Occurrence of virulence genes, 16S rRNA methylases, and plasmid-mediated quinolone resistance genes in CTX-M-producing Escherichia coli from Pakistan

The aim of the study was to conduct a comprehensive molecular characterization of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli collected from Pakistan. Genetic relatedness among 98 ESBL-producing E. coli was measured by pulsed-field gel electrophoresis (PFGE). The presence of genes encoding ESBLs, virulence factors (VFs), 16S rRNA methylases, plasmid-mediated quinolone resistance (PMQR) encoding elements, plasmid replicon types, phylogenetic groups of E. coli, prevalence of the worldwide disseminated clone E. coli ST131, and phylogrouping of CTX-M enzymes was investigated by polymerase chain reaction (PCR). All isolates carried bla (CTX-M) genes and, except for one isolate from CTX-M phylogroup 9, they all belonged to CTX-M phylogroup 1. The isolates were genetically diverse with PFGE. Phylogenetic group D (36 %) was most abundant in this collection of E. coli, whereas isolates belonging to B2 (22 %) had the highest content of virulence genes. PMQR genes were found in 84.6 % of the isolates; among them, 93 % isolates were positive for variants of acetyltransferases (aac(6')-lb-cr), whereas qnrB, qepA, and qnrS were present in 11 %, 5 %, and 4 % of the isolates, respectively. Only 3 % of the isolates contained genes encoding 16S rRNA methylases. The most abundant replicon type was IncF (96 %), and 18 % of the isolates belonged to the ST131 clone. Out of 34 investigated VFs, 24 genes encoding different types of adhesins, protectins, toxins, siderophores, and other VFs were found. Although the isolates in this collection were highly resistant to many antimicrobials, susceptibility to amikacin and meropenem was retained.