Comparative genomic analysis of Enterococcus faecalis: insights into their environmental adaptations

Abstract

BackgroundEnterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gastrointestinal tract, faeces, blood, urine, water, and fermented foods (such as dairy products). In order to elucidate the role of habitat in shaping the genome of Enterococcus faecalis, we performed a comparative genomic analysis of 78 strains of various origins.ResultsAlthough no correlation was found between the strain isolation habitat and the phylogeny of Enterococcus faecalis from our whole genome-based phylogenetic analysis, our results revealed some environment-associated features in the analysed Enterococcus faecalis genomes. Significant differences were found in the genome size and the number of predicted open reading frames (ORFs) between strains originated from different environments. In general, strains from water sources had the smallest genome size and the least number of predicted ORFs. We also identified 293 environment-specific genes, some of which might link to the adaptive strategies for survival in particular environments. In addition, the number of antibiotic resistance genes was significantly different between strains isolated from dairy products, water, and blood. Strains isolated from blood had the largest number of antibiotic resistance genes.ConclusionThese findings improve our understanding of the role of habitat in shaping the genomes of Enterococcus faecalis.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4887-3) contains supplementary material, which is available to authorized users.

Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

“…In general, no obvious differences arose from the profiles and sequences of virulence genes between strains obtained from foodstuffs/livestock and those causing human infections and only the occurrence of cyl and cpsC-K seemed lineage (ST)-specific (Table S5). These data support previous works indicating the generalist lifestyle of E. faecalis and the opportunist nature of the human infections they cause [31,51].…”

“…Intact or relics of prophages highly identical to sequences from common enterococcal prophages such as phiL1A and vB_IME197 were identified in most strains, but the exact phage(s) present in each genome cannot be ruled out with accuracy. The phiL1A and vB_IME197 phages are widespread in E. faecalis from variable sources [31] and were originally described in clinical settings in UK and China, respectively [54,55] [58]. In this study, this phage was putatively identified in three related ST476 strains from hospitalized patients, farm and retail chicken in China and Tunisia (Table S6), once more enphasizing the lack of a demarcation between clinical and non-clinical genomes in relevant mobile genetic elements (MGEs).…”

Comparative genomics of globaloptrA-carryingEnterococcus faecalisuncovers common genetic features and a chromosomal hotspot foroptrAacquisition

“…Based on SNP analysis, we observed an overall diverse population of optrA -positive E. faecalis (range 0-17.712 SNPs) with a correspondence between the sequence types identified (17 STs, 18 branches) (Figure 1, Table S1 in the Supplemental material). Strains originating from the same source or country were dispersed across the different tree branches, suggesting no significant correlation between strain origin and phylogeny as commonly observed in E. faecalis [31]. These results further confirm the easy promiscuity of optrA that has been identified in enterococci from highly variable epidemiological and genetic backgrounds [2, 32].…”

“…All of them are classified as temperate Siphoviridae bacteriophages originally obtained from variable sources (humans, farms, hospital sewage) [48–50]. The phiEf11 and LP-101 phages are not present in V583 in contrast to phiFL1A and vB_EfaS_IME197, which corresponded to the predominant prophages in the collection analysed and are also widespread in E. faecalis from variable sources [31]. Both phiFL1A and IME197 were originally described in clinical settings in UK and China, respectively [49, 51].…”

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

“…These results suggest alternating periods of genetic isolation and gene flow in different hosts for some E. faecalis lineages from wild birds. A reassessment of the population structure of the species through increased sampling of nonhuman isolates is therefore necessary to further identify host‐specific populations suggested here and elsewhere (He et al ., ). The presence and diversity of pheromone‐responsive plasmids in most birds, as well as in human isolates, confirms the relevance of this plasmid family in the biology of E. faecalis as a species.…”