Investigation and whole genome sequencing analysis of a cholera epidemic in Shaanxi, 2022

Objective To investigate the source of a cholera epidemic in Chenggu county, Shaanxi province in 2022.

Methods Case investigation and field hygienic survey were conducted, and local temperature and precipitation data were collected. Stool samples or anal swabs from the cases, dining companions and other diarrhea patients and samples of residual food, environmental water and aquatic products were collected for nucleic acid detection of V. cholerae and isolation and culture of V. cholerae. Serological test and mass spectrometry were conducted for the identification of isolated V. cholerae strains. Drug susceptibility testing was performed according to the guideline from national pathogenic bacterium identification network, virulence gene was detected by using the DNA extracted from the strains, The strains were sequenced using a second-generation sequencing platform, Virulence gene and drug resistance gene were predicted by using sequencing data, The sequencing data of previously isolated V. cholerae and domestic V. cholerae genome sequencing data from pubMLST were used for the analyses on core-genome multilocus sequence typing (cgMLST) and core-genome single nucleotide polymorphism (cgSNP).

Results Two strains of V. cholerae were isolated from 1 case and 1 carrier, both were V. cholerae O139, carrying ctxAB virulence genes, showing sensitivity to sulfonamides, carbapenems, three-generation cephalosporins, quinolones and β-lactaides and resistance to chloramphenicol, polymyxin, tetracycline and aminoglycoside. The cgMLST analysis after gene sequencing showed that the strains belonged to pandemic strain ST69, which had no association with previous cholera strains in Shaanxi. V. cholerae was not detected in 106 samples from the dining companions and other cases of diarrhea. In 96 water samples, 35 fish samples, 7 environmental samples and 7 livestock manure samples, 2 fish samples from Wenchuan River were positive for nucleic acid of V. cholerae hlyA and O139.The detection result of ctxAB virulence gene was negative.

Conclusion This epidemic was caused by V. cholerae O139 group, a pandemic strain, and the infection source might be the contamination of aquatic products, and high temperature, drought and others might be the associated factors.