Emergence of hybrid Escherichia coli with dual disease manifestations in intestinal and extraintestinal niches-Raw Data

Escherichia coli, a significant zoonotic pathogen, continuously evolves to produce hybrid strains with diverse pathogenic characteristics, threatening public health. Hybrid E. coli strains can cause multiple diseases in various tissues within a single individual or among different hosts with diverse genetic backgrounds. These strains have been reported to exhibit higher virulence, enhanced infectiousness, and increased resistance to environmental clearance. Here we identified a hybrid aEPEC/ExPEC isolate, PE164, from the blood and bloody stool of a piglet with severe diarrhea, which exhibited both intestinal and extraintestinal pathogenic traits. Monitoring the emergence of PE164-like hybrids in porcine-derived E. coli is crucial for animal production and public health safety. Phylogenetic and virulence gene analyses of nearly 300 clinical isolates from diseased pigs revealed eight hybrid strains categorized into four types, with significant variations in pathogenicity identified by in vitro and in vivo models. Notably, two O108 isolates, PE150 and PE164, were classified as highly virulent strains. A fused gene cluster of colanic acid and O108 antigen biosynthesis (CAO108) was identified as a key determinant of their extraintestinal pathogenicity, raising concerns about O-antigens linked to other exopolysaccharide components to create new high virulence factors. Additionally, the type III secretion system (T3SS), a classic pathway for pathogenic E. coli to optimally colonize the host gut, enhanced bacterial immune evasion and contributed to the extraintestinal pathogenicity of PE164. These findings underscore the prevalence of hybrid pathogenic E. coli strains in pigs, presenting new challenges for disease control.