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 ExPEC-associated virulence gene profiles and to contextualise these signals alongside mobilome proxies (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%). Using the Achtman 7-locus MLST scheme, 25/36 genomes were assigned a sequence type (ST), and 11/36 were unassigned due to ambiguous allele calls (predominantly affecting recA). The most frequent STs were ST131 (5/36), ST405 (4/36), ST617 (4/36) and ST69 (3/36), with additional lower-frequency STs including ST11176 and ST8767. Virulence screening detected a broad repertoire (1,001 distinct loci overall), with high within-genome burden (median ~193 virulence loci; range 173–251). Classical IPEC hallmarks (e.g., stx1/stx2, eae, bfpA, ipaH) were not detected, whereas ExPEC-associated markers were common, including iutA (27/36), iss2 (26/36), fyuA (24/36), kpsM (23/36), and ompT (18/36). Gene-based pathotype rules classified 19/36 genomes as ExPEC and 2/36 as EAEC, with 15/36 lacking sufficient defining markers. Plasmid replicon screening identified frequent IncF-family replicons (IncFII/IncFIB) alongside additional backbones (e.g., IncI1, IncHI2, IncY). Prophage prediction indicated widespread proviral content (3–7 regions/genome; median 6), with prophage-linked signals largely involving iron-acquisition (sit components) and serum-survival (iss2) loci, and no Shiga-toxin genes detected. Collectively, these findings provide a baseline view of ExPEC-associated virulence architectures in Zambian E. coli and highlight the potential contribution of mobile elements to the distribution of extraintestinal fitness traits.