Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species
Por:
León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Frances-Cuesta, C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, Gonzalez Candelas, F, Baquero F and Coque TM
Publicada:
1 ago 2019
Ahead of Print:
1 jul 2019
Resumen:
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.
Filiaciones:
León-Sampedro R:
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
Del Campo R:
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
Rodriguez-Baños M:
Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
Lanza VF:
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
Pozuelo MJ:
Department of Biology, Pharmacy Faculty, University San Pablo-CEU, Boadilla del Monte, Spain
:
Infection and Public Health Unit, FISABIO/University of Valencia, Spain
Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain
Tedim AP:
Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
Freitas AR:
UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
Novais C:
UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
Peixe L:
UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
Willems RJL:
Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
Corander J:
Department of Biostatistics, University of Oslo, Oslo, Norway
:
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
Baquero F:
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
Coque TM:
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
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