Objective To investigate the genomic characteristics of toxigenic Vibrio cholerae O139 strains in Fujian Province, and provide evidence for the prevention and control of cholera.

Methods From 2008 to 2022, toxigenic Vibrio cholerae O139 strains were collected from Fujian province. Minimal inhibit concentration (MIC) was detected for drug susceptibility testing. Whole-genome sequences of the strains were obtained by next-generation sequencing technology. The virulence genes and drug resistance genes of the strains were predicted by using online websites.The core genome sequences were analyzed by using tools such as Snippy, Prokka, and online analysis platforms and the data from global V. cholerae genome database of the United States National Center for Biotechnology Information（NCBI） for core genome multilocus sequence typing (cgMLST) and core genome single-nucleotide polymorphism (cgSNP) analysis.

Results All the 13 Vibrio. cholerae O139 strains collected in this study belonged to ST69. The cgMLST analysis revealed that all the 13 strains were in same cluster except strain FJ2008026 showing a close relationship with 2 Vibrio cholerae O1 strains isolated from Hangzhou. The cgSNP analysis classified the strains into two different genetic lineages, of which FJ2008026 was in the same genetic lineage as the strains from Shanghai in 2005 according to the NCBI database. The remaining 12 strains were in another genetic lineage. Overall, combined with the results of cgMLST and cgSNP analysis, the genetic relationship among the 13 strains of toxigenic Vibrio cholerae O139 collected in this study were close. The drug susceptibility test showed that the resistance phenotypes to quinolone and aminoglycoside were fully consist with the presence of resistance genes in the strains. However, the resistance phenotypes to other antibiotics were not fully consist with the presence of resistance genes in the strains. Unknown resistance mechanisms were also found.The strains all carried virulence genes such as ctxAB, ace, tcpA, rstR, rtxA, rtxC, hlyA-El, mshA, toxR, toxS, toxT, vasH, vasX, vgrG, as well as VSP-1, VSP-2 virulence islands, and type VI secretion system (T6SS). Notably, 7 Vibrio cholerae O139 strains isolated in 2014 and 2022 possessed the characteristic gene VC2346 associated with the seventh pandemic.

Conclusion The genomic features of toxigenic Vibrio cholerae O139 isolates in Fujian province were highly clonal and showed sereve drug resistance. The long-term distribution of such V. cholerae O139 starins in Fujian province, especially in coastal area, might cause cholera outbreaks. It is necessary to strengthen the surveillance for Vibrio cholerae O139.