Volume 21, Issue 8 p. 3046-3062
Research article

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

Ricardo León-Sampedro

Ricardo León-Sampedro

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

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Rosa del Campo

Rosa del Campo

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

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Mercedes Rodriguez-Baños

Mercedes Rodriguez-Baños

Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain

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Val F. Lanza

Val F. Lanza

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

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María José Pozuelo

María José Pozuelo

Department of Biology, Pharmacy Faculty, University San Pablo-CEU, Boadilla del Monte, Spain

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Carlos Francés-Cuesta

Carlos Francés-Cuesta

Infection and Public Health Unit, FISABIO/University of Valencia, Spain

Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain

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Ana P. Tedim

Ana P. Tedim

Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain

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Ana R. Freitas

Ana R. Freitas

UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal

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Carla Novais

Carla Novais

UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal

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Luísa Peixe

Luísa Peixe

UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal

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Rob J. L. Willems

Rob J. L. Willems

Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands

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Jukka Corander

Jukka Corander

Department of Biostatistics, University of Oslo, Oslo, Norway

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Fernando González Candelas

Fernando González Candelas

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

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Fernando Baquero

Fernando Baquero

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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Teresa M. Coque

Corresponding Author

Teresa M. Coque

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

For correspondence. E-mail [email protected] or E-mail [email protected]; Tel. (+34) 913368832.Search for more papers by this author
First published: 04 June 2019
Citations: 13

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.

Conflict of interest

The authors have no conflict of interest to declare.