Comparative phylogenomics of extended-spectrum beta-lactamase-producing Escherichia coli revealed a wide diversity of clones and plasmids in Spanish chicken meat

Abstract

Animal food products are important sources of zoonotic agents, increasing the risk of exposure to antibiotic-resistant bacteria from farm to fork. Therefore, we aimed to detect and fully characterise Extended-Spectrum Beta-Lactamase (ESBL)-producing E. coli from the poultry sector in a One Health approach. From December 2021 to March 2022, 48 chicken meat samples were collected from 16 establishments in La Rioja (Northern Spain). Antibiotic susceptibility testing was assessed by the disk-diffusion method. Forty E. coli isolates were recovered from 33 of the 48 chicken meat samples tested (68.8%) when plated on MacConkey-agar. In addition, six ESBL-E. coli (6/48, 12.5%) were obtained on cefotaxime-supplemented MacConkey-agar, which were Whole-Genome Sequenced. A large diversity of clones and ESBL genes was observed, namely ST1140-E/bla_CTX-M-32 (n = 1), ST752-A/bla_TEM-52 (n = 1), ST117-B2/bla_CTX-M-1/bla_SHV-12 (n = 2), ST10-A/bla_SHV-12 (n = 1) and ST223-B1/bla_SHV-12 (n = 1). Three IncI1-plasmids (pST3-CC3) were found carrying the bla_SHV-12/bla_CTX-M-1/bla_CTX-M-32 genes in two genetic environments: i) IS26-smc-glpR-bla_SHV-12-IS26; and ii) wbuC-bla_CTX-M-32/bla_CTX-M-1-ISEcp1. The bla_TEM-52 gene was carried on a P1-like phage-plasmid flanked by an IS4-mediated composite transposon. An IncHI2 plasmid harboured a bla_SHV-12 gene flanked by an IS26-mediated composite transposon but also additional genes conferring resistance to aminoglycosides, chloramphenicol, and sulphonamides. To analyse the cross-sectoral relatedness of our ESBL-E. coli isolates, our six genomes were mapped with publicly available genomes (n = 2588) related to the STs detected, revealing that one of our genomes (X3078-ST117) displayed strong similarities (34–40 allelic differences) with few genomes belonging to ST117 from the poultry sector from Germany and USA. This study demonstrated that the proportion of ESBL-E. coli is still high in chicken meat in Spain. In addition, the ST117 clone and the IncI1-bla_CTX-M-1-32/bla_SHV-12 plasmids might represent successful clones and plasmids adapted to the chicken host.