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by claude@2026-07, 2026-07-04
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This secondary in silico study analyzed 36 Escherichia coli draft genome assemblies from Zambia to profile ExPEC-associated virulence genes and to contextualize these with mobilome proxies including plasmid replicons and predicted prophage content. Most genomes passed assembly plausibility thresholds, and MLST assigned 25/36 strains to sequence types, with the most frequent being ST131, ST405, ST617 and ST69; a key limitation was that 11/36 remained unassigned due to ambiguous allele calls (mainly recA). Across the dataset, screening identified a broad virulence repertoire (1,001 distinct loci; median ~193 per genome), while classical IPEC/Shiga toxin and key adhesion markers (stx1/stx2, eae, bfpA, ipaH) were not detected; ExPEC-associated markers such as iutA, iss2, fyuA, kpsM, and ompT were common. Plasmid replicons frequently belonged to IncF-family backbones, prophage content was widespread (3–7 regions/genome), and prophage-linked signals involved iron acquisition (sit) and serum survival (iss2) with no Shiga-toxin genes detected. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.
Abstract
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.
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Abstract
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.
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