Genomic and epidemiological insights into a non-toxigenic Vibrio cholerae O1 Ogawa from an autochthonous case in Brazil.

UNLABELLED: Vibrio cholerae remains a global health threat, driven by epidemic strains and sporadic infections associated with non-toxigenic lineages. We report the genomic characterization of a V. cholerae O1 Ogawa isolate (V86/24) recovered from a human case in Brazil (2024) with no travel history. We performed antimicrobial susceptibility testing, whole-genome sequencing (WGS), and in silico analyses, including SNP-based phylogenetic and pangenome analyses (V86/24 + 62 public genomes; total N = 63), resistome, and virulome. The isolate showed intermediate susceptibility to imipenem but was susceptible to other tested antimicrobials. WGS identified V86/24 as sequence type ST170, lineage L3b.2, sublineage MX-2. It harbors pathogenicity islands VPI-1 and VPI-2 but lacks seventh-pandemic-associated islands (VSP-1, VSP-2) and classical CTXΦ-associated toxin genes (ctxA, ctxB, ace, zot). Pangenome analysis revealed 4,485 gene clusters; V86/24 carried eight unique clusters primarily mapped to a prophage-like region. Resistome profiling identified the intrinsic varG metallo-β-lactamase gene. The virulome retained alternative virulence and colonization factors, including TCP/ACF, RTX/MARTX, and an extensive type VI secretion system. Phylogenetically, V86/24 clusters with ST170 isolates circulating in the Americas, distinctly separated from seventh-pandemic lineages. Non-toxigenic V. cholerae O1 lineages can cause human infection. These findings underscore the critical need for integrated genomic surveillance, including pangenome profiling, beyond classical toxigenicity markers to detect emerging risks prior to epidemic spread.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10096-026-05495-4.