Enterococcus cecorum genome sequencing and assembly of French avian clinical isolates. undefined

Over the past twenty years, Enterococcus cecorum has become an increasingly important opportunistic pathogen in poultry. A collection of hundred French avian clinical isolates collected from 2007 to 2017, four avian commensal isolates, six human isolates and eight isolates from other countries project was analysed. The aims were to define the extent of genetic diversity of circulating clinical strains of E. cecorum in French flocks and detect genes associated with antimicrobial resistance. The overall genetic diversity of E. cecorum was investigated by pan-genome analysis. Moreover, ten genomes were sequenced in long and short reads, allowing the reconstruction of ten high-quality genome assemblies.