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

  1. León‐Sampedro, Ricardo 3910
  2. del Campo Moreno, Rosa 11015
  3. Rodriguez‐Baños, Mercedes 111
  4. Fernández Lanza, Val 123
  5. Pozuelo de Felipe, María José 12
  6. Francés Cuesta, Carlos 78
  7. Tedim, Ana P. 110
  8. Freitas, Ana R. 14
  9. Novais, Carla 14
  10. Peixe, Luísa 16
  11. Willems, Rob J. L. 13
  12. Corander, Jukka 6
  13. González Candelas, Fernando 7817
  14. Baquero, Fernando 345
  15. Coque, Teresa M. 345
  1. 1 Department of Microbiology University Hospital Ramón y Cajal
  2. 2 Ramón y Cajal Health Research Institute (IRYCIS)
  3. 3 Biomedical Research Networking Center for Epidemiology and Public Health (CIBER‐ESP)
  4. 4 Department of Microbiology University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS)
  5. 5 Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC)
  6. 6 Department of Biostatistics University of Oslo
  7. 7 Infection and Public Health Unit FISABIO/University of Valencia
  8. 8 Institute for Integrative Systems Biology, I2SysBio CSIC‐University of Valencia
  9. 9 Department of Microbiology University
  10. 10 Ramón y Cajal Health Research Institute (IRYCIS)
  11. 11 Ramón y Cajal Health Research Institute (IRYCIS) Madrid Spain
  12. 12 Department of Biology, Pharmacy Faculty University San Pablo‐CEU
  13. 13 Department of Medical Microbiology University Medical Center, Utrecht
  14. 14 UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty University of Porto Porto Portugal
  15. 15 Spanish Network for Research in Infectious Diseases (REIPI) Health Institute Carlos III
  16. 16 UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty University of Porto
  17. 17 Biomedical Research Networking Center for Epidemiology and Public Health (CIBER‐ESP)
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Revista:
Environmental Microbiology

ISSN: 1462-2912,  1462-2920

Año de publicación: 2019

Volumen: 21

Número: 8

Páginas: 3046-3062

Tipo: Artículo

DOI: 10.1111/1462-2920.14702 GOOGLE SCHOLAR lock_openAcceso abierto editor

Otras publicaciones en: Environmental Microbiology

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.

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