Genomic insights into multidrug-resistant extraintestinal pathogenic Escherichia coli O4:H12 harboring mcr-5 and blaSHV-12 on conjugative plasmids isolated from chicken meat in Japan.

Aims: This study aims to investigate the genomic profile of a multidrug-resistant Escherichia coli strain, 160-11H1, co-carrying an extended-spectrum β-lactamase (ESBL) and the plasmid-mediated mobile colistin resistance gene, mcr-5.

Methods and results: The entire genome of the strain was sequenced using Illumina MiSeq and Oxford Nanopore platforms, and de novo assembly was performed using Unicycler. The genome size was 5 031 330 bp and comprised 5140 coding sequences. mcr-5 and an ESBL-encoding gene, blaSHV-12, providing resistance to clinically important antimicrobials, including colistin (minimum inhibitory concentration [MIC]: 8 µg ml-1) and extended-spectrum cephalosporins (MIC: >32 µg ml-1) were detected. mcr-5 was carried on a Tn3-type transposase, being in an operon with a ChrB-domain protein and an uncharacterized major facilitator superfamily-type transporter on a conjugative plasmid of the IncFII backbone. The blaSHV-12 gene was inserted into tniA putative transposase gene in the IncFIA/FIB/FIC multireplicon plasmid. The strain belonged to sequence type (ST) 10, CH-type fumC11/fimH54, serotype O4:H12, and phylogroup A, and carried several virulence genes associated with heat survival, colonization, fitness, and conjugation.

Conclusions: This study presents the first identification of polymyxin-resistant E. coli co-carrying mcr-5 and ESBL genes in meat from Japan, highlighting the critical need for routine investigations of these genes within food ecosystems.