Abstract
Antimicrobial resistance (AMR) is an emerging public health problem and methods for surveillance are needed. We designed 85 sequence-specific PCR reactions to detect 79 genes or mutations associated with resistance across 10 major antimicrobial classes, with a focus on E. coli. The 85 qPCR assays demonstrated >99.9% concordance with sequencing. We evaluated the correlation between genotypic resistance markers and phenotypic susceptibility results on 239 E. coli isolates. Both sensitivity and specificity exceeded 90% for ampicillin, ceftriaxone, cefepime, imipenem, ciprofloxacin, azithromycin, gentamicin, amikacin, trimethoprim/sulfamethoxazole, tetracycline, and chloramphenicol phenotypic susceptibility results. We then evaluated the assays on direct stool specimens and observed a sensitivity of 97% ± 5 but, as expected, a lower specificity of 75% ± 31 versus the genotype of the E. coli cultured from stool. Finally, the assays were incorporated into a convenient TaqMan Array Card (TAC) format. These assays may be useful for tracking AMR in E. coli isolates or directly in stool for targeted testing of the fecal antibiotic resistome.
Highlights
Antimicrobial resistance (AMR) is a critical public health issue
We focused on E. coli because this was the most frequently reported bacteria in the World Health Organization (WHO) global antimicrobial resistance surveillance system (GLASS) [9] and has been associated with the greatest mortality and morbidity [10]
Correlation between genotypic and phenotypic antimicrobial susceptibility testing We evaluated the correlation between genotypic and phenotypic AST on 239 E.coli isolates
Summary
Antimicrobial resistance (AMR) is a critical public health issue. Antimicrobial-resistant infections can require prolonged treatments, extend hospital stays, and result in greater disability and death compared with susceptible infections [1]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The commercial company Charoen Pokphand Foods PCL provided support in the form of salaries for authors [TP] and animal derived sample materials but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section
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