Large-scale genomic analysis reveals the distribution and diversity of Type VI Secretion Systems in Escherichia coli
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The type VI secretion system (T6SS) is a versatile nanomachine that injects effectors into target cells, playing a role in bacterial competition and virulence. While widespread in Gram-negative bacteria, T6SS prevalence varies across species and strains, and its distribution in Escherichia coli remains underexplored despite E. coli being an important intestinal (IPEC) and extraintestinal (ExPEC) pathogen. Here, we examined the prevalence and distribution of T6SS subclasses (T6SS i ) across 131610 E. coli genomes, which we annotated for clinical relevance. T6SS genes were identified while focusing on the three subclasses of T6SS i gene clusters known to be present in E. coli: T6SS i1 , T6SS i2 , and T6SS i4b . Across phylogenetic groups, T6SS i1 was broadly present, while T6SS i2 showed associations with B1, B2, and G, and T6SS i4b was rare. T6SS i1 was primarily associated with IPEC, and T6SS i2 with ExPEC. Even clearer patterns emerged at the sequence type (ST) level or when strains were further categorized into pathovars. For example, both the most dominant ExPEC and IPEC ST (ST131 and ST11, respectively) displayed niche-specific T6SS trends, with non-complete T6SSs being more associated with humans. In a final step, we evaluated the co-occurrence of T6SSs with other virulence-associated genes (VAGs) and multidrug resistance (MDR). This analysis confirmed the association of T6SS i1 and T6SS i2 with IPEC- and ExPEC-associated VAGs, respectively, and revealed a negative correlation between complete T6SS i subclasses and MDR. Together, our work provides a comprehensive overview of the diversity of T6SSs across E. coli , shedding more light on their potential contribution to pathogenicity in this species.
Importance
Our study represents a large-scale analysis of T6SSs across one of the most comprehensive collections of E. coli genomes to date. In doing so, we updated several misconceptions on T6SSs distribution and other genomic properties of E. coli strains, which originated from smaller scale studies and were subsequently extrapolated in the literature. This includes the prevalence and distribution of T6SS i subclasses across phylogenetic groups (e.g., T6SS i2 is not prevalent in phylogroup D), the association of specific virulence factors with IPEC and/or ExPEC (e.g., hemolysin A is more often associated with IPEC and not a typical ExPEC characteristic), and characteristics of pathogenic STs (e.g., ST131 displays distinct genomic properties based on its environmental niche). As such, this study not only advances our understanding of T6SS in E. coli , but also serves as a valuable resource for future studies on the clinical relevance and distribution of other genetic elements.
