Novel sequence type 2040 non-O1/non-O139 Vibrio cholerae from southern China: genomic and phenotypic features with molecular epidemiological implications

Non-toxigenic non-O1/non-O139 Vibrio cholerae (NOVC) are opportunistic aquatic pathogens that cause extraintestinal infections including bacteremia, particularly in patients with underlying comorbidities. The incidence of NOVC bacteremia has increased in coastal China, yet the genomic diversity and population structure of clinical NOVC isolates remain poorly defined. This study aimed to characterize a clinical NOVC isolate from southern China at both phenotypic and genomic levels.

We recovered a clinical NOVC isolate (HL2601) from a bloodstream infection case in Xiamen, China. Antimicrobial susceptibility was determined by broth microdilution and disk diffusion. Whole-genome sequencing was performed, followed by multilocus sequence typing (MLST), average nucleotide identity (ANI) analysis, core-genome phylogeny reconstruction, virulence and resistance gene profiling, and quantitative genome collinearity and structural variation analysis.

The isolate was confirmed as V. cholerae and assigned to a novel sequence type, ST2040. It lacked cholera toxin and toxin-coregulated pilus genes but harbored multiple alternative virulence determinants, including intact type II and type VI secretion systems, RTX toxin, hemolysins, and iron uptake systems. HL2601 was susceptible to all 11 tested antibiotics and clustered phylogenetically with extraintestinal clinical and environmental NOVC strains, suggesting a potential environmental reservoir origin.

These findings expand the known genomic diversity of clinical NOVC in China. They provide a genomic baseline for surveillance of emerging NOVC clones and inform empirical antibiotic selection for extraintestinal vibriosis in coastal regions.