Publication: Genotypic antimicrobial resistance assays for use on E. Coli isolates and stool specimens
Issued Date
2019-05-01
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ISSN
19326203
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2-s2.0-85065834888
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Mahidol University
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SCOPUS
Bibliographic Citation
PLoS ONE. Vol.14, No.5 (2019)
Suggested Citation
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 Genotypic antimicrobial resistance assays for use on E. Coli isolates and stool specimens. PLoS ONE. Vol.14, No.5 (2019). doi:10.1371/journal.pone.0216747 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/49775
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Title
Genotypic antimicrobial resistance assays for use on E. Coli isolates and stool specimens
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.