| Summary: | ABSTRACT: Objectives: Colistin is considered a last-resort antibiotic against carbapenem-resistant isolates. Currently, this antibiotic is facing the emergence of mobilised colistin resistance (mcr) genes, which confer colistin resistance. This study conducted genomic characterisation of an atypical multidrug-resistant Escherichia coli harbouring two mcr genes in France. Samples collected from a pig farm in Avignon (Vaucluse department) were subjected to molecular screening targeting mcr variants. Methods: Samples were cultured on selective Lucie-Bardet-Jean-Marc-Rolain medium. Growing bacteria were identified using MALDI-TOF, followed by antibiotic susceptibility testing. Whole-genome sequencing and bioinformatic genome analysis were performed. Results: Selective culture of stools revealed the presence of an E. coli strain named Q4552 harbouring mcr-1.1 and mcr-3.5 genes, which is also resistant to 14 antibiotics. Genome sequencing and assembly yielded a complete and circular chromosome and eight different plasmids. Sequence analysis demonstrated an integration of a mobile genetic element carrying mcr-1.1 in the chromosome, whereas mcr-3.5 was in the plasmid and its resistome was composed of 22 resistance genes. The Q4552 strain was identified as an ST-843 clone that belonged to the clonal complex Cplx-568 and is the only ST type of this cplx-568 that has been isolated from animals, humans, and the environment. Conclusion: We report the first co-occurrence of mcr-1 and mcr-3 genes in France from a pathogenic E. coli isolated from a pig. Because this clone (ST-843) has been reported in zoonotic transmissions, programs to monitor the bacterium are urgently required to avoid its spread and zoonotic transmission to humans.
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