ABSTRACTCertain strains ofEnterococcus faeciumandEnterococcus faecaliscontribute 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 31E. faeciumand 38E. faecalisstrains. Hierarchical clustering of 7,017 orthologs found in theE. faeciumpangenome revealed that NC strains clustered into two clades and are distinct from CL strains. NCE. faeciumgenomes 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. faeciumortholog 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 CL-enriched loci. Genes in 23 functional groups are also differentially enriched between NC and CLE. faeciumgenomes. In contrast, differences were not observed between NC and CLE. faecalisgenomes despite their having larger genomes thanE. faecium. Our findings show that unlikeE. faecalis, NC and CLE. faeciumstrains are equipped with distinct structural and functional genomic features indicative of adaptation to different environments.
Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features
