Premium
Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species
Author(s) -
LeónSampedro Ricardo,
del Campo Rosa,
RodriguezBaños Mercedes,
Lanza Val F.,
Pozuelo María José,
FrancésCuesta Carlos,
Tedim Ana P.,
Freitas Ana R.,
Novais Carla,
Peixe Luísa,
Willems Rob J. L.,
Corander Jukka,
González Candelas Fernando,
Baquero Fernando,
Coque Teresa M.
Publication year - 2019
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.14702
Subject(s) - biology , phylogenomics , enterococcus faecalis , genome , host (biology) , evolutionary biology , core (optical fiber) , phylogenetics , genetics , gene , clade , escherichia coli , materials science , composite material
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.