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Title: Genotypic antimicrobial resistance assays for use on E. Coli isolates and stool specimens
Authors: Suporn Pholwat
Jie Liu
Mami Taniuchi
Rattapha Chinli
Tawat Pongpan
Iyarit Thaipisutikul
Parntep Ratanakorn
James A. Platts-Mills
Molly Fleece
Suzanne Stroup
Jean Gratz
Esto Mduma
Buliga Mujaga
Thomas Walongo
Rosemary Nshama
Caroline Kimathi
Suporn Foongladda
Eric R. Houpt
Haydom Lutheran Hospital
University of Virginia
Mahidol University
Faculty of Medicine, Siriraj Hospital, Mahidol University
Swine Veterinarian Service
Kilimanjaro Clinical Research Institute
Keywords: Agricultural and Biological Sciences;Biochemistry, Genetics and Molecular Biology
Issue Date: 1-May-2019
Citation: PLoS ONE. Vol.14, No.5 (2019)
Abstract: © 2019 Pholwat et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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.
ISSN: 19326203
Appears in Collections:Scopus 2019

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