Certain strains of Enterococcus faecium and Enterococcus faecalis contribute beneficially to animal health and food production, while others are associated with nosocomial infections. To determine whether there are structural and functional genomic features that are distinct between nonclinical (NC) and clinical (CL) strains of those species, we analyzed the genomes of 31 E. faecium and 38 E. faecalis strains. Hierarchical clustering of 7,017 orthologs found in the E. faecium pangenome revealed that NC strains clustered into two clades and are distinct from CL strains. NC E. faecium genomes are significantly smaller than CL genomes, and this difference was partly explained by significantly fewer mobile genetic elements (ME), virulence factors (VF), and antibiotic resistance (AR) genes. E. faecium ortholog comparisons identified 68 and 153 genes that are enriched for NC and CL strains, respectively. Proximity analysis showed that CL-enriched loci, and not NC-enriched loci, are more frequently colocalized on the genome with ME. In CL genomes, AR genes are also colocalized with ME, and VF are more frequently associated with CLenriched loci. Genes in 23 functional groups are also differentially enriched between NC and CL E. faecium genomes. In contrast, differences were not observed between NC and CL E. faecalis genomes despite their having larger genomes than E. faecium. Our findings show that unlike E. faecalis, NC and CL E. faecium strains are equipped with distinct structural and functional genomic features indicative of adaptation to different environments.
Enterococcus faecium and Enterococcus faecalis are Gram-positive bacteria in the Firmicutes phylum and are found on plants, in foods, and in the gastrointestinal tracts (GIT) of animals (1). These species are members of the polyphyletic group of bacteria known as lactic acid bacteria and have important roles in food and beverage fermentations. Certain strains of E. faecium confer beneficial or probiotic effects on animal and human health (2). Conversely, strains of E. faecium and E. faecalis are also associated with nosocomial infections resulting in endocarditis and bacteremia and represent a significant reservoir of antibiotic resistance genes (2).The genetic features of E. faecium and E. faecalis were investigated previously to identify lineages specific to community and clinical environments (3-7). Virulence factors (VF), antibiotic resistance (AR) genes, mobile genetic elements (ME), and multilocus sequence typing (MLST) patterns are associated with the potential of E. faecium and E. faecalis to cause disease in humans (8, 9). Despite such studies, the structural and functional features of enterococcal genomes are not fully understood. We hypothesized that the lineage-specific differences observed previously were only a fraction of the greater, more significant distinctions between nonclinical (NC) and clinical (CL) strains, and the opposing environmental and health-specific associations are the result of broader niche-specific adaptations that can be o...