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Environ Microbiol

Title:		Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species
Author(s):		Leon-Sampedro R; Del Campo R; Rodriguez-Banos 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; Coque TM;
Address:		"Department of Microbiology, University Hospital Ramon y Cajal, Ramon y Cajal Health Research Institute (IRYCIS), Madrid, Spain. Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain. Spanish Network for Research in Infectious Diseases (REIPI), Health Institute Carlos III, Madrid, Spain. 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. UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal. Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands. Department of Biostatistics, University of Oslo, Oslo, Norway. Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain"
Journal Title:		Environ Microbiol
Year:		2019
Volume:		20190704
Issue:		8
Page Number:		3046 - 3062
DOI:		10.1111/1462-2920.14702
ISSN/ISBN:		1462-2920 (Electronic) 1462-2912 (Linking)
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"
Keywords:		"Animals Animals, Wild Birds/*microbiology Enterococcus faecalis/*genetics Gene Expression Regulation, Bacterial Gene Transfer, Horizontal Genome, Bacterial Host Specificity *Phylogeny;"
Notes:		"MedlineLeon-Sampedro, Ricardo Del Campo, Rosa Rodriguez-Banos, Mercedes Lanza, Val F Pozuelo, Maria Jose Frances-Cuesta, Carlos Tedim, Ana P Freitas, Ana R Novais, Carla Peixe, Luisa Willems, Rob J L Corander, Jukka Gonzalez Candelas, Fernando Baquero, Fernando Coque, Teresa M eng Instituto de Salud Carlos III of Spain/Ministry of Economy and Competitiveness/International European Development Regional Fund 'A way to achieve Europe' (ERDF)/International PI15-0512/Spanish R& D National Plan Estatal de I + D + i 2013-2016/International JPIAMR2016-AC16/00039/Joint Programming Initiative in Antimicrobial Resistance (JPIAMR)/International Sociedad Espanola de Enfermedades Infecciosas y Microbiologia Clinica (SEIMC)/International Research Support, Non-U.S. Gov't England 2019/06/05 Environ Microbiol. 2019 Aug; 21(8):3046-3062. doi: 10.1111/1462-2920.14702. Epub 2019 Jul 4"