Enterococcus lactis is ecologically and genetically distinct from the major opportunistic pathogen Enterococcus faecium

Abstract

Enterococcus faecium is a major human opportunistic bacterial pathogen and a close relative of the recently established species Enterococcus lactis. As a species, commensal E. lactis remains relatively understudied, and its genetic connectivity with E. faecium is not thoroughly understood. Here, we introduce a large collection of whole-genome sequenced isolates comprising 894 E. faecium and 392 E. lactis genomes. Using these genomes to complement publicly available data, we studied the genome content and the evolutionary relationship between these species. A wider range of host species was observed in E. faecium; in particular, there is a radiation of E. faecium clades specialized to domesticated and pet animals among which E. lactis is uncommon. Of note, pangenome analyses reveal that E. lactis has significantly more allelic variation and lower recombination rates in core genes compared with E. faecium. These observations suggest that E. lactis represents a population that has occupied its ecological niche longer than E. faecium has. This study enhances understanding of the evolutionary histories of these species and highlights the importance of sampling and studying closely related commensal bacteria in addition to clinically relevant opportunistic pathogens.

Keywords: Enterococcus faecium; Enterococcus lactis; evolution; genomics.

Fig. 1.. Midpoint-rooted maximum likelihood phylogenies of the E. lactis (n=454) (top) and E. faecium (n=2,538) (bottom) populations. Population clusters as determined with fastbaps were computed independently for each species and are displayed in the tree panels. The coloured leaf tips correspond to circularized assemblies collected from the NCBI. The isolation source and phenotypic AMRs are displayed for all isolates that had such data available. Elac = E. lactis; Efm = E. faecium.

Fig. 2.. Relative distributions of isolation sources that make up each population group in the combined study population.

Fig. 3.. Functional categories of COGs that are in the soft core (>95%) in one species and cloud (<15%) in the other. The colours correspond to the species in which the genes are commonly found. Hypothetical proteins of unknown function were not included in this chart.

Fig. 4.. Tukey box plots displaying the diversity (left) and consistency (right) indices of the core COGs in each population group. Efm, E. faecium; Elac, E. lactis.

Fig. 5.. Summary of models produced with Panstripe using the estimated pangenome and a combined population phylogeny computed with FastTree. (a) Estimated gene gain and loss events computed by Panstripe. (b) Parameters of the gene exchange models fitted to each clade. The ‘core’ parameter describes the association between gene gain and loss events with core phylogeny branch length. The ‘tip’ parameter describes gene exchange events that occur only at the tips of the phylogenies.