Genomic characterization of the type VI secretion system in extraintestinal pathogenic <i>Escherichia coli</i>

ABSTRACT Extraintestinal pathogenic Escherichia coli (ExPEC) is a distinctive group of Escherichia coli strains capable of causing infections outside the gastrointestinal tract of humans and certain animals. ExPEC includes the pathotypes avian pathogenic E. coli (APEC), neonatal meningitis E. coli (NMEC), sepsis-associated E. coli (SEPEC), and uropathogenic E. coli (UPEC). These pathotypes share multiple virulence factors, including the Type VI Secretion System (T6SS), a nanomachinery that has been described as important for E. coli pathogenesis. In this study, we applied genome-wide association analysis to evaluate the prevalence and evolution of T6SS across 399 ExPEC genomes, including new NMEC ( n = 78) and APEC ( n = 68) sequences ( n = 146). Our findings suggest that among ExPEC, T6SS is more prevalent in NMEC and is more conserved between NMEC and APEC in terms of loci organization and gene content, whereas greater structural variation was observed in SEPEC and UPEC. Additionally, our findings indicate an inverse relationship between T6SS presence and antimicrobial resistance, suggesting that harboring both may incur a fitness cost. Our study provides new insights into the ecological and evolutionary pressures shaping the distribution of T6SS among ExPEC lineages and supports its relevance for further in vitro investigation regarding its expression and function in Escherichia coli . IMPORTANCE Extraintestinal pathogenic Escherichia coli (ExPEC) is responsible for severe infections in humans and animals. However, the distribution of the Type VI Secretion System (T6SS) among these pathotypes remains unclear. The T6SS has been implicated in E. coli pathogenicity, but its prevalence and structural diversity across ExPEC are still poorly understood due to the lack of genomes available from some pathotypes, especially neonatal meningitis E. coli (NMEC) strains. This study introduces new NMEC and avian pathogenic E. coli (APEC) genomes among a total of 399 ExPEC genomes analyzed, including sepsis-associated E. coli (SEPEC) and uropathogenic E. coli (UPEC). Our findings indicate the T6SS as a conserved and predominant virulence factor in NMEC compared with other pathotypes. Moreover, an inverse association between T6SS presence and antimicrobial resistance suggests a potential fitness trade-off that may influence ExPEC evolution. These findings advance our understanding of T6SS in ExPEC and identify this secretion system as a relevant target for future functional and mechanistic studies.