Higher accuracy of genotypic identification compared to phenotyping in the diagnosis of coagulase-negative staphylococcus infection in orthopedic surgery. Muñoz-Gamito, G.; Cuchí, E.; Roigé, J.; Gómez, L.; Jaén, À.; Matamala, A.; Pedro-Botet, M. L.; Capdevila, J. A.; Anglès, F.; and Pérez, J. Infectious Diseases, 0(0):1–8, July, 2020. Publisher: Taylor & Francis _eprint: https://doi.org/10.1080/23744235.2020.1799069
Higher accuracy of genotypic identification compared to phenotyping in the diagnosis of coagulase-negative staphylococcus infection in orthopedic surgery [link]Paper  doi  abstract   bibtex   
Purpose To determine whether Repetitive Extragenic Palindromic PCR (rep-PCR) genotyping can improve the diagnosis of coagulase-negative staphylococcal (CoNS) orthopaedic infections in comparison to phenotyping. Methods Prospective study comparing the results of phenotypic/genotypic (rep-PCR) testing in patients with suspected CoNS infection. Each strain was analysed using both methods. Strains identified as identical in ≥2 samples were considered as pathogenic. Results 255 CoNS strains from 52 surgical episodes were included. Infection was diagnosed by phenotyping in 38(73%) cases and by genotyping in 40(77%). The Kappa index was 0.59. Sensitivity, Specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV) for phenotyping (vs. rep-PCR) were: 88%, 75%, 92%, and 64%. 5/14(36%) of cases not considered as true infections by phenotyping were diagnosed as infections with genotyping. In a subgroup of 203 strains from 41 surgical procedures with orthopaedic implants, the kappa index was 0.68. Sensitivity, Specificity, PPV, and NPV for phenotyping were: 93%, 73%, 90% and 80%. Again, 2/10 episodes in which CoNS were considered non-infective by phenotyping were diagnosed as infected by genotyping. Conclusions Rep-PCR genotyping can identify identical CoNS strains that differ in their phenotype and should be used as a complementary technique. One-third of infected cases may be misdiagnosed without genotypic analysis.
@article{munoz-gamito_higher_2020,
	title = {Higher accuracy of genotypic identification compared to phenotyping in the diagnosis of coagulase-negative staphylococcus infection in orthopedic surgery},
	volume = {0},
	issn = {2374-4235},
	url = {https://doi.org/10.1080/23744235.2020.1799069},
	doi = {10.1080/23744235.2020.1799069},
	abstract = {Purpose To determine whether Repetitive Extragenic Palindromic PCR (rep-PCR) genotyping can improve the diagnosis of coagulase-negative staphylococcal (CoNS) orthopaedic infections in comparison to phenotyping. Methods Prospective study comparing the results of phenotypic/genotypic (rep-PCR) testing in patients with suspected CoNS infection. Each strain was analysed using both methods. Strains identified as identical in ≥2 samples were considered as pathogenic. Results 255 CoNS strains from 52 surgical episodes were included. Infection was diagnosed by phenotyping in 38(73\%) cases and by genotyping in 40(77\%). The Kappa index was 0.59. Sensitivity, Specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV) for phenotyping (vs. rep-PCR) were: 88\%, 75\%, 92\%, and 64\%. 5/14(36\%) of cases not considered as true infections by phenotyping were diagnosed as infections with genotyping. In a subgroup of 203 strains from 41 surgical procedures with orthopaedic implants, the kappa index was 0.68. Sensitivity, Specificity, PPV, and NPV for phenotyping were: 93\%, 73\%, 90\% and 80\%. Again, 2/10 episodes in which CoNS were considered non-infective by phenotyping were diagnosed as infected by genotyping. Conclusions Rep-PCR genotyping can identify identical CoNS strains that differ in their phenotype and should be used as a complementary technique. One-third of infected cases may be misdiagnosed without genotypic analysis.},
	number = {0},
	urldate = {2020-08-25},
	journal = {Infectious Diseases},
	author = {Muñoz-Gamito, Gema and Cuchí, Eva and Roigé, Jordi and Gómez, Lucía and Jaén, Àngels and Matamala, Alfredo and Pedro-Botet, M. Lluïsa and Capdevila, Josep Anton and Anglès, Francesc and Pérez, Josefa},
	month = jul,
	year = {2020},
	pmid = {32735157},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/23744235.2020.1799069},
	keywords = {Article, Bone and joint infection, Laboratori Biologia Molecular, Orthopaedic infection, coagulase-negative staphylococci infection, genotyping, molecular diagnostic techniques},
	pages = {1--8},
}
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