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

Abstract

Summary Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone‐responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

“…While MDR Enterococci are often overrepresented in HA lineages 14,30 , our data also revealed AMR traits to be highly prevalent in E. faecalis isolates from non-hospital settings and of non-human origin, again consistent with it being a generalist organism where lineages can survive across multiple niches. Traits conveying AMR have been shown to be abundant in E. faecalis isolates from migratory wild birds 20 , and we accordingly detected majority of wild bird isolates in the present collection to carry multiple ARGs, unlike what has been found even in domesticated poultry when screening for ARGs in S. aureus isolates 3 . Intriguingly, flightless birds in locations remote from anthropogenic impact carried E. faecalis isolates lacking other but intrinsic ARGs, in agreement with lack of selection driven by human-applied antimicrobials in the population and its environment 58 .…”

“…The top three largest PopPUNK clusters (PP) overlapped with three major sequence types (STs) in E. faecalis, ST6 (PP2), ST16 (PP3) and ST40 (PP1), of which the two latter have been isolated from various sources both human and non-human, while ST6 has been described as human-associated [20][21][22][23][24] . Phylogenetically closely related to PP3, PP9 exclusively included ST179, a humanassociated single-locus variant of ST16 20 , and PP10 solely contained ST58 and ST63. The other PP clusters included a broader set of STs, of up to 12 different STs in PP4, with the most prevalent being ST21 and ST22 (PP5), ST28 (PP6), ST9 (PP7) and ST8 and ST64 (PP8).…”

Evolutionary Pathways and Trajectories in Antibiotic Resistance

“…A gradient of host ranges for different PTUs has been inferred from comprehensive genome databases, with the number of mobilizable and conjugative plasmids able to propagate between species of different bacterial genera and families being higher than that of plasmids able to move between orders (e.g., 9 PTUs that include emblematic IncL/M, IncN1, IncW, IncHI2, IncX1), classes (e.g., PTUs-IncC, previously known as A/C; and PTU-Q2) and phylum (e.g., PTU-P1). Epidemiological data complement (and confirm) the heterogeneity of plasmidomes in bacterial populations, from species to the microbiome level (33,65,743,744), which is influenced not only by the plasmids' "conduciveness" but also by that of the host (745). Maintenance of plasmid heterogeneity has obvious benefits for the robustness and evolvability of bacterial communities (746).…”

Evolutionary Pathways and Trajectories in Antibiotic Resistance

“…We will briefly address the interesting case of mobile promoters, MGEs transferring entirely noncoding DNA sequences, resulting in horizontal regulatory transfer (718), which can increase ARG expression. (33,65,743,744), which is influenced not only by the plasmids' "conduciveness" but also by that of the host (745). Maintenance of plasmid heterogeneity has obvious benefits for the robustness and evolvability of bacterial communities (746).…”