Rapid Genomic Profiling of Staphylococcus aureus Antibiotic Resistance and Virulence Determinants from Massively Parallel Sequencing Reads. Gene Godbold, Hasan, N. A., Yang, B., Nitcher, S., Choi, S. Y., Subramanian, P., Rebeil, R., Li, H., Faith, S., Young, B., Colwell, R., & Cebula, T. May, 2014. abstract bibtex The increase in antibiotic resistance among bacteria is one of the more serious public health concerns globally. Health care practitioners use antibiotics even when there is an uncertainty in pathogen diagnosis, when the infection is viral, or when the bacterial infection is self-limiting. Whole genome sequencing (WGS) can identify precisely the phylogenetic lineage of a bacterial isolate and determine its virulence and antibiotic resistance gene profiles. However, labor costs for data analysis discourages routine use of WGS in a clinical setting. Our approach uses characteristics of the entire genome along with specialized databases of antibiotic resistance elements and virulence genes to determine (i) its most likely phylogenetic lineage and the spectrum of (ii) antibiotic resistance and (iii) virulence genes harbored within a bacterial genome. Our Staphylococcus aureus genomic database consists of 221 genomes supplemented by WGS of 13 isolates obtained from NARSA. The antibiotic resistance database consists of more than 250,000 genetic elements from more than 2000 species of bacteria that cover most major types of clinically relevant resistance. A more narrowly tailored database of staphylococcal virulence elements (~16,000 sequences) was also developed. Systematic interrogation of these resources with custom software allows identification of the phylogenetic lineage of a given S. aureus isolate as well as its complement of antibiotic resistance and virulence genes. The software distinguishes in silico WGS reads from various single S. aureus isolates down to the strain level in less than two minutes and can ascertain their antibiotic resistance and virulence content in less than ten minutes. This approach provides, within minutes, more accurate identification of S. aureus isolates at a resolution unattainable by any existing typing methods. The method developed is general and can be applied to any set of bacteria.
@misc{gene_godbold_rapid_2014,
address = {Boston, MA},
title = {Rapid {Genomic} {Profiling} of {Staphylococcus} aureus {Antibiotic} {Resistance} and {Virulence} {Determinants} from {Massively} {Parallel} {Sequencing} {Reads}},
abstract = {The increase in antibiotic resistance among bacteria is one of the more serious public health concerns globally. Health care practitioners use antibiotics even when there is an uncertainty in pathogen diagnosis, when the infection is viral, or when the bacterial infection is self-limiting. Whole genome sequencing (WGS) can identify precisely the phylogenetic lineage of a bacterial isolate and determine its virulence and antibiotic resistance gene profiles. However, labor costs for data analysis discourages routine use of WGS in a clinical setting. Our approach uses characteristics of the entire genome along with specialized databases of antibiotic resistance elements and virulence genes to determine (i) its most likely phylogenetic lineage and the spectrum of (ii) antibiotic resistance and (iii) virulence genes harbored within a bacterial genome. Our Staphylococcus aureus genomic database consists of 221 genomes supplemented by WGS of 13 isolates obtained from NARSA. The antibiotic resistance database consists of more than 250,000 genetic elements from more than 2000 species of bacteria that cover most major types of clinically relevant resistance. A more narrowly tailored database of staphylococcal virulence elements ({\textasciitilde}16,000 sequences) was also developed. Systematic interrogation of these resources with custom software allows identification of the phylogenetic lineage of a given
S. aureus isolate as well as its complement of antibiotic resistance and virulence genes. The software distinguishes
in silico WGS reads from various single S. aureus isolates down to the strain level in less than two minutes and can ascertain their antibiotic resistance and virulence content in less than ten minutes. This approach provides, within minutes, more accurate identification of S. aureus isolates at a resolution unattainable by any existing typing methods. The method developed is general and can be applied to any set of bacteria.},
author = {{Gene Godbold} and Hasan, Nur A. and Yang, Boyu and Nitcher, Sara and Choi, Seon Young and Subramanian, Poorani and Rebeil, Roberto and Li, Huai and Faith, Seth and Young, Brian and Colwell, Rita and Cebula, Thomas},
month = may,
year = {2014},
keywords = {mrsa, publications},
}
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