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Whole-Genome Sequencing and Comparative Genomic Analysis of Enterococcus spp. Isolated from Dairy Products: Genomic Diversity, Functional Characteristics, and Pathogenic Potential

Enterococci are commensal organisms that have probiotic effects for their hosts and can be used as adjunct cultures in fermented dairy products. The dark side of Enterococci is manifested in E. faecium and E. faecalis, which are the causative agents of nosocomial infections, and thus Enterococci have not been granted a safety status as food additives. In this context, we aimed to assess the safety and functional profile of an Enterococci collection retrieved from traditional dairy products through a high-resolution genomic characterization and comparative genomic analysis. Analysis did not reveal major differences in the main cellular processes of Enterococci. Moreover, a diverse repertoire of resistance and virulence genes was present, though known hallmark pathogenicity factors were either absent or occurred rarely. The abundance of bacteriocins and CRISPR/Cas systems suggested the ability of the isolates to suppress pathogens and evade bacteriophages, respectively. Presence–absence patterns of genes suggested that dairy-originated E. faecium are not associated with pathogenicity factors, while those of human origin are strongly linked with notorious resistance and virulence determinants. Our comparative analysis provided some notable insights regarding the genomic composition of Enterococci in the context of their origin. However, their pathogenic lifestyle is likely to be explained by the interplay of multiple genomic factors.