species and pairwise nucleotide variation in the HA, NA, and NS genes of 70 isolates of H5N1 highly pathogenic avian influenza virus (HPAIV) collected from October 2005 to December  2007 from birds in Romania. A mixed-binomial Bayesian regression model was used to quantify the probability of nucleotide variation between isolates and its association with space, time, and host species. As expected for the three target  genes, a higher probability of nucleotide differences (odds ratios [ORs] {\textgreater} 1) was found between viruses sampled from places at greater geographical distances from  each other, viruses sampled over greater periods of time, and viruses derived from different species. The modeling approach in the present study maybe useful in further understanding the molecular epidemiology of H5N1 HPAI virus in bird populations. The methodology presented here will be useful in predicting the most likely genetic distance for any of the three gene segments of viruses that have not yet been isolated or sequenced based on space, time, and host species during  the course of an epidemic.},
	language = {eng},
	number = {3},
	journal = {Avian diseases},
	author = {Alkhamis, Mohammad and Perez, Andres and Batey, Nicole and Howard, Wendy and Baillie, Greg and Watson, Simon and Franz, Stephanie and Focosi-Snyman, Raffaella and Onita, Iuliana and Cioranu, Raluca and Turcitu, Mihai and Kellam, Paul and Brown, Ian H. and Breed, Andrew C.},
	month = sep,
	year = {2013},
	pmid = {24283126},
	pmcid = {PMC3980047},
	keywords = {*Genetic Variation, Animals, Bayes Theorem, Birds, Geography, Hemagglutinin Glycoproteins, Influenza Virus/*genetics/metabolism, Influenza A Virus, H5N1 Subtype/*genetics/metabolism, Influenza in Birds/virology, Models, Theoretical, Molecular Epidemiology/*methods, Neuraminidase/*genetics/metabolism, Regression Analysis, Romania, Sequence Analysis, RNA/veterinary, Species Specificity, Time Factors, Viral Nonstructural Proteins/*genetics/metabolism, Viral Proteins/*genetics/metabolism},
	pages = {612--621},
}

Molecular characterization studies of a diverse collection of avian influenza viruses (AIVs) have demonstrated that AIVs' greatest genetic variability lies in the HA, NA, and NS genes. The objective here was to quantify the association between geographical locations, periods of time, and host species and pairwise nucleotide variation in the HA, NA, and NS genes of 70 isolates of H5N1 highly pathogenic avian influenza virus (HPAIV) collected from October 2005 to December 2007 from birds in Romania. A mixed-binomial Bayesian regression model was used to quantify the probability of nucleotide variation between isolates and its association with space, time, and host species. As expected for the three target genes, a higher probability of nucleotide differences (odds ratios [ORs] \textgreater 1) was found between viruses sampled from places at greater geographical distances from each other, viruses sampled over greater periods of time, and viruses derived from different species. The modeling approach in the present study maybe useful in further understanding the molecular epidemiology of H5N1 HPAI virus in bird populations. The methodology presented here will be useful in predicting the most likely genetic distance for any of the three gene segments of viruses that have not yet been isolated or sequenced based on space, time, and host species during the course of an epidemic.

@article{le_migration_2013,
	title = {Migration and persistence of human influenza {A} viruses, {Vietnam}, 2001-2008.},
	volume = {19},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid1911.130349},
	abstract = {Understanding global influenza migration and persistence is crucial for vaccine strain selection. Using 240 new human influenza A virus whole genomes collected in Vietnam during 2001-2008, we looked for persistence patterns and migratory connections between Vietnam and other countries. We found that viruses in Vietnam migrate to and from China, Hong Kong, Taiwan, Cambodia, Japan, South Korea, and the United States. We attempted to reduce geographic bias by generating phylogenies subsampled at the year and country levels. However, migration events  in these phylogenies were still driven by the presence or absence of sequence data, indicating that an epidemiologic study design that controls for prevalence  is required for robust migration analysis. With whole-genome data, most migration events are not detectable from the phylogeny of the hemagglutinin segment alone,  although general migratory relationships between Vietnam and other countries are  visible in the hemagglutinin phylogeny. It is possible that virus lineages in Vietnam persisted for {\textgreater}1 year.},
	language = {eng},
	number = {11},
	journal = {Emerging infectious diseases},
	author = {Le, Mai Quynh and Lam, Ha Minh and Cuong, Vuong Duc and Lam, Tommy Tsan-Yuk and Halpin, Rebecca A. and Wentworth, David E. and Hien, Nguyen Tran and Thanh, Le Thi and Phuong, Hoang Vu Mai and Horby, Peter and Boni, Maciej F.},
	month = nov,
	year = {2013},
	pmid = {24188643},
	pmcid = {PMC3837676},
	keywords = {Genome, Viral, Hemagglutinin Glycoproteins, Influenza Virus/genetics, Humans, Influenza A Virus, H1N1 Subtype, Influenza A Virus, H3N2 Subtype, Influenza A virus/*classification/*genetics, Influenza, Human/*epidemiology/*transmission, Molecular Sequence Data, Phylogeny, Phylogeography, Public Health Surveillance, Vietnam, Vietnam/epidemiology, influenza, migration, persistence, tropics, viruses},
	pages = {1756--1765},
}

Understanding global influenza migration and persistence is crucial for vaccine strain selection. Using 240 new human influenza A virus whole genomes collected in Vietnam during 2001-2008, we looked for persistence patterns and migratory connections between Vietnam and other countries. We found that viruses in Vietnam migrate to and from China, Hong Kong, Taiwan, Cambodia, Japan, South Korea, and the United States. We attempted to reduce geographic bias by generating phylogenies subsampled at the year and country levels. However, migration events in these phylogenies were still driven by the presence or absence of sequence data, indicating that an epidemiologic study design that controls for prevalence is required for robust migration analysis. With whole-genome data, most migration events are not detectable from the phylogeny of the hemagglutinin segment alone, although general migratory relationships between Vietnam and other countries are visible in the hemagglutinin phylogeny. It is possible that virus lineages in Vietnam persisted for \textgreater1 year.

@article{tan_identification_2013,
	title = {Identification of a new cyclovirus in cerebrospinal fluid of patients with acute  central nervous system infections.},
	volume = {4},
	issn = {2150-7511},
	doi = {10.1128/mBio.00231-13},
	abstract = {Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified and characterized the full genome of a novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) in cerebrospinal fluid (CSF) specimens of two Vietnamese patients with CNS infections of unknown etiology. CyCV-VN was subsequently detected in 4\% of 642 CSF specimens from Vietnamese patients with suspected CNS infections and none of 122 CSFs from patients with noninfectious neurological disorders. Detection rates were similar in patients with CNS infections of unknown etiology and those in whom other pathogens were detected. A similar detection rate in feces from healthy children suggested food-borne or orofecal transmission routes, while high detection rates in feces from pigs and poultry (average, 58\%) suggested the existence of animal reservoirs for such transmission. Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus.},
	language = {eng},
	number = {3},
	journal = {mBio},
	author = {Tan, Le Van and van Doorn, H. Rogier and Nghia, Ho Dang Trung and Chau, Tran Thi Hong and Tu, Le Thi Phuong and de Vries, Michel and Canuti, Marta and Deijs, Martin and Jebbink, Maarten F. and Baker, Stephen and Bryant, Juliet E. and Tham, Nguyen Thi and BKrong, Nguyen Thi Thuy Chinh and Boni, Maciej F. and Loi, Tran Quoc and Phuong, Le Thi and Verhoeven, Joost T. P. and Crusat, Martin and Jeeninga, Rienk E. and Schultsz, Constance and Chau, Nguyen Van Vinh and Hien, Tran Tinh and van der Hoek, Lia and Farrar, Jeremy and de Jong, Menno D.},
	month = jun,
	year = {2013},
	pmid = {23781068},
	pmcid = {PMC3684831},
	keywords = {Adolescent, Adult, Aged, Animals, Central Nervous System Infections/epidemiology/*virology, Child, Child, Preschool, Circoviridae Infections/epidemiology/*virology, Circoviridae/*classification/genetics/*isolation \& purification, Cluster Analysis, DNA, Viral/chemistry/genetics, Female, Genome, Viral, Humans, Infant, Male, Middle Aged, Molecular Sequence Data, Phylogeny, Prevalence, Prospective Studies, Sequence Analysis, DNA, Vietnam, Young Adult},
	pages = {e00231--00213},
}

Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified and characterized the full genome of a novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) in cerebrospinal fluid (CSF) specimens of two Vietnamese patients with CNS infections of unknown etiology. CyCV-VN was subsequently detected in 4% of 642 CSF specimens from Vietnamese patients with suspected CNS infections and none of 122 CSFs from patients with noninfectious neurological disorders. Detection rates were similar in patients with CNS infections of unknown etiology and those in whom other pathogens were detected. A similar detection rate in feces from healthy children suggested food-borne or orofecal transmission routes, while high detection rates in feces from pigs and poultry (average, 58%) suggested the existence of animal reservoirs for such transmission. Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus.

@article{assiri_hospital_2013,
	title = {Hospital outbreak of {Middle} {East} respiratory syndrome coronavirus.},
	volume = {369},
	issn = {1533-4406 0028-4793},
	doi = {10.1056/NEJMoa1306742},
	abstract = {BACKGROUND: In September 2012, the World Health Organization reported the first cases of pneumonia caused by the novel Middle East respiratory syndrome coronavirus (MERS-CoV). We describe a cluster of health care-acquired MERS-CoV infections. METHODS: Medical records were reviewed for clinical and demographic information and determination of potential contacts and exposures. Case patients  and contacts were interviewed. The incubation period and serial interval (the time between the successive onset of symptoms in a chain of transmission) were estimated. Viral RNA was sequenced. RESULTS: Between April 1 and May 23, 2013, a  total of 23 cases of MERS-CoV infection were reported in the eastern province of  Saudi Arabia. Symptoms included fever in 20 patients (87\%), cough in 20 (87\%), shortness of breath in 11 (48\%), and gastrointestinal symptoms in 8 (35\%); 20 patients (87\%) presented with abnormal chest radiographs. As of June 12, a total  of 15 patients (65\%) had died, 6 (26\%) had recovered, and 2 (9\%) remained hospitalized. The median incubation period was 5.2 days (95\% confidence interval  [CI], 1.9 to 14.7), and the serial interval was 7.6 days (95\% CI, 2.5 to 23.1). A total of 21 of the 23 cases were acquired by person-to-person transmission in hemodialysis units, intensive care units, or in-patient units in three different  health care facilities. Sequencing data from four isolates revealed a single monophyletic clade. Among 217 household contacts and more than 200 health care worker contacts whom we identified, MERS-CoV infection developed in 5 family members (3 with laboratory-confirmed cases) and in 2 health care workers (both with laboratory-confirmed cases). CONCLUSIONS: Person-to-person transmission of},
	language = {eng},
	number = {5},
	journal = {The New England journal of medicine},
	author = {Assiri, Abdullah and McGeer, Allison and Perl, Trish M. and Price, Connie S. and Al Rabeeah, Abdullah A. and Cummings, Derek A. T. and Alabdullatif, Zaki N. and Assad, Maher and Almulhim, Abdulmohsen and Makhdoom, Hatem and Madani, Hossam and Alhakeem, Rafat and Al-Tawfiq, Jaffar A. and Cotten, Matthew and Watson, Simon J. and Kellam, Paul and Zumla, Alimuddin I. and Memish, Ziad A.},
	month = aug,
	year = {2013},
	pmid = {23782161},
	pmcid = {PMC4029105},
	keywords = {*Disease Outbreaks, Adult, Aged, Aged, 80 and over, Base Sequence, Coronavirus Infections/epidemiology/*transmission/virology, Coronavirus/*genetics/isolation \& purification, Cross Infection/epidemiology/*transmission/virology, DNA, Viral/analysis, Disease Transmission, Infectious, Female, Humans, Infectious Disease Incubation Period, Infectious Disease Transmission, Patient-to-Professional, Intensive Care Units, Male, Middle Aged, Phylogeny, Pneumonia, Viral/*epidemiology/transmission/virology, Renal Dialysis, Saudi Arabia/epidemiology},
	pages = {407--416},
}

BACKGROUND: In September 2012, the World Health Organization reported the first cases of pneumonia caused by the novel Middle East respiratory syndrome coronavirus (MERS-CoV). We describe a cluster of health care-acquired MERS-CoV infections. METHODS: Medical records were reviewed for clinical and demographic information and determination of potential contacts and exposures. Case patients and contacts were interviewed. The incubation period and serial interval (the time between the successive onset of symptoms in a chain of transmission) were estimated. Viral RNA was sequenced. RESULTS: Between April 1 and May 23, 2013, a total of 23 cases of MERS-CoV infection were reported in the eastern province of Saudi Arabia. Symptoms included fever in 20 patients (87%), cough in 20 (87%), shortness of breath in 11 (48%), and gastrointestinal symptoms in 8 (35%); 20 patients (87%) presented with abnormal chest radiographs. As of June 12, a total of 15 patients (65%) had died, 6 (26%) had recovered, and 2 (9%) remained hospitalized. The median incubation period was 5.2 days (95% confidence interval [CI], 1.9 to 14.7), and the serial interval was 7.6 days (95% CI, 2.5 to 23.1). A total of 21 of the 23 cases were acquired by person-to-person transmission in hemodialysis units, intensive care units, or in-patient units in three different health care facilities. Sequencing data from four isolates revealed a single monophyletic clade. Among 217 household contacts and more than 200 health care worker contacts whom we identified, MERS-CoV infection developed in 5 family members (3 with laboratory-confirmed cases) and in 2 health care workers (both with laboratory-confirmed cases). CONCLUSIONS: Person-to-person transmission of

@article{horby_h7n9_2013,
	title = {{H7N9} is a virus worth worrying about.},
	volume = {496},
	issn = {1476-4687 0028-0836},
	doi = {10.1038/496399a},
	language = {eng},
	number = {7446},
	journal = {Nature},
	author = {Horby, Peter},
	month = apr,
	year = {2013},
	pmid = {23619655},
	keywords = {Adaptation, Physiological, Animals, China/epidemiology, Disease Transmission, Infectious/statistics \& numerical data, Host Specificity, Humans, Influenza A Virus, H1N1 Subtype/pathogenicity/physiology, Influenza A Virus, H5N1 Subtype/pathogenicity/physiology, Influenza A virus/pathogenicity/*physiology, Influenza, Human/*epidemiology/prevention \& control/transmission/*virology, Poultry/virology, Swine/virology, Zoonoses/*epidemiology/transmission/*virology},
	pages = {399},
}

@article{cotten_full-genome_2013,
	title = {Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus.},
	volume = {19},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid1905.130057},
	abstract = {A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient's sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events.},
	language = {eng},
	number = {5},
	journal = {Emerging infectious diseases},
	author = {Cotten, Matthew and Lam, Tommy T. and Watson, Simon J. and Palser, Anne L. and Petrova, Velislava and Grant, Paul and Pybus, Oliver G. and Rambaut, Andrew and Guan, Yi and Pillay, Deenan and Kellam, Paul and Nastouli, Eleni},
	month = may,
	year = {2013},
	pmid = {23693015},
	pmcid = {PMC3647518},
	keywords = {*Genome, Viral, Animals, Base Sequence, Chiroptera/virology, Coronavirus Infections/*diagnosis/virology, Coronavirus/classification/*genetics/isolation \& purification, DNA Primers, DNA, Complementary/genetics, Evolution, High-Throughput Nucleotide Sequencing, Humans, Jordan, Molecular Sequence Data, Phylogeny, Qatar, RNA, Viral/*genetics, Reverse Transcriptase Polymerase Chain Reaction, Saudi Arabia, computer-aided design, coronavirus infections, disease transmission, infectious, molecular, respiratory tract infections, viruses, zoonoses},
	pages = {736--742B},
}

A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient's sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events.

@article{thompson_epidemiological_2013,
	title = {Epidemiological features and risk factors of {Salmonella} gastroenteritis in children resident in {Ho} {Chi} {Minh} {City}, {Vietnam}.},
	volume = {141},
	issn = {1469-4409 0950-2688},
	doi = {10.1017/S0950268812002014},
	abstract = {Non-typhoidal Salmonella are an important but poorly characterized cause of paediatric diarrhoea in developing countries. We conducted a hospital-based case-control study in children aged {\textless}5 years in Ho Chi Minh City to define the epidemiology and examine risk factors associated with Salmonella diarrhoeal infections. From 1419 diarrhoea cases and 571 controls enrolled between 2009 and  2010, 77 (54\%) diarrhoea cases were stool culture-positive for non-typhoidal Salmonella. Salmonella patients were more likely to be younger than controls (median age 10 and 12 months, respectively) [odds ratio (OR) 097; 95\% confidence  interval (CI) 094-099], to report a recent diarrhoeal contact (81\% cases, 18\% controls; OR 598, 95\% CI 18-204) and to live in a household with {\textgreater}2 children (cases 208\%, controls 102\%; OR 232, 95\% CI 12-47). Our findings indicate that Salmonella are an important cause of paediatric gastroenteritis in this setting and we suggest that transmission may occur through direct human contact in the home.},
	language = {eng},
	number = {8},
	journal = {Epidemiology and infection},
	author = {Thompson, C. N. and Phan, V. T. M. and Le, T. P. T. and Pham, T. N. T. and Hoang, L. P. and Ha, V. and Nguyen, V. M. H. and Pham, V. M. and Nguyen, T. V. and Cao, T. T. and Tran, T. T. N. and Nguyen, T. T. H. and Dao, M. T. and Campbell, J. I. and Nguyen, T. C. and Tang, C. T. and Ha, M. T. and Farrar, J. and Baker, S.},
	month = aug,
	year = {2013},
	pmid = {23010148},
	pmcid = {PMC3733064},
	keywords = {*Developing Countries, Bacterial Typing Techniques, Case-Control Studies, Child, Preschool, Diarrhea/*epidemiology/microbiology, Feces/microbiology, Female, Gastroenteritis/*epidemiology/microbiology, Humans, Infant, Male, Prevalence, Risk Factors, Salmonella Infections/*epidemiology/microbiology/transmission, Salmonella/*isolation \& purification, Surveys and Questionnaires, Urban Population, Vietnam/epidemiology},
	pages = {1604--1613},
}

Non-typhoidal Salmonella are an important but poorly characterized cause of paediatric diarrhoea in developing countries. We conducted a hospital-based case-control study in children aged \textless5 years in Ho Chi Minh City to define the epidemiology and examine risk factors associated with Salmonella diarrhoeal infections. From 1419 diarrhoea cases and 571 controls enrolled between 2009 and 2010, 77 (54%) diarrhoea cases were stool culture-positive for non-typhoidal Salmonella. Salmonella patients were more likely to be younger than controls (median age 10 and 12 months, respectively) [odds ratio (OR) 097; 95% confidence interval (CI) 094-099], to report a recent diarrhoeal contact (81% cases, 18% controls; OR 598, 95% CI 18-204) and to live in a household with \textgreater2 children (cases 208%, controls 102%; OR 232, 95% CI 12-47). Our findings indicate that Salmonella are an important cause of paediatric gastroenteritis in this setting and we suggest that transmission may occur through direct human contact in the home.

@article{my_endemic_2013,
	title = {Endemic norovirus infections in children, {Ho} {Chi} {Minh} {City}, {Vietnam}, 2009-2010.},
	volume = {19},
	issn = {1080-6059 1080-6040},
	doi = {10.3201/eid1906.111862},
	abstract = {We performed a case-control investigation to identify risk factors for norovirus  infections among children in Vietnam. Of samples from 1,419 children who had diarrhea and 609 who were asymptomatic, 20.6\% and 2.8\%, respectively, were norovirus positive. Risk factors included residential crowding and symptomatic contacts, indicating person-to-person transmission of norovirus.},
	language = {eng},
	number = {6},
	journal = {Emerging infectious diseases},
	author = {My, Phan Vu Tra and Thompson, Corinne and Phuc, Hoang Le and Tuyet, Pham Thi Ngoc and Vinh, Ha and Hoang, Nguyen Van Minh and Minh, Pham Van and Vinh, Nguyen Thanh and Thuy, Cao Thu and Nga, Tran Thi Thu and Hau, Nguyen Thi Thu and Campbell, James and Chinh, Nguyen Tran and Thuong, Tang Chi and Tuan, Ha Manh and Farrar, Jeremy and Baker, Stephen},
	month = jun,
	year = {2013},
	pmid = {23735160},
	pmcid = {PMC3713809},
	keywords = {*Norovirus/classification/genetics/isolation \& purification, Caliciviridae Infections/*epidemiology/history/transmission, Case-Control Studies, Child, Diarrhea/*epidemiology/history/virology, Gastroenteritis/*epidemiology/history/virology, History, 21st Century, Humans, Prevalence, Prospective Studies, Risk Factors, Seasons, Vietnam, Vietnam/epidemiology, asymptomatic, children, diarrhea, gastroenteritis, norovirus, pediatric, symptomatic, viruses},
	pages = {977--980},
}

We performed a case-control investigation to identify risk factors for norovirus infections among children in Vietnam. Of samples from 1,419 children who had diarrhea and 609 who were asymptomatic, 20.6% and 2.8%, respectively, were norovirus positive. Risk factors included residential crowding and symptomatic contacts, indicating person-to-person transmission of norovirus.

@article{creanga_emergence_2013,
	title = {Emergence of multiple clade 2.3.2.1 influenza {A} ({H5N1}) virus subgroups in {Vietnam} and detection of novel reassortants.},
	volume = {444},
	copyright = {Published by Elsevier Inc.},
	issn = {1096-0341 0042-6822},
	doi = {10.1016/j.virol.2013.06.005},
	abstract = {Phylogenetic analyses of 169 influenza A(H5N1) virus genomes were conducted for samples collected through active surveillance and outbreak responses in Vietnam between September 2010 and September 2012. While clade 1.1 viruses persisted in southern regions, three genetically distinct subgroups of clade 2.3.2.1 were found in northern and central Vietnam. The identification of each subgroup corresponded with detection of novel reassortants, likely due to their overlapping circulation throughout the country. While the previously identified clade 1.1 and A/Hubei/1/2010-like 2.3.2.1 genotypes remained the predominant viruses detected, four viruses were found to be reassortants between A/Hubei/1/2010-like (HA, NA, PB2, PB1, PA, NP) and A/duck/Vietnam/NCVD-885/2010-like (M, NS) viruses and one virus was identified as having A/duck/Vietnam/NCVD-885/2010-like HA, NA, PB1, and NP with A/Hubei/1/2010-like PB2 and PA genes. Additionally, clade 2.3.2.1 A/Hong Kong/6841/2010-like viruses, first detected in mid-2012, were identified as reassortants comprised of A/Hubei/1/2010-like PB2 and PA and A/duck/Vietnam/NCVD-885/2010-like PB1, NP, NA, M, NS genes.},
	language = {eng},
	number = {1-2},
	journal = {Virology},
	author = {Creanga, Adrian and Thi Nguyen, Diep and Gerloff, Nancy and Thi Do, Hoa and Balish, Amanda and Dang Nguyen, Hoang and Jang, Yunho and Thi Dam, Vui and Thor, Sharmi and Jones, Joyce and Simpson, Natosha and Shu, Bo and Emery, Shannon and Berman, LaShondra and Nguyen, Ha T. and Bryant, Juliet E. and Lindstrom, Steve and Klimov, Alexander and Donis, Ruben O. and Davis, C. Todd and Nguyen, Tung},
	month = sep,
	year = {2013},
	pmid = {23849789},
	keywords = {*Phylogeography, Animals, Cluster Analysis, Evolution, Genotype, Geographic distribution, H5N1, Highly pathogenic avian influenza virus, Influenza A Virus, H5N1 Subtype/*classification/*genetics/isolation \& purification, Influenza in Birds/*virology, Molecular Sequence Data, Orthomyxovirus, Phylogenetics, Poultry, RNA, Viral/*genetics, Real-Time Polymerase Chain Reaction, Reassortant Viruses/*classification/*genetics/isolation \& purification, Reassortment, Sequence Analysis, DNA, Vietnam},
	pages = {12--20},
}

Phylogenetic analyses of 169 influenza A(H5N1) virus genomes were conducted for samples collected through active surveillance and outbreak responses in Vietnam between September 2010 and September 2012. While clade 1.1 viruses persisted in southern regions, three genetically distinct subgroups of clade 2.3.2.1 were found in northern and central Vietnam. The identification of each subgroup corresponded with detection of novel reassortants, likely due to their overlapping circulation throughout the country. While the previously identified clade 1.1 and A/Hubei/1/2010-like 2.3.2.1 genotypes remained the predominant viruses detected, four viruses were found to be reassortants between A/Hubei/1/2010-like (HA, NA, PB2, PB1, PA, NP) and A/duck/Vietnam/NCVD-885/2010-like (M, NS) viruses and one virus was identified as having A/duck/Vietnam/NCVD-885/2010-like HA, NA, PB1, and NP with A/Hubei/1/2010-like PB2 and PA genes. Additionally, clade 2.3.2.1 A/Hong Kong/6841/2010-like viruses, first detected in mid-2012, were identified as reassortants comprised of A/Hubei/1/2010-like PB2 and PA and A/duck/Vietnam/NCVD-885/2010-like PB1, NP, NA, M, NS genes.

@article{woolhouse_ecological_2013,
	title = {Ecological and taxonomic variation among human {RNA} viruses.},
	volume = {58},
	copyright = {Copyright (c) 2013 Elsevier B.V. All rights reserved.},
	issn = {1873-5967 1386-6532},
	doi = {10.1016/j.jcv.2013.02.019},
	abstract = {Only a minority of RNA viruses that can infect humans are capable of spreading in human populations independently of a zoonotic reservoir. This is especially true  of vector-borne RNA viruses; the majority of these are not transmissible (via the vector) between humans at all. Understanding the biology underlying this observation will help us evaluate the public health risk associated with novel vector-borne RNA viruses.},
	language = {eng},
	number = {2},
	journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
	author = {Woolhouse, Mark E. J. and Adair, Kyle},
	month = oct,
	year = {2013},
	pmid = {23518441},
	pmcid = {PMC3793856},
	keywords = {*Disease Vectors, *Ecology, Animals, Discovery, Emerging, Humans, Infectious Disease Transmission, Vertical, One health, RNA Virus Infections/*epidemiology/*transmission/virology, RNA Viruses/*physiology, Zoonoses/*epidemiology/*transmission/virology},
	pages = {344--345},
}

Only a minority of RNA viruses that can infect humans are capable of spreading in human populations independently of a zoonotic reservoir. This is especially true of vector-borne RNA viruses; the majority of these are not transmissible (via the vector) between humans at all. Understanding the biology underlying this observation will help us evaluate the public health risk associated with novel vector-borne RNA viruses.

@article{phan_detection_2013,
	title = {Detection of {HPAI} {H5N1} viruses in ducks sampled from live bird markets in {Vietnam}.},
	volume = {141},
	issn = {1469-4409 0950-2688},
	doi = {10.1017/S0950268812001112},
	abstract = {In Vietnam, highly pathogenic avian influenza (HPAI) H5N1 infections in poultry often occur without concomitant clinical signs and outbreaks are not consistently reported. Live bird markets represent a convenient site for surveillance that does not rely on farmers' notifications. Two H5N1 surveys were conducted at live  bird markets/slaughter points in 39 districts (five provinces) in the Red River,  Mekong delta, and central Vietnam during January and May 2011. Oropharyngeal and  rectal swab samples from 12 480 ducks were tested for H5N1 by reverse transcription-polymerase chain reaction in pools of five. Traders and stallholders were interviewed using standardized questionnaires; 3.3\% of pools tested positive. The highest prevalence (6.6\%) corresponded to the Mekong delta,  and no H5N1 was detected in the two Red River provinces. The surveys identified key risk behaviours of traders and stallholders. It is recommended that market surveys are implemented over time as a tool to evaluate progress in HPAI control  in Vietnam.},
	language = {eng},
	number = {3},
	journal = {Epidemiology and infection},
	author = {Phan, M. Q. and Henry, W. and Bui, C. B. and DO, D. H. and Hoang, N. V. and Thu, N. T. and Nguyen, T. T. and LE, T. D. and Diep, T. Q. and Inui, K. and Weaver, J. and Carrique-Mas, J.},
	month = mar,
	year = {2013},
	pmid = {22651930},
	keywords = {Age Factors, Animals, Commerce, Ducks/*virology, Humans, Influenza A Virus, H5N1 Subtype/*isolation \& purification, Influenza in Birds/*epidemiology/*virology, Oropharynx/virology, Prevalence, Rectum/virology, Reverse Transcriptase Polymerase Chain Reaction/veterinary, Surveys and Questionnaires, Vietnam/epidemiology},
	pages = {601--611},
}

In Vietnam, highly pathogenic avian influenza (HPAI) H5N1 infections in poultry often occur without concomitant clinical signs and outbreaks are not consistently reported. Live bird markets represent a convenient site for surveillance that does not rely on farmers' notifications. Two H5N1 surveys were conducted at live bird markets/slaughter points in 39 districts (five provinces) in the Red River, Mekong delta, and central Vietnam during January and May 2011. Oropharyngeal and rectal swab samples from 12 480 ducks were tested for H5N1 by reverse transcription-polymerase chain reaction in pools of five. Traders and stallholders were interviewed using standardized questionnaires; 3.3% of pools tested positive. The highest prevalence (6.6%) corresponded to the Mekong delta, and no H5N1 was detected in the two Red River provinces. The surveys identified key risk behaviours of traders and stallholders. It is recommended that market surveys are implemented over time as a tool to evaluate progress in HPAI control in Vietnam.

@article{rabaa_dengue_2013,
	title = {Dengue virus in sub-tropical northern and central {Viet} {Nam}: population immunity and climate shape patterns of viral invasion and maintenance.},
	volume = {7},
	issn = {1935-2735 1935-2727},
	doi = {10.1371/journal.pntd.0002581},
	abstract = {Dengue virus transmission occurs in both epidemic and endemic cycles across tropical and sub-tropical regions of the world. Incidence is particularly high in much of Southeast Asia, where hyperendemic transmission plagues both urban and rural populations. However, endemicity has not been established in some areas with climates that may not support year-round viral transmission. An understanding of how dengue viruses (DENV) enter these environments and whether the viruses persist in inapparent local transmission cycles is central to understanding how dengue emerges in areas at the margins of endemic transmission. Dengue is highly endemic in tropical southern Vietnam, while increasingly large seasonal epidemics have occurred in northern Viet Nam over the last decade. We have investigated the spread of DENV-1 throughout Vietnam to determine the routes by which the virus enters northern and central regions of the country. Phylogeographic analysis of 1,765 envelope (E) gene sequences from Southeast Asia revealed frequent movement of DENV between neighboring human populations and strong local clustering of viral lineages. Long-distance migration of DENV between human population centers also occurred regularly and on short time-scales, indicating human-mediated viral invasion into northern Vietnam. Human populations in southern Vietnam were found to be the primary source of DENV circulating throughout the country, while central and northern Vietnam acted as sink populations, likely due to reduced connectedness to other populations in the case of the central regions and to the influence of temperature variability on DENV replication and vector survival and competence in the north. Finally, phylogeographic analyses suggested that viral movement follows a gravity model and indicates that population immunity and physical and economic connections between populations may play important roles in shaping patterns of DENV transmission.},
	language = {eng},
	number = {12},
	journal = {PLoS neglected tropical diseases},
	author = {Rabaa, Maia A. and Simmons, Cameron P. and Fox, Annette and Le, Mai Quynh and Nguyen, Thuy Thi Thu and Le, Hai Yen and Gibbons, Robert V. and Nguyen, Xuyen Thanh and Holmes, Edward C. and Aaskov, John G.},
	year = {2013},
	pmid = {24340118},
	pmcid = {PMC3854975},
	keywords = {Climate, Cluster Analysis, Dengue Virus/classification/genetics/*immunology/isolation \& purification, Dengue/*epidemiology/*immunology, Humans, Molecular Epidemiology, Molecular Sequence Data, Phylogeography, Sequence Analysis, DNA, Sequence Homology, Vietnam/epidemiology, Viral Envelope Proteins/genetics},
	pages = {e2581},
}

Dengue virus transmission occurs in both epidemic and endemic cycles across tropical and sub-tropical regions of the world. Incidence is particularly high in much of Southeast Asia, where hyperendemic transmission plagues both urban and rural populations. However, endemicity has not been established in some areas with climates that may not support year-round viral transmission. An understanding of how dengue viruses (DENV) enter these environments and whether the viruses persist in inapparent local transmission cycles is central to understanding how dengue emerges in areas at the margins of endemic transmission. Dengue is highly endemic in tropical southern Vietnam, while increasingly large seasonal epidemics have occurred in northern Viet Nam over the last decade. We have investigated the spread of DENV-1 throughout Vietnam to determine the routes by which the virus enters northern and central regions of the country. Phylogeographic analysis of 1,765 envelope (E) gene sequences from Southeast Asia revealed frequent movement of DENV between neighboring human populations and strong local clustering of viral lineages. Long-distance migration of DENV between human population centers also occurred regularly and on short time-scales, indicating human-mediated viral invasion into northern Vietnam. Human populations in southern Vietnam were found to be the primary source of DENV circulating throughout the country, while central and northern Vietnam acted as sink populations, likely due to reduced connectedness to other populations in the case of the central regions and to the influence of temperature variability on DENV replication and vector survival and competence in the north. Finally, phylogeographic analyses suggested that viral movement follows a gravity model and indicates that population immunity and physical and economic connections between populations may play important roles in shaping patterns of DENV transmission.

@article{harada_avian_2013,
	title = {Avian influenza {A}({H7N9}): information-sharing through government web sites in the  {Western} {Pacific} {Region}.},
	volume = {4},
	issn = {2094-7313 2094-7321},
	doi = {10.5365/WPSAR.2013.4.2.010},
	language = {eng},
	number = {2},
	journal = {Western Pacific surveillance and response journal : WPSAR},
	author = {Harada, Nahoko and Alexander, Nyka and Olowokure, Babatunde},
	month = jun,
	year = {2013},
	pmid = {24015371},
	pmcid = {PMC3762963},
	keywords = {*Government Agencies, *Influenza A Virus, H7N9 Subtype, Animals, Birds, Consumer Health Information/*statistics \& numerical data, Humans, Influenza in Birds/epidemiology/*prevention \& control, Influenza, Human/epidemiology/*prevention \& control, Internet/*utilization, Pacific Islands, Patient Education as Topic/statistics \& numerical data},
	pages = {44--46},
}

@article{murhekar_avian_2013,
	title = {Avian influenza {A}({H7N9}) and the closure of live bird markets.},
	volume = {4},
	issn = {2094-7313 2094-7321},
	doi = {10.5365/WPSAR.2013.4.2.008},
	language = {eng},
	number = {2},
	journal = {Western Pacific surveillance and response journal : WPSAR},
	author = {Murhekar, Manoj and Arima, Yuzo and Horby, Peter and Vandemaele, Katelijn A. H. and Vong, Sirenda and Zijian, Feng and Lee, Chin-Kei and Li, Ailan},
	month = jun,
	year = {2013},
	pmid = {24015364},
	pmcid = {PMC3762972},
	keywords = {*Marketing, Agriculture, Animals, China, Disease Reservoirs/*statistics \& numerical data/virology, Humans, Influenza A Virus, H7N9 Subtype/*isolation \& purification, Influenza in Birds/*diagnosis/epidemiology/virology, Influenza, Human/*diagnosis/epidemiology/virology, Poultry/*virology},
	pages = {4--7},
}

@article{horby_updated_2013,
	title = {An updated systematic review of the role of host genetics in susceptibility to influenza.},
	volume = {7 Suppl 2},
	copyright = {(c) 2013 Blackwell Publishing Ltd.},
	issn = {1750-2659 1750-2640},
	doi = {10.1111/irv.12079},
	abstract = {The World Health Organization has identified studies of the role of host genetics on susceptibility to severe influenza as a priority. A systematic review was conducted in June 2011 to summarise the evidence on the role of host genetics in  susceptibility to influenza, and this report updates that previously published review. Animal studies suggest that genetic control of susceptibility to severe influenza in mice is complex and not controlled by a single locus, but there is encouraging evidence that some of the host genetic determinants of susceptibility to severe disease may be common across influenza subtypes. Although a number of studies on genetic susceptibility to influenza in humans have been published recently, all are underpowered and unreplicated, so do not provide robust statistical evidence of an association between the identified genetic loci and susceptibility. One study does however present convincing functional evidence for an important role for IFITM3 in susceptibility to severe influenza in mice, and some evidence that this may also be important in human A/H1N1/pdm2009 infection.},
	language = {eng},
	journal = {Influenza and other respiratory viruses},
	author = {Horby, Peter and Nguyen, Nhu Y. and Dunstan, Sarah J. and Baillie, John Kenneth},
	month = sep,
	year = {2013},
	pmid = {24034482},
	keywords = {*Genetic Predisposition to Disease, Animal model, Animals, Disease Models, Animal, Humans, Influenza, Human/*genetics, Membrane Proteins/genetics/immunology, Mice, RNA-Binding Proteins/genetics/immunology, host genetics, human influenza, susceptibility, systematic review},
	pages = {37--41},
}

The World Health Organization has identified studies of the role of host genetics on susceptibility to severe influenza as a priority. A systematic review was conducted in June 2011 to summarise the evidence on the role of host genetics in susceptibility to influenza, and this report updates that previously published review. Animal studies suggest that genetic control of susceptibility to severe influenza in mice is complex and not controlled by a single locus, but there is encouraging evidence that some of the host genetic determinants of susceptibility to severe disease may be common across influenza subtypes. Although a number of studies on genetic susceptibility to influenza in humans have been published recently, all are underpowered and unreplicated, so do not provide robust statistical evidence of an association between the identified genetic loci and susceptibility. One study does however present convincing functional evidence for an important role for IFITM3 in susceptibility to severe influenza in mice, and some evidence that this may also be important in human A/H1N1/pdm2009 infection.

@article{oude_munnink_autologous_2013,
	title = {Autologous antibody capture to enrich immunogenic viruses for viral discovery.},
	volume = {8},
	issn = {1932-6203 1932-6203},
	doi = {10.1371/journal.pone.0078454},
	abstract = {Discovery of new viruses has been boosted by novel deep sequencing technologies.  Currently, many viruses can be identified by sequencing without knowledge of the  pathogenicity of the virus. However, attributing the presence of a virus in patient material to a disease in the patient can be a challenge. One approach to  meet this challenge is identification of viral sequences based on enrichment by autologous patient antibody capture. This method facilitates identification of viruses that have provoked an immune response within the patient and may increase the sensitivity of the current virus discovery techniques. To demonstrate the utility of this method, virus discovery deep sequencing (VIDISCA-454) was performed on clinical samples from 19 patients: 13 with a known respiratory viral infection and 6 with a known gastrointestinal viral infection. Patient sera was collected from one to several months after the acute infection phase. Input and antibody capture material was sequenced and enrichment was assessed. In 18 of the 19 patients, viral reads from immunogenic viruses were enriched by antibody capture (ranging between 1.5x to 343x in respiratory material, and 1.4x to 53x in stool). Enriched reads were also determined in an identity independent manner by  using a novel algorithm Xcompare. In 16 of the 19 patients, 21\% to 100\% of the enriched reads were derived from infecting viruses. In conclusion, the technique  provides a novel approach to specifically identify immunogenic viral sequences among the bulk of sequences which are usually encountered during virus discovery  metagenomics.},
	language = {eng},
	number = {11},
	journal = {PloS one},
	author = {Oude Munnink, Bas B. and Jazaeri Farsani, Seyed Mohammad and Deijs, Martin and Jonkers, Jiri and Verhoeven, Joost T. P. and Ieven, Margareta and Goossens, Herman and de Jong, Menno D. and Berkhout, Ben and Loens, Katherine and Kellam, Paul and Bakker, Margreet and Canuti, Marta and Cotten, Matthew and van der Hoek, Lia},
	year = {2013},
	pmid = {24223808},
	pmcid = {PMC3817278},
	keywords = {Algorithms, Antibodies, Viral/*blood, DNA, Viral/immunology/*isolation \& purification, Feces/virology, Gastroenteritis/*diagnosis/immunology/virology, Humans, Metagenomics, Molecular Typing/*methods, Respiratory Tract Infections/*diagnosis/immunology/virology, Sequence Analysis, DNA, Virus Diseases/*diagnosis/immunology/virology, Viruses/immunology/*isolation \& purification},
	pages = {e78454},
}

Discovery of new viruses has been boosted by novel deep sequencing technologies. Currently, many viruses can be identified by sequencing without knowledge of the pathogenicity of the virus. However, attributing the presence of a virus in patient material to a disease in the patient can be a challenge. One approach to meet this challenge is identification of viral sequences based on enrichment by autologous patient antibody capture. This method facilitates identification of viruses that have provoked an immune response within the patient and may increase the sensitivity of the current virus discovery techniques. To demonstrate the utility of this method, virus discovery deep sequencing (VIDISCA-454) was performed on clinical samples from 19 patients: 13 with a known respiratory viral infection and 6 with a known gastrointestinal viral infection. Patient sera was collected from one to several months after the acute infection phase. Input and antibody capture material was sequenced and enrichment was assessed. In 18 of the 19 patients, viral reads from immunogenic viruses were enriched by antibody capture (ranging between 1.5x to 343x in respiratory material, and 1.4x to 53x in stool). Enriched reads were also determined in an identity independent manner by using a novel algorithm Xcompare. In 16 of the 19 patients, 21% to 100% of the enriched reads were derived from infecting viruses. In conclusion, the technique provides a novel approach to specifically identify immunogenic viral sequences among the bulk of sequences which are usually encountered during virus discovery metagenomics.

@article{nguyen_antibiotic_2013,
	title = {Antibiotic use and resistance in emerging economies: a situation analysis for {Viet} {Nam}.},
	volume = {13},
	issn = {1471-2458 1471-2458},
	doi = {10.1186/1471-2458-13-1158},
	abstract = {BACKGROUND: Antimicrobial resistance is a major contemporary public health threat. Strategies to contain antimicrobial resistance have been comprehensively  set forth, however in developing countries where the need for effective antimicrobials is greatest implementation has proved problematic. A better understanding of patterns and determinants of antibiotic use and resistance in emerging economies may permit more appropriately targeted interventions.Viet Nam, with a large population, high burden of infectious disease and relatively unrestricted access to medication, is an excellent case study of the difficulties faced by emerging economies in controlling antimicrobial resistance. METHODS: Our working group conducted a situation analysis of the current patterns and determinants of antibiotic use and resistance in Viet Nam. International publications and local reports published between 1-1-1990 and 31-8-2012 were reviewed. All stakeholders analyzed the findings at a policy workshop and feasible recommendations were suggested to improve antibiotic use in Viet Nam.Here we report the results of our situation analysis focusing on: the healthcare system, drug regulation and supply; antibiotic resistance and infection control; and agricultural antibiotic use. RESULTS: Market reforms have  improved healthcare access in Viet Nam and contributed to better health outcomes. However, increased accessibility has been accompanied by injudicious antibiotic use in hospitals and the community, with predictable escalation in bacterial resistance. Prescribing practices are poor and self-medication is common - often  being the most affordable way to access healthcare. Many policies exist to regulate antibiotic use but enforcement is insufficient or lacking.Pneumococcal penicillin-resistance rates are the highest in Asia and carbapenem-resistant bacteria (notably NDM-1) have recently emerged. Hospital acquired infections, predominantly with multi-drug resistant Gram-negative organisms, place additional strain on limited resources. Widespread agricultural antibiotic use further propagates antimicrobial resistance. CONCLUSIONS: Future legislation regarding antibiotic access must alter incentives for purchasers and providers and ensure effective enforcement. The Ministry of Health recently initiated a national action plan and approved a multicenter health improvement project to strengthen national capacity for antimicrobial stewardship in Viet Nam. This analysis provided important input to these initiatives. Our methodologies and findings may be of use to others across the world tackling the growing threat of antibiotic resistance.},
	language = {eng},
	journal = {BMC public health},
	author = {Nguyen, Kinh Van and Thi Do, Nga Thuy and Chandna, Arjun and Nguyen, Trung Vu and Pham, Ca Van and Doan, Phuong Mai and Nguyen, An Quoc and Thi Nguyen, Chuc Kim and Larsson, Mattias and Escalante, Socorro and Olowokure, Babatunde and Laxminarayan, Ramanan and Gelband, Hellen and Horby, Peter and Thi Ngo, Ha Bich and Hoang, Mai Thanh and Farrar, Jeremy and Hien, Tran Tinh and Wertheim, Heiman F. L.},
	month = dec,
	year = {2013},
	pmid = {24325208},
	pmcid = {PMC4116647},
	keywords = {*Developing Countries, *Drug Resistance, Bacterial, Anti-Bacterial Agents/*therapeutic use, Bacterial Infections/*drug therapy, Drug Utilization/standards, Health Policy, Humans, Vietnam},
	pages = {1158},
}

BACKGROUND: Antimicrobial resistance is a major contemporary public health threat. Strategies to contain antimicrobial resistance have been comprehensively set forth, however in developing countries where the need for effective antimicrobials is greatest implementation has proved problematic. A better understanding of patterns and determinants of antibiotic use and resistance in emerging economies may permit more appropriately targeted interventions.Viet Nam, with a large population, high burden of infectious disease and relatively unrestricted access to medication, is an excellent case study of the difficulties faced by emerging economies in controlling antimicrobial resistance. METHODS: Our working group conducted a situation analysis of the current patterns and determinants of antibiotic use and resistance in Viet Nam. International publications and local reports published between 1-1-1990 and 31-8-2012 were reviewed. All stakeholders analyzed the findings at a policy workshop and feasible recommendations were suggested to improve antibiotic use in Viet Nam.Here we report the results of our situation analysis focusing on: the healthcare system, drug regulation and supply; antibiotic resistance and infection control; and agricultural antibiotic use. RESULTS: Market reforms have improved healthcare access in Viet Nam and contributed to better health outcomes. However, increased accessibility has been accompanied by injudicious antibiotic use in hospitals and the community, with predictable escalation in bacterial resistance. Prescribing practices are poor and self-medication is common - often being the most affordable way to access healthcare. Many policies exist to regulate antibiotic use but enforcement is insufficient or lacking.Pneumococcal penicillin-resistance rates are the highest in Asia and carbapenem-resistant bacteria (notably NDM-1) have recently emerged. Hospital acquired infections, predominantly with multi-drug resistant Gram-negative organisms, place additional strain on limited resources. Widespread agricultural antibiotic use further propagates antimicrobial resistance. CONCLUSIONS: Future legislation regarding antibiotic access must alter incentives for purchasers and providers and ensure effective enforcement. The Ministry of Health recently initiated a national action plan and approved a multicenter health improvement project to strengthen national capacity for antimicrobial stewardship in Viet Nam. This analysis provided important input to these initiatives. Our methodologies and findings may be of use to others across the world tackling the growing threat of antibiotic resistance.

@article{campbell_successful_2013,
	title = {A successful antimicrobial regime for {Chromobacterium} violaceum induced bacteremia.},
	volume = {13},
	issn = {1471-2334 1471-2334},
	doi = {10.1186/1471-2334-13-4},
	abstract = {BACKGROUND: Chromobacterium violaceum is a proteobacterium found in soil and water in tropical regions. The organism rarely causes infection in humans, yet can cause a severe systemic infection by entering the bloodstream via an open wound. CASE PRESENTATION: We recently identified a case of severe bacteremia caused by Chromobacterium violaceum at the Hospital for Tropical Diseases (HTD) in Ho Chi Minh City, Vietnam. Here, we describe how rapid microbiological identification and a combination of antimicrobials was used to successfully treat this life threatening infection in a four-year-old child. CONCLUSIONS: This case  shows the need for rapid diagnosis when there is the suspicion of a puncture wound contaminated with water and soil in tropical regions. We suggest that the aggressive antimicrobial combination used here is considered when this infection  is suspected.},
	language = {eng},
	journal = {BMC infectious diseases},
	author = {Campbell, James I. and Lan, Nguyen Phu Huong and Qui, Phan Tu and Dung, Le Thi and Farrar, Jeremy J. and Baker, Stephen},
	month = jan,
	year = {2013},
	pmid = {23286235},
	pmcid = {PMC3543835},
	keywords = {Anti-Bacterial Agents/*therapeutic use, Bacteremia/*drug therapy/microbiology, Bacterial Typing Techniques, Child, Preschool, Chromobacterium/*isolation \& purification, Drug Therapy, Combination, Gram-Negative Bacterial Infections/*drug therapy/microbiology, Humans, Male, Vietnam, Wounds, Penetrating/microbiology},
	pages = {4},
}

BACKGROUND: Chromobacterium violaceum is a proteobacterium found in soil and water in tropical regions. The organism rarely causes infection in humans, yet can cause a severe systemic infection by entering the bloodstream via an open wound. CASE PRESENTATION: We recently identified a case of severe bacteremia caused by Chromobacterium violaceum at the Hospital for Tropical Diseases (HTD) in Ho Chi Minh City, Vietnam. Here, we describe how rapid microbiological identification and a combination of antimicrobials was used to successfully treat this life threatening infection in a four-year-old child. CONCLUSIONS: This case shows the need for rapid diagnosis when there is the suspicion of a puncture wound contaminated with water and soil in tropical regions. We suggest that the aggressive antimicrobial combination used here is considered when this infection is suspected.

@article{carrique-mas_review_2013,
	title = {A {Review} of {Foodborne} {Bacterial} and {Parasitic} {Zoonoses} in {Vietnam}},
	volume = {10},
	issn = {1612-9202},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3938847/},
	doi = {10.1007/s10393-013-0884-9},
	abstract = {Vietnam has experienced unprecedented economic and social development in recent years, and the livestock sector is undergoing significant transformations. Although food animal production is still dominated by small-scale ‘backyard’ enterprises with mixed crop–livestock or livestock–aquatic systems, there is a trend towards more intensive and vertically integrated operations. Changes in animal production, processing and distribution networks for meat and animal products, and the shift from wet markets to supermarkets will undoubtedly impact food safety risks in Vietnam in unforeseen and complex ways. Here, we review the available published literature on bacterial and parasitic foodborne zoonoses (FBZ) in Vietnam. We report on clinical disease burden and pathogen prevalence in animal reservoirs for a number of important FBZ, and outline opportunities for future research.},
	number = {4},
	journal = {Ecohealth},
	author = {Carrique-Mas, Juan J and Bryant, J E},
	year = {2013},
	pages = {465--489},
}

Vietnam has experienced unprecedented economic and social development in recent years, and the livestock sector is undergoing significant transformations. Although food animal production is still dominated by small-scale ‘backyard’ enterprises with mixed crop–livestock or livestock–aquatic systems, there is a trend towards more intensive and vertically integrated operations. Changes in animal production, processing and distribution networks for meat and animal products, and the shift from wet markets to supermarkets will undoubtedly impact food safety risks in Vietnam in unforeseen and complex ways. Here, we review the available published literature on bacterial and parasitic foodborne zoonoses (FBZ) in Vietnam. We report on clinical disease burden and pathogen prevalence in animal reservoirs for a number of important FBZ, and outline opportunities for future research.

@article{taylor_spectrum_2012,
	title = {The spectrum of central nervous system infections in an adult referral hospital in {Hanoi}, {Vietnam}.},
	volume = {7},
	issn = {1932-6203 1932-6203},
	doi = {10.1371/journal.pone.0042099},
	abstract = {OBJECTIVES: To determine prospectively the causative pathogens of central nervous system (CNS) infections in patients admitted to a tertiary referral hospital in Hanoi, Vietnam. METHODS: From May 2007 to December 2008, cerebrospinal fluid (CSF) samples from 352 adults with suspected meningitis or encephalitis underwent routine testing, staining (Gram, Ziehl-Nielsen, India ink), bacterial culture and polymerase chain reaction targeting Neisseria meningitidis, Streptococcus pneumoniae, S. suis, Haemophilus influenzae type b, Herpes simplex virus (HSV), Varicella Zoster virus (VZV), enterovirus, and 16S ribosomal RNA. Blood cultures  and clinically indicated radiology were also performed. Patients were classified  as having confirmed or suspected bacterial (BM), tuberculous (TBM), cryptococcal  (CRM), eosinophilic (EOM) meningitis, aseptic encephalitis/meningitis (AEM), neurocysticercosis and others. RESULTS: 352 (male: 66\%) patients were recruited:  median age 34 years (range 13-85). 95/352 (27.3\%) diagnoses were laboratory confirmed and one by cranial radiology: BM (n = 62), TBM (n = 9), AEM (n = 19), CRM (n = 5), and neurocysticercosis (n = 1, cranial radiology). S. suis predominated as the cause of BM [48/62 (77.4\%)]; Listeria monocytogenese (n = 1), S. pasteurianus (n = 1) and N. meningitidis (n = 2) were infrequent. AEM viruses  were: HSV (n = 12), VZV (n = 5) and enterovirus (n = 2). 5 patients had EOM. Of 262/352 (74.4\%) patients with full clinical data, 209 (79.8\%) were hospital referrals and 186 (71\%) had been on antimicrobials. 21 (8\%) patients died: TBM (15.2\%), AEM (10\%), and BM (2.8\%). CONCLUSIONS: Most infections lacked microbiological confirmation. S. suis was the most common cause of BM in this setting. Improved diagnostics are needed for meningoencephalitic syndromes to inform treatment and prevention strategies.},
	language = {eng},
	number = {8},
	journal = {PloS one},
	author = {Taylor, Walter R. and Nguyen, Kinh and Nguyen, Duc and Nguyen, Huyen and Horby, Peter and Nguyen, Ha L. and Lien, Trinh and Tran, Giang and Tran, Ninh and Nguyen, Ha M. and Nguyen, Thai and Nguyen, Ha H. and Nguyen, Thanh and Tran, Giap and Farrar, Jeremy and de Jong, Menno and Schultsz, Constance and Tran, Huong and Nguyen, Diep and Vu, Bich and Le, Hoa and Dao, Trinh and Nguyen, Trung and Wertheim, Heiman},
	year = {2012},
	pmid = {22952590},
	pmcid = {PMC3431395},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Central Nervous System Infections/cerebrospinal fluid/*epidemiology/*microbiology, Encephalitis/cerebrospinal fluid/*epidemiology/*microbiology, Female, Humans, Male, Meningitis/cerebrospinal fluid/*epidemiology/*microbiology, Middle Aged, Polymerase Chain Reaction/methods, Prospective Studies, Referral and Consultation, Streptococcus suis/*metabolism, Treatment Outcome, Vietnam},
	pages = {e42099},
}

OBJECTIVES: To determine prospectively the causative pathogens of central nervous system (CNS) infections in patients admitted to a tertiary referral hospital in Hanoi, Vietnam. METHODS: From May 2007 to December 2008, cerebrospinal fluid (CSF) samples from 352 adults with suspected meningitis or encephalitis underwent routine testing, staining (Gram, Ziehl-Nielsen, India ink), bacterial culture and polymerase chain reaction targeting Neisseria meningitidis, Streptococcus pneumoniae, S. suis, Haemophilus influenzae type b, Herpes simplex virus (HSV), Varicella Zoster virus (VZV), enterovirus, and 16S ribosomal RNA. Blood cultures and clinically indicated radiology were also performed. Patients were classified as having confirmed or suspected bacterial (BM), tuberculous (TBM), cryptococcal (CRM), eosinophilic (EOM) meningitis, aseptic encephalitis/meningitis (AEM), neurocysticercosis and others. RESULTS: 352 (male: 66%) patients were recruited: median age 34 years (range 13-85). 95/352 (27.3%) diagnoses were laboratory confirmed and one by cranial radiology: BM (n = 62), TBM (n = 9), AEM (n = 19), CRM (n = 5), and neurocysticercosis (n = 1, cranial radiology). S. suis predominated as the cause of BM [48/62 (77.4%)]; Listeria monocytogenese (n = 1), S. pasteurianus (n = 1) and N. meningitidis (n = 2) were infrequent. AEM viruses were: HSV (n = 12), VZV (n = 5) and enterovirus (n = 2). 5 patients had EOM. Of 262/352 (74.4%) patients with full clinical data, 209 (79.8%) were hospital referrals and 186 (71%) had been on antimicrobials. 21 (8%) patients died: TBM (15.2%), AEM (10%), and BM (2.8%). CONCLUSIONS: Most infections lacked microbiological confirmation. S. suis was the most common cause of BM in this setting. Improved diagnostics are needed for meningoencephalitic syndromes to inform treatment and prevention strategies.

@article{horby_epidemiology_2012,
	title = {The epidemiology of interpandemic and pandemic influenza in {Vietnam}, 2007-2010: the {Ha} {Nam} household cohort study {I}.},
	volume = {175},
	issn = {1476-6256 0002-9262},
	doi = {10.1093/aje/kws121},
	abstract = {Prospective community-based studies have provided fundamental insights into the epidemiology of influenza in temperate regions, but few comparable studies have been undertaken in the tropics. The authors conducted prospective influenza surveillance and intermittent seroprevalence surveys in a household-based cohort  in Vietnam between December 2007 and April 2010, resulting in 1,793 person-seasons of influenza surveillance. Age- and sex-standardized estimates of  the risk of acquiring any influenza infection per season in persons 5 years of age or older were 21.1\% (95\% confidence interval: 17.4, 24.7) in season 1, 26.4\%  (95\% confidence interval: 22.6, 30.2) in season 2, and 17.0\% (95\% confidence interval: 13.6, 20.4) in season 3. Some individuals experienced multiple episodes of infection with different influenza types/subtypes in the same season (n = 27)  or reinfection with the same subtype in different seasons (n = 22). The highest risk of influenza infection was in persons 5-9 years old, in whom the risk of influenza infection per season was 41.8\%. Although the highest infection risk was in school-aged children, there were important heterogeneities in the age of infection by subtype and season. These heterogeneities could influence the impact of school closure and childhood vaccination on influenza transmission in tropical areas, such as Vietnam.},
	language = {eng},
	number = {10},
	journal = {American journal of epidemiology},
	author = {Horby, Peter and Mai, Le Quynh and Fox, Annette and Thai, Pham Quang and Thi Thu Yen, Nguyen and Thanh, Le Thi and Le Khanh Hang, Nguyen and Duong, Tran Nhu and Thoang, Dang Dinh and Farrar, Jeremy and Wolbers, Marcel and Hien, Nguyen Tran},
	month = may,
	year = {2012},
	pmid = {22411862},
	pmcid = {PMC3353138},
	keywords = {*Pandemics, Adolescent, Adult, Age Factors, Aged, Child, Child, Preschool, Female, Humans, Incidence, Infant, Infant, Newborn, Influenza A Virus, H1N1 Subtype/*isolation \& purification, Influenza, Human/*epidemiology, Longitudinal Studies, Male, Middle Aged, Population Surveillance, Prospective Studies, RNA, Viral/analysis, Reverse Transcriptase Polymerase Chain Reaction, Risk, Seroepidemiologic Studies, Sex Factors, Tropical Climate, Vietnam/epidemiology, Young Adult},
	pages = {1062--1074},
}

Prospective community-based studies have provided fundamental insights into the epidemiology of influenza in temperate regions, but few comparable studies have been undertaken in the tropics. The authors conducted prospective influenza surveillance and intermittent seroprevalence surveys in a household-based cohort in Vietnam between December 2007 and April 2010, resulting in 1,793 person-seasons of influenza surveillance. Age- and sex-standardized estimates of the risk of acquiring any influenza infection per season in persons 5 years of age or older were 21.1% (95% confidence interval: 17.4, 24.7) in season 1, 26.4% (95% confidence interval: 22.6, 30.2) in season 2, and 17.0% (95% confidence interval: 13.6, 20.4) in season 3. Some individuals experienced multiple episodes of infection with different influenza types/subtypes in the same season (n = 27) or reinfection with the same subtype in different seasons (n = 22). The highest risk of influenza infection was in persons 5-9 years old, in whom the risk of influenza infection per season was 41.8%. Although the highest infection risk was in school-aged children, there were important heterogeneities in the age of infection by subtype and season. These heterogeneities could influence the impact of school closure and childhood vaccination on influenza transmission in tropical areas, such as Vietnam.

@article{vien_co-selection_2012,
	title = {The co-selection of fluoroquinolone resistance genes in the gut flora of {Vietnamese} children.},
	volume = {7},
	issn = {1932-6203 1932-6203},
	doi = {10.1371/journal.pone.0042919},
	abstract = {Antimicrobial consumption is one of the major contributing factors facilitating the development and maintenance of bacteria exhibiting antimicrobial resistance.  Plasmid-mediated quinolone resistance (PMQR) genes, such as the qnr family, can be horizontally transferred and contribute to reduced susceptibility to fluoroquinolones. We performed an observational study, investigating the copy number of PMQR after antimicrobial therapy. We enrolled 300 children resident in  Ho Chi Minh City receiving antimicrobial therapy for acute respiratory tract infections (ARIs). Rectal swabs were taken on enrollment and seven days subsequently, counts for Enterobacteriaceae were performed and qnrA, qnrB and qnrS were quantified by using real-time PCR on metagenomic stool DNA. On enrollment, we found no association between age, gender or location of the participants and the prevalence of qnrA, qnrB or qnrS. Yet, all three loci demonstrated a proportional increase in the number of samples testing positive between day 0 and day 7. Furthermore, qnrB demonstrated a significant increase in copy number between paired samples (p{\textless}0.001; Wilcoxon rank-sum), associated with  non-fluoroquinolone combination antimicrobial therapy. To our knowledge, this is  the first study describing an association between the use of non-fluoroquinolone  antimicrobials and the increasing relative prevalence and quantity of qnr genes.  Our work outlines a potential mechanism for the selection and maintenance of PMQR genes and predicts a strong effect of co-selection of these resistance determinants through the use of unrelated and potentially unnecessary antimicrobial regimes.},
	language = {eng},
	number = {8},
	journal = {PloS one},
	author = {Vien, Le Thi Minh and Minh, Ngo Ngoc Quang and Thuong, Tang Chi and Khuong, Huynh Duy and Nga, Tran Vu Thieu and Thompson, Corinne and Campbell, James I. and de Jong, Menno and Farrar, Jeremy J. and Schultsz, Constance and van Doorn, H. Rogier and Baker, Stephen},
	year = {2012},
	pmid = {22937000},
	pmcid = {PMC3427306},
	keywords = {Anti-Bacterial Agents/*pharmacology, Bacterial Proteins/genetics, Child, Preschool, Citrobacter/drug effects/genetics, Drug Resistance, Bacterial/immunology, Enterobacteriaceae/drug effects/genetics, Escherichia coli/drug effects/genetics, Female, Fluoroquinolones/*pharmacology, Gastrointestinal Tract/*microbiology, Humans, Infant, Klebsiella/drug effects/genetics, Male, Microbial Sensitivity Tests, Pantoea/drug effects/genetics, Plasmids/genetics, Proteus/drug effects/genetics, Real-Time Polymerase Chain Reaction, Shigella/drug effects/genetics},
	pages = {e42919},
}

Antimicrobial consumption is one of the major contributing factors facilitating the development and maintenance of bacteria exhibiting antimicrobial resistance. Plasmid-mediated quinolone resistance (PMQR) genes, such as the qnr family, can be horizontally transferred and contribute to reduced susceptibility to fluoroquinolones. We performed an observational study, investigating the copy number of PMQR after antimicrobial therapy. We enrolled 300 children resident in Ho Chi Minh City receiving antimicrobial therapy for acute respiratory tract infections (ARIs). Rectal swabs were taken on enrollment and seven days subsequently, counts for Enterobacteriaceae were performed and qnrA, qnrB and qnrS were quantified by using real-time PCR on metagenomic stool DNA. On enrollment, we found no association between age, gender or location of the participants and the prevalence of qnrA, qnrB or qnrS. Yet, all three loci demonstrated a proportional increase in the number of samples testing positive between day 0 and day 7. Furthermore, qnrB demonstrated a significant increase in copy number between paired samples (p\textless0.001; Wilcoxon rank-sum), associated with non-fluoroquinolone combination antimicrobial therapy. To our knowledge, this is the first study describing an association between the use of non-fluoroquinolone antimicrobials and the increasing relative prevalence and quantity of qnr genes. Our work outlines a potential mechanism for the selection and maintenance of PMQR genes and predicts a strong effect of co-selection of these resistance determinants through the use of unrelated and potentially unnecessary antimicrobial regimes.

@article{farrar_h5n1_2012,
	title = {{H5N1} surveillance: {Shift} expertise to where it matters.},
	volume = {483},
	issn = {1476-4687 0028-0836},
	doi = {10.1038/483534a},
	language = {eng},
	number = {7391},
	journal = {Nature},
	author = {Farrar, Jeremy},
	month = mar,
	year = {2012},
	pmid = {22460881},
	keywords = {*Geography, Animals, Humans, Influenza A Virus, H5N1 Subtype/genetics/*isolation \& purification/pathogenicity, Influenza, Human/epidemiology/transmission/*virology, Orthomyxoviridae Infections/epidemiology/transmission/*veterinary/virology, Population Surveillance/*methods, Poultry/virology, Vietnam/epidemiology, Zoonoses/epidemiology/transmission/virology},
	pages = {534--535},
}

@article{morse_prediction_2012,
	title = {Prediction and prevention of the next pandemic zoonosis.},
	volume = {380},
	copyright = {Copyright (c) 2012 Elsevier Ltd. All rights reserved.},
	issn = {1474-547X 0140-6736},
	doi = {10.1016/S0140-6736(12)61684-5},
	abstract = {Most pandemics--eg, HIV/AIDS, severe acute respiratory syndrome, pandemic influenza--originate in animals, are caused by viruses, and are driven to emerge  by ecological, behavioural, or socioeconomic changes. Despite their substantial effects on global public health and growing understanding of the process by which they emerge, no pandemic has been predicted before infecting human beings. We review what is known about the pathogens that emerge, the hosts that they originate in, and the factors that drive their emergence. We discuss challenges to their control and new efforts to predict pandemics, target surveillance to the most crucial interfaces, and identify prevention strategies. New mathematical modelling, diagnostic, communications, and informatics technologies can identify  and report hitherto unknown microbes in other species, and thus new risk assessment approaches are needed to identify microbes most likely to cause human  disease. We lay out a series of research and surveillance opportunities and goals that could help to overcome these challenges and move the global pandemic strategy from response to pre-emption.},
	language = {eng},
	number = {9857},
	journal = {Lancet (London, England)},
	author = {Morse, Stephen S. and Mazet, Jonna A. K. and Woolhouse, Mark and Parrish, Colin R. and Carroll, Dennis and Karesh, William B. and Zambrana-Torrelio, Carlos and Lipkin, W. Ian and Daszak, Peter},
	month = dec,
	year = {2012},
	pmid = {23200504},
	pmcid = {PMC3712877},
	keywords = {Animals, Blood-Borne Pathogens, Communicable Diseases, Emerging/epidemiology/prevention \& control, Environmental Monitoring, Global Health, Health Policy, Humans, International Cooperation, Pandemics/*prevention \& control, Travel, Virus Diseases/epidemiology/prevention \& control, Zoonoses/*epidemiology},
	pages = {1956--1965},
}

Most pandemics–eg, HIV/AIDS, severe acute respiratory syndrome, pandemic influenza–originate in animals, are caused by viruses, and are driven to emerge by ecological, behavioural, or socioeconomic changes. Despite their substantial effects on global public health and growing understanding of the process by which they emerge, no pandemic has been predicted before infecting human beings. We review what is known about the pathogens that emerge, the hosts that they originate in, and the factors that drive their emergence. We discuss challenges to their control and new efforts to predict pandemics, target surveillance to the most crucial interfaces, and identify prevention strategies. New mathematical modelling, diagnostic, communications, and informatics technologies can identify and report hitherto unknown microbes in other species, and thus new risk assessment approaches are needed to identify microbes most likely to cause human disease. We lay out a series of research and surveillance opportunities and goals that could help to overcome these challenges and move the global pandemic strategy from response to pre-emption.

@article{boni_no_2012,
	title = {No evidence for intra-segment recombination of 2009 {H1N1} influenza virus in swine.},
	volume = {494},
	copyright = {Copyright (c) 2011 Elsevier B.V. All rights reserved.},
	issn = {1879-0038 0378-1119},
	doi = {10.1016/j.gene.2011.10.041},
	abstract = {Hao (2011) reported that the PB2 genes of three swine influenza A viruses were likely generated through homologous recombination between two closely related parental strains. However, we show that Hao's observation is an artifact of incorrect taxon sampling arising through the lack of an appropriate evolutionary  context. Through rigorous phylogenetic analyses we explain the evolutionary origins of these stains and confirm the lack of any statistical support for intra-segmental recombination.},
	language = {eng},
	number = {2},
	journal = {Gene},
	author = {Boni, Maciej F. and Smith, Gavin J. D. and Holmes, Edward C. and Vijaykrishna, Dhanasekaran},
	month = feb,
	year = {2012},
	pmid = {22226809},
	pmcid = {PMC3427013},
	keywords = {*Evolution, Molecular, *Recombination, Genetic, Influenza A virus/*genetics},
	pages = {242--245},
}

Hao (2011) reported that the PB2 genes of three swine influenza A viruses were likely generated through homologous recombination between two closely related parental strains. However, we show that Hao's observation is an artifact of incorrect taxon sampling arising through the lack of an appropriate evolutionary context. Through rigorous phylogenetic analyses we explain the evolutionary origins of these stains and confirm the lack of any statistical support for intra-segmental recombination.

@article{cauchemez_influenza_2012,
	title = {Influenza infection rates, measurement errors and the interpretation of paired serology.},
	volume = {8},
	issn = {1553-7374 1553-7366},
	doi = {10.1371/journal.ppat.1003061},
	abstract = {Serological studies are the gold standard method to estimate influenza infection  attack rates (ARs) in human populations. In a common protocol, blood samples are  collected before and after the epidemic in a cohort of individuals; and a rise in haemagglutination-inhibition (HI) antibody titers during the epidemic is considered as a marker of infection. Because of inherent measurement errors, a},
	language = {eng},
	number = {12},
	journal = {PLoS pathogens},
	author = {Cauchemez, Simon and Horby, Peter and Fox, Annette and Mai, Le Quynh and Thanh, Le Thi and Thai, Pham Quang and Hoa, Le Nguyen Minh and Hien, Nguyen Tran and Ferguson, Neil M.},
	year = {2012},
	pmid = {23271967},
	pmcid = {PMC3521724},
	keywords = {Adolescent, Adult, Aged, Antibodies, Viral/blood/*immunology, Cohort Studies, Female, Hemagglutinin Glycoproteins, Influenza Virus/blood/*immunology, Humans, Influenza, Human/blood/*epidemiology/*immunology, Male, Middle Aged, Observer Variation, Seroepidemiologic Studies, Serologic Tests, Vietnam/epidemiology},
	pages = {e1003061},
}

Serological studies are the gold standard method to estimate influenza infection attack rates (ARs) in human populations. In a common protocol, blood samples are collected before and after the epidemic in a cohort of individuals; and a rise in haemagglutination-inhibition (HI) antibody titers during the epidemic is considered as a marker of infection. Because of inherent measurement errors, a

@article{tham_comparison_2012,
	title = {Comparison of the {Roche} {RealTime} ready {Influenza} {A}/{H1N1} {Detection} {Set} with {CDC} {A}/{H1N1pdm09} {RT}-{PCR} on samples from three hospitals in {Ho} {Chi} {Minh} {City}, {Vietnam}.},
	volume = {74},
	copyright = {Copyright (c) 2012 Elsevier Inc. All rights reserved.},
	issn = {1879-0070 0732-8893},
	doi = {10.1016/j.diagmicrobio.2012.06.003},
	abstract = {Real-time polymerase chain reaction (PCR) can be considered the gold standard for detection of influenza viruses due to its high sensitivity and specificity. Roche has developed the RealTime ready Influenza A/H1N1 Detection Set, consisting of a  generic influenza virus A PCR targeting the M2 gene (M2 PCR) and a specific PCR targeting the hemagglutinin (HA) of A/H1N1-pdm09 (HA PCR, 2009 H1N1), with the intention to make a reliable, rapid, and simple test to detect and quantify 2009  H1N1 in clinical samples. We evaluated this kit against the US Centers for Disease Control and Prevention (USCDC)/World Health Organization real-time PCR for influenza virus using 419 nose and throat swabs from 210 patients collected in 3 large hospitals in Ho Chi Minh City, Vietnam. In the per-patient analysis, when compared to CDC PCR, the sensitivity and specificity of the M2 PCR were 85.8\% and 97.6\%, respectively; the sensitivity and specificity of HA PCR were 88.2\% and 100\%, respectively. In the per-sample analysis, the sensitivity and specificity in nose swabs were higher than those in throat swabs for both M2 and  HA PCRs. The viral loads as determined with the M2 and HA PCRs correlated well with the Ct values of the CDC PCR. Compared with the CDC PCR, the kit has a reasonable sensitivity and very good specificity for the detection and quantification of influenza A virus and A/H1N1-pdm09. However, given the current  status of 2009 H1N1, a kit that can detect all circulating seasonal influenza viruses would be preferable.},
	language = {eng},
	number = {2},
	journal = {Diagnostic microbiology and infectious disease},
	author = {Tham, Nguyen thi and Hang, Vu thi Ty and Khanh, Trong Huu and Viet, Do Chau and Hien, Tran Tinh and Farrar, Jeremy and Chau, Nguyen van Vinh and van Doorn, H. Rogier},
	month = oct,
	year = {2012},
	pmid = {22785431},
	pmcid = {PMC3444637},
	keywords = {Adolescent, Adult, Aged, Child, Child, Preschool, Female, Hospitals, Humans, Infant, Influenza A Virus, H1N1 Subtype/*isolation \& purification, Influenza, Human/*diagnosis, Male, Middle Aged, Molecular Diagnostic Techniques/*methods, Nose/virology, Pharynx/virology, Real-Time Polymerase Chain Reaction/*methods, Sensitivity and Specificity, Vietnam, Virology/*methods, Young Adult},
	pages = {131--136},
}

Real-time polymerase chain reaction (PCR) can be considered the gold standard for detection of influenza viruses due to its high sensitivity and specificity. Roche has developed the RealTime ready Influenza A/H1N1 Detection Set, consisting of a generic influenza virus A PCR targeting the M2 gene (M2 PCR) and a specific PCR targeting the hemagglutinin (HA) of A/H1N1-pdm09 (HA PCR, 2009 H1N1), with the intention to make a reliable, rapid, and simple test to detect and quantify 2009 H1N1 in clinical samples. We evaluated this kit against the US Centers for Disease Control and Prevention (USCDC)/World Health Organization real-time PCR for influenza virus using 419 nose and throat swabs from 210 patients collected in 3 large hospitals in Ho Chi Minh City, Vietnam. In the per-patient analysis, when compared to CDC PCR, the sensitivity and specificity of the M2 PCR were 85.8% and 97.6%, respectively; the sensitivity and specificity of HA PCR were 88.2% and 100%, respectively. In the per-sample analysis, the sensitivity and specificity in nose swabs were higher than those in throat swabs for both M2 and HA PCRs. The viral loads as determined with the M2 and HA PCRs correlated well with the Ct values of the CDC PCR. Compared with the CDC PCR, the kit has a reasonable sensitivity and very good specificity for the detection and quantification of influenza A virus and A/H1N1-pdm09. However, given the current status of 2009 H1N1, a kit that can detect all circulating seasonal influenza viruses would be preferable.

@article{van_doorn_clinical_2012,
	title = {Clinical validation of a point-of-care multiplexed in vitro immunoassay using monoclonal antibodies (the {MSD} influenza test) in four hospitals in {Vietnam}.},
	volume = {50},
	issn = {1098-660X 0095-1137},
	doi = {10.1128/JCM.00085-12},
	abstract = {Point-of-care (POC) diagnostic tests for influenza can considerably shorten the time to clinical decision making. An investigational POC test based on a multiplexed immunoassay was developed by Meso Scale Diagnostics, LLC (MSD), with  the objective to make a more sensitive rapid test that can also subtype influenza A viruses (1977 H1, H3, and H5). Between February and November 2010, we conducted a prospective multicenter study at four hospitals in Vietnam and compared the performance of this test to that of the WHO/CDC real-time reverse transcriptase PCR (RT-PCR) on nasal and throat swab specimens from patients presenting with influenza-like illness. Five hundred sixty-three adults and children with a median age of 25 months were enrolled. Sensitivity and specificity of the test with combined results from nasal and throat swab samples were 74.0\% (131/177) and 99.7\% (351/352), respectively, compared to RT-PCR. The POC test was as sensitive  for influenza virus B as for influenza virus A (74.4\% [64/86] versus 73.6\% [67/91]). The positivity rate was associated with lower cycle threshold values (a marker for higher viral loads), sample type (73.6\% for nasal swab versus 52.4\% for throat swab), and younger age. A total of 210 (18.7\%) out of 1,126 MSD tests  failed, and for 34 (6\%) of patients, both test samples failed (these were excluded from the performance analysis). Subtyping could be assessed only for influenza virus A/H3N2, as 1977 H1N1 was not circulating at the time and no},
	language = {eng},
	number = {5},
	journal = {Journal of clinical microbiology},
	author = {van Doorn, H. Rogier and Kinh, Nguyen van and Tuan, Ha Manh and Tuan, Tran Anh and Minh, Ngo Ngoc Quang and Bryant, Juliet E. and Hang, Vu thi Ty and Uyen, Le thi Tham and Thinh, Le Quoc and Anh, Tran thi Ngoc and Lan, Nguyen Phu Huong and Trung, Nguyen Vu and Taylor, Walter and Merson, Laura and Wertheim, Heiman F. L. and Farrar, Jeremy and Wolbers, Marcel and Chau, Nguyen van Vinh and de Jong, Menno D.},
	month = may,
	year = {2012},
	pmid = {22357497},
	pmcid = {PMC3347120},
	keywords = {*Point-of-Care Systems, Adolescent, Adult, Aged, Antibodies, Monoclonal, Antibodies, Viral, Antigens, Viral/*analysis/immunology, Child, Child, Preschool, Female, Hospitals, Humans, Immunoassay/methods, Infant, Influenza, Human/*diagnosis, Male, Middle Aged, Orthomyxoviridae/classification/immunology/*isolation \& purification, Sensitivity and Specificity, Vietnam, Young Adult},
	pages = {1621--1625},
}

Point-of-care (POC) diagnostic tests for influenza can considerably shorten the time to clinical decision making. An investigational POC test based on a multiplexed immunoassay was developed by Meso Scale Diagnostics, LLC (MSD), with the objective to make a more sensitive rapid test that can also subtype influenza A viruses (1977 H1, H3, and H5). Between February and November 2010, we conducted a prospective multicenter study at four hospitals in Vietnam and compared the performance of this test to that of the WHO/CDC real-time reverse transcriptase PCR (RT-PCR) on nasal and throat swab specimens from patients presenting with influenza-like illness. Five hundred sixty-three adults and children with a median age of 25 months were enrolled. Sensitivity and specificity of the test with combined results from nasal and throat swab samples were 74.0% (131/177) and 99.7% (351/352), respectively, compared to RT-PCR. The POC test was as sensitive for influenza virus B as for influenza virus A (74.4% [64/86] versus 73.6% [67/91]). The positivity rate was associated with lower cycle threshold values (a marker for higher viral loads), sample type (73.6% for nasal swab versus 52.4% for throat swab), and younger age. A total of 210 (18.7%) out of 1,126 MSD tests failed, and for 34 (6%) of patients, both test samples failed (these were excluded from the performance analysis). Subtyping could be assessed only for influenza virus A/H3N2, as 1977 H1N1 was not circulating at the time and no

@article{ho_dang_trung_aetiologies_2012,
	title = {Aetiologies of central nervous system infection in {Viet} {Nam}: a prospective provincial hospital-based descriptive surveillance study.},
	volume = {7},
	issn = {1932-6203 1932-6203},
	doi = {10.1371/journal.pone.0037825},
	abstract = {BACKGROUND: Infectious diseases of the central nervous system (CNS) remain common and life-threatening, especially in developing countries. Knowledge of the aetiological agents responsible for these infections is essential to guide empiric therapy and develop a rational public health policy. To date most data has come from patients admitted to tertiary referral hospitals in Asia and there  is limited aetiological data at the provincial hospital level where most patients are seen. METHODS: We conducted a prospective Provincial Hospital-based descriptive surveillance study in adults and children at thirteen hospitals in central and southern Viet Nam between August 2007-April 2010. The pathogens of CNS infection were confirmed in CSF and blood samples by using classical microbiology, molecular diagnostics and serology. RESULTS: We recruited 1241 patients with clinically suspected infection of the CNS. An aetiological agent was identified in 640/1241 (52\%) of the patients. The most common pathogens were  Streptococcus suis serotype 2 in patients older than 14 years of age (147/617, 24\%) and Japanese encephalitis virus in patients less than 14 years old (142/624, 23\%). Mycobacterium tuberculosis was confirmed in 34/617 (6\%) adult patients and  11/624 (2\%) paediatric patients. The acute case fatality rate (CFR) during hospital admission was 73/617 (12\%) in adults and to 42/624 (7\%) in children. CONCLUSIONS: Zoonotic bacterial and viral pathogens are the most common causes of CNS infection in adults and children in Viet Nam.},
	language = {eng},
	number = {5},
	journal = {PloS one},
	author = {Ho Dang Trung, Nghia and Le Thi Phuong, Tu and Wolbers, Marcel and Nguyen Van Minh, Hoang and Nguyen Thanh, Vinh and Van, Minh Pham and Thieu, Nga Tran Vu and Van, Tan Le and Song, Diep To and Thi, Phuong Le and Thi Phuong, Thao Nguyen and Van, Cong Bui and Tang, Vu and Ngoc Anh, Tuan Hoang and Nguyen, Dong and Trung, Tien Phan and Thi Nam, Lien Nguyen and Kiem, Hao Tran and Thi Thanh, Tam Nguyen and Campbell, James and Caws, Maxine and Day, Jeremy and de Jong, Menno D. and Van Vinh, Chau Nguyen and Van Doorn, H. Rogier and Tinh, Hien Tran and Farrar, Jeremy and Schultsz, Constance},
	year = {2012},
	pmid = {22662232},
	pmcid = {PMC3360608},
	keywords = {Adult, Central Nervous System Infections/*epidemiology/*etiology, Child, Child, Preschool, Encephalitis, Viral/epidemiology, Female, Humans, Infant, Male, Meningitis, Bacterial/epidemiology, Meningitis, Viral/epidemiology, Middle Aged, Population Surveillance, Prospective Studies, Vietnam/epidemiology, Young Adult},
	pages = {e37825},
}

BACKGROUND: Infectious diseases of the central nervous system (CNS) remain common and life-threatening, especially in developing countries. Knowledge of the aetiological agents responsible for these infections is essential to guide empiric therapy and develop a rational public health policy. To date most data has come from patients admitted to tertiary referral hospitals in Asia and there is limited aetiological data at the provincial hospital level where most patients are seen. METHODS: We conducted a prospective Provincial Hospital-based descriptive surveillance study in adults and children at thirteen hospitals in central and southern Viet Nam between August 2007-April 2010. The pathogens of CNS infection were confirmed in CSF and blood samples by using classical microbiology, molecular diagnostics and serology. RESULTS: We recruited 1241 patients with clinically suspected infection of the CNS. An aetiological agent was identified in 640/1241 (52%) of the patients. The most common pathogens were Streptococcus suis serotype 2 in patients older than 14 years of age (147/617, 24%) and Japanese encephalitis virus in patients less than 14 years old (142/624, 23%). Mycobacterium tuberculosis was confirmed in 34/617 (6%) adult patients and 11/624 (2%) paediatric patients. The acute case fatality rate (CFR) during hospital admission was 73/617 (12%) in adults and to 42/624 (7%) in children. CONCLUSIONS: Zoonotic bacterial and viral pathogens are the most common causes of CNS infection in adults and children in Viet Nam.