Emergence and Clonal Spread of CTX-M-65-Producing Escherichia coli From Retail Meat in Portugal

Abstract

The emergence and dissemination of resistance to third- and fourth-generation cephalosporins among Enterobacteriaceae from different sources impose a global public health threat. Here, we characterized by whole-genome sequencing four Escherichia coli strains harboring the blaCTX–M–65 gene identified among 49 isolates from beef and pork collected at retail. The genomic content was determined using the Center for Genomic Epidemiology web tools. Additionally, the prediction and reconstruction of plasmids were conducted, the genetic platform of the blaCTX–M–65 genes was investigated, and phylogenetic analysis was carried out using 17 other genomes with the same sequence type and harboring the blaCTX–M–65 gene. All strains harbored blaCTX–M–65, blaOXA–1, and blaTEM–1B, and one also carried the blaSHV–12 gene. Other resistance genes, namely, qnrS2, aac(6′)-Ib-c, dfrA14, sul2, tetA, and mphA, were present in all the genomes; the mcr-1.1 gene was identified in the colistin-resistant strains. They belong to sequence type 2179, phylogenetic group B1, and serotype O9:H9 and carried plasmids IncI, IncFIC(FII), and IncFIB. All strains share an identical genetic environment with IS903 and ISEcp1 flanking the blaCTX–M–65 gene. It seems likely that the blaCTX–M–65 gene is located in the chromosome in all isolates based on deep in silico analysis. Our findings showed that the strains are clonally related and belong to two sub-lineages. This study reports the emergence of CTX-M-65-producing E. coli in Portugal in food products of animal origin. The chromosomal location of the blaCTX–M–65 gene may ensure a stable spread of resistance in the absence of selective pressure.

Are Virulence and Antibiotic Resistance Genes Linked? A Comprehensive Analysis of Bacterial Chromosomes and Plasmids

“…The link between antimicrobial use and resistance is complex, but the emergence of resistance is likely to be specific to each drug and to each microorganism [ 34 ]. Therefore, horizontal gene transfer and clonal expansion are giving rise to highly resistant microorganisms [ 5 , 35 ]. Nevertheless, other factors, such as cross-selection and co-selection, are highly pertinent while addressing antibiotic resistance [ 34 ].…”

First Report of blaCTX–M–167, blaSHV–1, and blaTEM–1B Carrying Klebsiella pneumonia Showing High-Level Resistance to Carbapenems

“…The genetic platform analysis revealed that the bla CTX–M gene was flanked by Tn2-like transposase and ISEcp1 downstream and upstream in both genetic environments, respectively. IS Ecp1 , belonging to the IS 1380 family, is one of the most important insertion sequences associated with bla CTX–M genes ( Zhao and Hu, 2013 ; Leão et al, 2021 ). Tn3 transposon, which is conjugative, was also detected.…”

Prevalence and Characterization of ESBL/AmpC Producing Escherichia coli from Fresh Meat in Portugal

“…In this study, it was identified in four isolates, three from beef and one from pork. Genomic characterization by whole genome sequencing and genetic relatedness with other E. coli genomes suggest a clonal spread in Europe [ 72 ]. This enzyme is widely distributed in the Asian and North and South American continents [ 73 , 74 , 75 , 76 ], and only scarce studies reported its presence in Europe in humans, animals, and food [ 47 , 71 , 77 , 78 , 79 ].…”

“…In 89 resistant isolates with a wide range of MICs (0.25 to ≥8 mg/L), PMQR were detected in 52, being qnrB the most frequent ( n = 27), followed by qnrS ( n = 21) and aac(6′)-Ib-cr ( n = 4), in agreement with other studies [ 20 ]. Of note, the four CTX-M-65 producers co-harbored qnrS and aac(6′)-Ib-cr [ 72 ]. Studies in China in Enterobacteriaceae ESBL producers identified strains co-harboring two and three PMQR-encoding mechanisms simultaneously [ 76 , 101 ].…”