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

Célia Leão; Lurdes Clemente; Laura Moura; Anne Mette Seyfarth; Inge M Hansen; Rene S Hendriksen; Ana Amaro

doi:10.3389/fmicb.2021.653595

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

Front Microbiol. 2021 Jul 20:12:653595. doi: 10.3389/fmicb.2021.653595. eCollection 2021.

Authors

Célia Leão^{1

2}, Lurdes Clemente^{1

3}, Laura Moura^{1

4}, Anne Mette Seyfarth⁵, Inge M Hansen⁵, Rene S Hendriksen⁵, Ana Amaro¹

Affiliations

¹ Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal.
² MED - Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal.
³ Faculty of Veterinary Science, CIISA- Centre for Interdisciplinary Research in Animal Health, Lisbon, Portugal.
⁴ Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal.
⁵ EURL-AR, European Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark (DTU), National Food Institute, Lyngby, Denmark.

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 bla _CTX-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 bla _CTX-M-65 genes was investigated, and phylogenetic analysis was carried out using 17 other genomes with the same sequence type and harboring the bla _CTX-M-65 gene. All strains harbored bla _CTX-M-65, bla _OXA-1, and bla _TEM-1B, and one also carried the bla _SHV-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 bla _CTX-M-65 gene. It seems likely that the bla _CTX-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 bla _CTX-M-65 gene may ensure a stable spread of resistance in the absence of selective pressure.

Keywords: CTX-M-65; ESBL; Escherichia coli; WGS; chromosome; retail meat.