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

• Type: Article in International Scientific Journal
• Date: 2019

Authors

Leon Sampedro, R (Author) Other; del Campo, R (Author) Other; Rodriguez Banos, M (Author) Other; Lanza, VF (Author) Other; Jose Pozuelo, MJ (Author) Other; Frances Cuesta, C (Author) Other; Tedim, AP (Author) Other; Freitas, AR (Author) Other; Novais, Carla (Author) FFUP; Luisa Peixe (Author) FFUP; Willems, RJL (Author) Other; Corander, J (Author) Other; Gonzalez Candelas, FG (Author) Other; Baquero, F (Author) Other; Coque, TM (Author) Other

Journal

Title: Environmental Microbiology

Vol. 21

Pages: 3046-3062

ISSN: 1462-2912

Publisher: Wiley-Blackwell

Indexing

ISI Web of Knowledge - 1 Citation

Scopus - 2 Citations

Other information

Authenticus ID: P-00Q-TKK

DOI: 10.1111/1462-2920.14702

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 17