Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages

Abstract

Non-toxigenic Vibrio cholerae isolates have been found associated with diarrheal disease globally, however, the global picture of non-toxigenic infections is largely unknown. Among non-toxigenic V. cholerae, ctxAB negative, tcpA positive (CNTP) isolates have the highest risk of disease. From 2001 to 2012, 71 infectious diarrhea cases were reported in Hangzhou, China, caused by CNTP serogroup O1 isolates. We sequenced 119 V. cholerae genomes isolated from patients, carriers and the environment in Hangzhou between 2001 and 2012, and compared them with 850 publicly available global isolates. We found that CNTP isolates from Hangzhou belonged to two distinctive lineages, named L3b and L9. Both lineages caused disease over a long time period with usually mild or moderate clinical symptoms. Within Hangzhou, the spread route of the L3b lineage was apparently from rural to urban areas, with aquatic food products being the most likely medium. Both lineages had been previously reported as causing local endemic disease in Latin America, but here we show that global spread of them has occurred, with the most likely origin of L3b lineage being in Central Asia. The L3b lineage has spread to China on at least three occasions. Other spread events, including from China to Thailand and to Latin America were also observed. We fill the missing links in the global spread of the two non-toxigenic serogroup O1 V. cholerae lineages that can cause human infection. The results are important for the design of future disease control strategies: surveillance of V. cholerae should not be limited to ctxAB positive strains.

Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae

“…The case in the Chaco region during 2005, which was caused by non-epidemic V. cholerae O1 of the MX-2 lineage 7 and failed to cause epidemic cholera, exemplifies this point. Similar observations have recently been made in China 48 . Relative risk of V. cholerae lineages should be accounted for in the magnitude of epidemic preparedness responses to such outbreaks, as is now being done in Argentina.…”

“…1 d, 4a, b ; Supplementary Data 3 ). Thus, we placed these into context with a more diverse collection of V. cholerae sequences 7 , together with genomes from a recently-published study of non-epidemic V. cholerae O1 in China 48 , and then calculated a pangenome using these sequences (Fig. 4 ).…”

Emergence of Vibrio cholerae O1 Sequence Type 75, South Africa, 2018–2020

“…We further compared the ST75 isolates from South Africa with a larger global collection of 144 ST75, or closely related ST169, ST170, and ST182, genomes (Appendix 2), and constructed a maximum-likelihood phylogeny by using 49,540 SNPs (Figure). Our phylogenetic analysis showed that the 7 isolates from South Africa clustered in the L3b.1 clade, defined by H. Wang et al (9), with a maximum pairwise distance of 22 SNPs. Isolates from Limpopo Province had a maximum pairwise distance of 1-6, but KwaZulu-Natal Province isolates had no SNP differences.…”

Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis

“…All the software settings used were the default parameters, unless otherwise stated. A gene/segment was considered present if the overall hit coverage and identity were both ≥70 % [ 48 ].…”