| Background Cholera is a food-borne disease that causes acute diarrhea and dehydration in patients.There has been seven global pandemics in human modern history,causing huge losses to the lives and health of people in developing countries and regions.The pathogen of cholera,Vibrio cholerae,mainly exists in the water environment such as estuaries in nature,and infects humans by polluted water and aquatic products such as shrimp and crabs.There are three spread patterns of V.cholerae in the human population,the first is pandemic,caused by the classical and EI Tor biotypes of V.cholerae in the O1 serogroup,the second is endemic or epidemic,and the third is sporadic,which is usually associated with environmental strains,and the pathogenicity is weaker than the first two.Compared with pandemic V.cholerae,the endemic strains,which are generally less infectious,pathogenic and are easily neglected but continually infecting humans,and some studies have pointed out that the V.cholerae of second pattern has spread worldwide and has a potential disease risk that needs to pay attention to,in which most of them were non-toxigenic V.cholerae.Non-toxigenic V.cholerae refers to the V.cholerae that cannot produce cholera toxin due to the lack of ctxAB genes which encode the cholera toxin.The disease risk of non-toxigenic V.cholerae will rise if the toxin co-regulator pilus（TCP）,which was encoded by tcpA gene and helps V.cholerae to colonize the human intestine,exists in their genomes.The V.cholerae in Hangzhou conformed to the second pattern,and the main population was non-toxigenic V.cholerae.From 2001 to 2018,the number of cases caused by V.cholerae in Hangzhou generally showed a tendency of first increased,decreased later,and then increased again.In this study,we conducted a genomic epidemiology study of V.cholerae in Hangzhou,in order to clarify the population diversity of V.cholerae and its dynamics which would provide help for disease prevention.Results and discussion 1 The population shift and its genetic mechanism of V.cholerae in Hangzhou In this study,we performed whole-genome sequencing of 88 V.cholerae isolates from Hangzhou from 2013 to 2018,which were included in the dataset together with 119 isolates from 2001 to 2012 used in previous study and 1573 publicly published genomes.From 2001 to 2018,the epidemic of V.cholerae in Hangzhou can be divided into two waves（named wave1 and wave2）,both caused by ctxAB gene negative and tcpA positive non-toxigenic V.cholerae,the main pathogenic lineages were L3 b and L9,and we found that the L3 b and L9 lineages jointly led to wave1 and wave2,but the dominant lineage in different waves changed from L3 b to L9.During wave1,119 strains were isolated,of which 82 strains were L3 b strains,accounting for 69%,and 88 strains were isolated during wave2,including 44 L9 strains,accounting for 50%.We further found that in wave2,the L9 lineage acquired type I tcp F genes,which can improve the colonization efficiency of V.cholerae in the human gut and may play a key role in the shift of dominant populations.2 Non-toxigenic V.cholerae lineage strains can acquire CTXφ phage to form toxigenic strains We found that the ratio of cholera toxin producing V.cholerae was surprisingly 21% in the L3 b and L9 lineages,and we also found the appearance of toxigenic L3 b strains in Hangzhou.In order to detect the origin of toxigenic V.cholerae in the L3 b lineage in Hangzhou,we detected the genetic mechanism of integration of the ctxAB gene in the representative genomes and found that they acquired CTXφ phages carrying the ctxAB gene,rather than the ctxAB gene alone integrated in the genomes,further phylogenetic analysis of CTXφs showed that Hangzhou L3 b.4 CTXφs had high homology with CTXφs in the pandemic lineage L2,which means that the change from non-toxigenic to toxigenic V.cholerae in the Hangzhou L3 b lineage was caused by the integration of the CTXφs of the pandemic group into their genome via horizontal gene transfer,rather than the evolution from pre-CTXφs carried in other L3 b strains.Conclusion We used genomic epidemiological methods to analyze the composition and dynamic changes of V.cholerae populations in Hangzhou from 2001 to 2018.We found that the main epidemic lineages in Hangzhou were L3 b and L9,but after 2013,the dominant population shifted from L3 b to L9,we found that the tcp F gene was a factor related with the shift of the dominant population,which provides new clues for the surveillance work and epidemic prediction of V.cholerae.In addition,we found that 21% of the toxigenic strains were present in the L3 b and L9 lineages,and we detected the genetic mechanisms by which the CTXφs were acquired.L3 b and L9 lineage strains are capable of causing long-term epidemics and have spread worldwide,indicating that they pose a potential risk to public health.Our study provides insights into the genetic diversity,epidemic patterns and pathogenic mechanisms of strains of L3 b and L9 lineages,which provides a theoretical basis for future disease prevention and control work. |
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