Whole genome sequencing (WGS) potentially offers a single, comprehensive, and cost-effective approach to characterize bacterial pathogens. The technology has transformed our understanding of antimicrobial resistance, helping us to better track and identify the genetic mechanisms underlying resistance. In our pilot study, we used traditional phenotypic in vitro antimicrobial susceptibility testing methods and WGS to evaluate correlations among resistance phenotypes and genotypes of Campylobacter, E. coli and Salmonella isolates from NARMS. Resistance genotypes were determined using assembled WGS sequences through BLAST analysis with the cutoff set at 50% sequence length and 85% amino acid identity with known resistance proteins. A comprehensive resistance genotype was identified for each isolate. The correlations between phenotypic resistance to a given drug and presence of one or more genes conferring resistance to that drug ranged from 90%-100% for all 19 drugs tested. In additional, many virulence genes and structure of MDR plasmids were identified. The results showed that WGS offers high resolution for detection and characterization of full components of antimicrobial resistance and virulence determinants. WGS shows promise as a useful tool for antimicrobial resistance surveillance programs.

Tracking ntimicrobial resistance in foodborne bacteria: Application of WGS in the US NARMS program

2019 Spring National Meeting

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