Escherichia coli Strains Originating from Raw Sheep Milk, with Special Reference to Their Genomic Characterization, Such as Virulence Factors (VFs) and Antimicrobial Resistance (AMR) Genes, Using Whole-Genome Sequencing (WGS)

The objective of this work was to deliver a comprehensive genetic characterization of a collection of <i>E. coli</i> strains isolated from raw sheep milk. To complete our purpose, the technique of whole-genome sequencing, coupled with bioinformatics and phenotypic characterization of antimicrobial resistance, was performed. These Gram-negative, facultative anaerobic bacteria belong to the family <i>Enterobacteriaceae</i>, together with other intestinal pathogens, such as <i>Shigella</i> spp. and <i>Salmonella</i> spp. Genetic analysis was carried out on all strains (phylogram, sequence types, VFs, AMR genes, and pangenome). The results showed the presence of various genetic traits that are related to virulence factors contributing to their pathogenic potential. In addition, genes conferring resistance to antibiotics were also detected and confirmed using phenotypic tests. Finally, the genome of the <i>E. coli</i> strains was characterized by the presence of several mobile genetic elements, thus facilitating the exchange of various genetic elements, associated with virulence and antimicrobial resistance, within and beyond the species, through horizontal gene transfer. Contaminated raw sheep milk with pathogenic <i>E. coli</i> strains is particularly alarming for cheese production in artisan dairies.