Genome-wide investigation of outbreak-associated Vibrio cholerae in Gujarat, India identifies antimicrobial resistance genes, virulence determinants, and mobile genetic elements.

内容摘要

This study investigates the 2024 cholera outbreak in Gujarat, India, utilizing combined whole-genome analysis of clinical Vibrio cholerae isolates and wastewater surveillance. A total of, 69 V. cholerae isolates were recovered from affected patients, predominantly belonging to the O1 serogroup (51 isolates). Antimicrobial susceptibility test (AST) of 34 isolates revealed complete resistance to ampicillin and partial resistance to cotrimoxazole, whereas all isolates were susceptible to doxycycline, ciprofloxacin, chloramphenicol, tetracycline, and gentamicin. Whole-genome sequencing of 20 selected isolates revealed that the isolates belong to the seventh pandemic El Tor (7PET) lineage, sequence type ST69. Phylogenomic analyses using a multi-method approach, core genes, Composition Vector (CV) Tree, SNPs, and multilocus sequence typing (MLST) showed tight clustering with limited diversity among the isolates. All isolates contained 13-15 antimicrobial resistance genes, with high consistency between genotype-phenotype for most antibiotics, although discordance was observed for ciprofloxacin, cotrimoxazole, and chloramphenicol. Sixteen genes were identified as virulence factors, and 11 isolates also had ctxA/ctxB. All isolates also had two to four integrative conjugative elements (ICEs) containing antimicrobial resistance genes (ARGs) and important Vibrio cholerae pathogenicity islands (VPI-1, VPI-2) and Vibrio cholerae seventh pandemic islands (VSP-1, VSP-2). The pangenome analysis highlights extensive genomic flexibility within species, likely driven by horizontal gene transfer and ecological adaptation; however, further outbreak-specific investigations are required to determine their direct role in current outbreak. The detection of ctxA-positive signals in wastewater, 20% (28/140) of the samples, suggests a possible surveillance signal during the outbreak. These results highlight the presence of antimicrobial-resistant 7PET O1 El Tor strains in Gujarat outbreaks and support continued genomic monitoring to guide focused public health interventions in endemic areas. Furthermore, this study also underscores the importance of wastewater surveillance for monitoring V. cholerae.