Genotypic antimicrobial resistance assays for use on E. coli isolates and stool specimens.

Academic Article


  • 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.
  • Authors

    Published In

  • PLoS One  Journal
  • Keywords

  • Anti-Bacterial Agents, Drug Resistance, Bacterial, Escherichia coli, Feces, Genotype, Humans, Phenotype, Polymerase Chain Reaction, Sequence Analysis, DNA
  • Digital Object Identifier (doi)

    Author List

  • Pholwat S; Liu J; Taniuchi M; Chinli R; Pongpan T; Thaipisutikul I; Ratanakorn P; Platts-Mills JA; Fleece M; Stroup S
  • Start Page

  • e0216747
  • Volume

  • 14
  • Issue

  • 5