Analysis of global genomes revealed that strains carrying T6SS are more common in human gastroenteritis than in environmental sources and are often phylogenetically related.

is an emerging human enteric pathogen. However, the genomic features and virulence genes of strains from human gastroenteritis and other sources have not been fully elucidated. Here, we conducted a genomic analysis of 565 global strains isolated from different sources, including 261 strains isolated from faecal samples of gastroenteritis patients, of which 18 genomes were sequenced in this study. The presence of bacterial virulence genes and secretion systems in strains from different sources was compared, and the phylogenetic relationship of strains was assessed based on the core genome. The complete genome of strain A20-9 isolated from a gastroenteritis patient was obtained in this study, from which 300 putative virulence factors and a T4SS-encoding plasmid, pAC, were identified. Genes encoding T4SS were also identified in a novel genomic island, ACI-1, from other T4SS-positive strains. The prevalence of T4SS was significantly lower in strains from gastroenteritis patients than in environmental strains (3 %, <0.0001 vs 14 %, <0.01). Conversely, the prevalence of T6SS was significantly higher in strains isolated from gastroenteritis patients than in environmental strains (25 %, <0.05 vs 13  %, <0.01). Four phylogenetic clusters were formed based on the core genome of 565 . strains, and strains carrying T6SS often showed close phylogenetic relationships. T3SS, aerolysin and thermostable cytotonic enterotoxin were absent in all 565 . strains. Our findings provide novel information on the genomic features of and suggest that T6SS may play a role in -induced human gastroenteritis.