Phylogenomics of Enterococcus faecalis from wild birds: New insights into host-associated differences in core and accessory genomes of the species

Earlier studies have painted a picture of E. faecalis populations having high recombination and mutation rates, suggesting a frequent gene flow between strains from disparate origins, which is important information for interpreting epidemiological data. The verification of this hypothesis has been hampered by the scarcity of available sequences from nonhuman host strains. We studied 97 E. faecalis isolates from 35 species of wild migratory and raptor birds and we also compared five newly determined genomes from various wild bird species with 441 E. faecalis genomes from diverse human (majority) and nonhuman sources available from public databases. We have identified many unique sequence types (STs) in wild birds and also a proportion of STs previously found in other hosts, including some predominant in poultry (ST82, ST16, ST290). Using a combination of novel phylogenetic and population structure methods to analyze genomes, we have obtained new insights into the core and accessory genome of the species. The ST82 lineage, represented here by genomes of wild migratory birds and previously associated with severe infections in poultry, clustered separately, reflecting some degree of “adaptive isolation.” Other overrepresented E. faecalis lineages in various hosts, including birds (ST16, ST40, ST55) exhibited host-associated differences in core and accessory genomes. Core genome divergence, frequent events of differential gene introgression and occasional epidemic peaks appear to explain the population structure of the species. These findings indicate the need to carefully reassess the low level of host specialization of this enterococcal species that was proposed in previous studies.