High Diversity of Antimicrobial Resistance Genes, Class 1 Integrons, and Genotypes of Multidrug-ResistantEscherichia coliin Beef Carcasses

Abstract

Multidrug-resistant Escherichia coli can contaminate food meat during processing and cause human infection. Phenotypic and genotypic characterization of the antimicrobial resistance were conducted for 45 multidrug-resistant E. coli isolates from 208 samples of beef carcasses. The mechanisms of resistance were evaluated using polymerase chain reaction and sequencing methods, and the clonal relationship among isolates was evaluated using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Different variants of bla, tet, flo, dfrA, and aadA genes were detected in most of the strains resistant to β-lactam, tetracycline, chloramphenicol, sulfonamides, and aminoglycosides, respectively. Extended-spectrum β-lactamase (ESBL)-producing E. coli was found in 42.2% of the 45 E. coli isolates and the most commonly detected ESBL genotypes were CTX-M group 1 and 9. Class 1 integrons with nine different arrangements of gene cassettes were present in 28 of 45 E. coli isolates. Twenty-nine PFGE groups and 24 MLST types were identified in their clonal structure. This study revealed that E. coli isolates from beef contained high diversity of antimicrobial resistance genes, integrons, and genotypes. These results highlighted the role of beef meat as a potential source for multidrug-resistant E. coli strains and the need for controlling beef safety.

DeepARG: A deep learning approach for predicting antibiotic resistance genes from metagenomic data

“…On the other hand, the best hit approach showed a higher precision (0.44), but a much lower recall (0.44). The multidrug category contains genes that confer resistance to multiple antibiotic classes such as macrolides, beta-lactamases, glycopeptides, quinolones, as well as other antimicrobials such as metals (Chen et al, 2017;Linhares et al, 2015). These genes often share similar sequences, which makes it challenging for computational methods to determine the true source of a short read.…”

Drivers of antimicrobial resistance amongst intestinalEscherichia coliisolated from children in South Asia and sub-Saharan Africa

“…Here we present the first comprehensive AMR phenotypic data and molecular characterization for multiple antimicrobials, detecting several common mobile elements mediating the AMR including small plasmids, class I integrons with different cassettes and transposons including Tn6029, Tn10 and Tn1721 ( Fig S3). Many of the common mobile elements we detected have been reported widely in E. coli and other Enterobacteriaceae from human intestinal and extra-intestinal and animal samples [32][33][34][35][36] . Thus, while not conducted for the specific purpose of AMR surveillance, these aEPEC are likely represent a holistic overview of E. coli, and possibly other Enterobacteriaceae, in circulation at the study sites.…”

Diverse Gene Cassette Arrays Prevail in Commensal Escherichia coli From Intensive Farming Swine in Four Provinces of China

“…There are nine arrays that are summarized from swine farming settings and pork products ( dfrA1–aadA1 , aadA22 , dfr17–aadA5 , dfrA12–orfF–aadA2 , dfrXII–orfF–aadA2 , aadA2 , dfrA1–catB3–aacA4 , aadB–aadA2 , and dfrA12–aadA2–cmlA1–aadA1 ; Chen, 2013 ; Wei, 2014 ; Zhang et al, 2017 ). Nine arrays were present in E. coli isolates from beef carcasses, including linF–aadA2 , dfrA17–aadA5 , aadB–blaOXA-10 , dfr12–orfF–aadA2 , dfrA1–aadA1 , dfrA12–aadA2 , aadA2 , dfr12 , and aadB–aadA2 ( Chen et al, 2017 ). Five arrays were in E. coli isolates from waterfowls ( dfrA1–orfC , aadA2 , aadA1 , dfrA1–aadA1 , and dfrA1–orfC–aadA1 ; Zhang et al, 2019b ).…”