Genomic analyses of enteroinvasive Escherichia coli revealed the circulation of conjugative virulence plasmids and emergence of novel clones

Abstract

Enteroinvasive Escherichia coli (EIEC) is a diarrhoeagenic E. coli pathotype that shares key virulence traits with Shigella, including the invasion plasmid (pINV). In Thailand, an outbreak caused by the EIEC serotype O8:H19—the first reported in the country—occurred in 2023, affecting over 150 patients. To elucidate the emergence, clinical relevance, and epidemiological distribution of EIEC in Thailand, we conducted a comprehensive investigation. We isolated and genomically characterised 63 isolates, comprising 28 EIEC (eight serotypes, including O96:H19 from a 2024 outbreak) and 35 Shigella (25 S. sonnei and 10 S. flexneri), along with 85 global reference strains. Comparative genomics revealed that the 2023 and 2024 EIEC outbreak isolates, along with a novel OX18:H25 EIEC lineage, harboured highly similar pINV plasmids with conserved invasion genes and complete conjugation elements. These isolates retained several biochemical traits that were more typical of commensal E. coli than classical EIEC. Limited chromosomal genome reduction—a hallmark of Shigella— was observed, which suggests that these lineages are in an early stage of adaptation toward a pathogenic lifestyle. Phylogenomic analysis showed that OX18:H25 is closely related to livestock-associated E. coli, supporting the hypothesis that pINV was recently acquired via horizontal gene transfer. These findings highlight the active circulation of putatively conjugative virulence plasmids among E. coli populations and the ongoing emergence of novel EIEC clones with epidemic-inducing potential.