Phylogenetic Analysis of Serogroup O5 Vibrio cholerae that Caused Successive Cholera Outbreaks - Guangdong Province, China, 2020-2021

Gastroenteritis caused by non-O1/non-O139 exhibited an increasing trend in recent years in China. Whole genome sequence (WGS) data could play an important role both in the identification of the outbreaks and in the determination of the serogroup. Here, we present the employment of WGS data in the investigation of two outbreaks caused by non-O1/non-O139 in Guangdong, China, 2020-2021. We obtained the whole genome sequence of 66 strains isolated in two outbreaks with next generation sequencing technology. We retrieved the publicly available WGS data of non-O1/non-O139 from public database. We used a pipeline integrated in China Pathogen Identification Net (PIN) to complete the phylogenetic analysis. Two outbreaks caused by non-O1/non-O139 were identified using WGS data. These strains were determined as serogroup O5. Type 3 and 6 secretion systems were detected in these serogroup O5 strains. These serogroup O5 strains belonged to sequence type (ST) 88. Our analysis indicated the risk of non-O1/non-O139 leading to outbreaks of diarrheal diseases. The application of genomic data played an important role in the identification of the serogroup of non-O1/non-O139 in the lack of antiserum, which gave an example of the application of genome data in disease surveillance and public health emergency response.