Abstract
Enterococcus faecium is a part of the native microbiota in fermented and dairy products. However, the acquisition of virulence determinants turns this bacterium into a pathogen. To evaluate the genetic relatedness and virulence profile, we performed whole-genome sequencing of four E. faecium strains isolated from the dairy industry and compared them with clinical and environmental isolates reported in Mexico. Our findings revealed close genetic relationships between certain dairy-associated and clinical isolates, with shared antibiotic-resistance determinants and prophages. Notably, the tetL, tetM, lnuA, and lsaE genes, associated with tetracycline and lincosamide resistance, were present in the two dairy-related strains. Clinical isolates exhibited a higher prevalence of adhesion and biofilm-related genes, including acm, ecbA, fss3, and sgrA. Additionally, the identification of prophages in dairy-related strains suggests their potential for genetic exchange. Thus, it is crucial to assess the risk posed by E. faecium as a potential pathogen in the dairy plant environment.
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