Virulence gene profiles of extraintestinal pathogenic Escherichia coli (ExPEC) from Zambia: a secondary in silico study

This secondary in silico study analysed 36 Escherichia coli draft genome assemblies from Zambia to characterise the virulence gene profiles of extraintestinal pathogenic E. coli (ExPEC) and to relate them to mobilome proxies, namely plasmid replicons and prophage content. All assemblies met plausibility thresholds for E. coli (1–17 contigs; 4.85–5.77 Mb; GC 50.47–50.96%), and species identity was confirmed by average nucleotide identity to the E. coli type strain (96.6–98.9%). Using the Achtman seven-locus multilocus sequence typing scheme applied to the reads, 35 of 36 genomes were assigned a sequence type (ST), and one remained untypeable at a single locus. The most frequent type was ST69 (9/36) rather than the globally dominant ST131 (6/36), followed by ST405 (5/36) and ST617 (5/36). Phylogroup D was most frequent (12/36), followed by the commensal-associated phylogroup A (8/36) and the pandemic phylogroup B2 (6/36). Classical intestinal-pathotype hallmarks (stx1, stx2, eae, bfpA, ipaH) were not detected. In contrast, ExPEC-associated markers were common, including iutA (27/36), iss2 (26/36), fyuA (24/36), kpsM (23/36) and ompT (18/36), with a high within-genome burden (median approximately 193 loci; range 173–251). Gene-based rules classified 19 of 36 genomes as ExPEC and 2 as enteroaggregative E. coli, and source-informed analysis identified uropathogenic, neonatal-meningitis-associated and sepsis-associated subpathotypes. IncF-family replicons predominated, sitABCD occurred in both chromosomal and IncF-plasmid contexts, and iss2 was recurrently prophage-associated. These findings indicate that extraintestinal virulence in this population is distributed and modular rather than confined to ST131. This virulence is carried across diverse lineages and phylogroups, including classically commensal backgrounds, and is mobilised by plasmids and prophages. Ultimately, these data provide a baseline for the genomic surveillance of virulent E. coli in Zambia.