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Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species |
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| Authors: | Ricardo León-Sampedro Rosa del Campo Mercedes Rodriguez-Baños Val F. Lanza María José Pozuelo Carlos Francés-Cuesta Ana P. Tedim Ana R. Freitas Carla Novais Luísa Peixe Rob J. L. Willems Jukka Corander Fernando González Candelas Fernando Baquero Teresa M. Coque |
| Affiliation: | 1. Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain;2. Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain Spanish Network for Research in Infectious Diseases (REIPI), Health Institute Carlos III, Madrid, Spain;3. Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain;4. Department of Biology, Pharmacy Faculty, University San Pablo-CEU, Boadilla del Monte, Spain;5. Infection and Public Health Unit, FISABIO/University of Valencia, Spain;6. UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal;7. Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands;8. Department of Biostatistics, University of Oslo, Oslo, Norway;9. Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain Infection and Public Health Unit, FISABIO/University of Valencia, Spain Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain;10. Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain |
| Abstract: | 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. |
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