<i>Vibrio cholerae</i>genomic diversity within and between patients

Levade, Inès; Terrat, Yves; Leducq, Jean-Baptiste; Weil, Ana A.; Mayo-Smith, Leslie M.; Chowdhury, Fahima; Khan, Ashraful Islam; Boncy, Jacques; Buteau, Josiane; Ivers, Louise C.; Ryan, Edward T.; Charles, Richelle C.; Calderwood, Stephen B.; Qadri, Firdausi; Harris, Jason B.; LaRocque, Regina C.; Shapiro, Ben

doi:10.1101/169292

Cited by 5 publications

(2 citation statements)

References 84 publications

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“…To exclude the possibility of mixed infection of ctxAB positive and negative strains, we selected three colonies for each sample to test the presence/absence of ctxAB by PCR amplification separately. No sample showed co-existence of both ctxAB positive and negative colonies in all 119 Hangzhou samples, which was consistent with a previous report of low within host diversity of V. cholerae (zero to three SNPs within each patient) [30]. Finally, the samples of ctxAB negative and tcpA positive were defined as CNTP strains.…”

Section: Cholerae Isolatessupporting

confidence: 89%

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

et al. 2020

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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.

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Section: Cholerae Isolatessupporting

confidence: 89%

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

et al. 2020

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“…2C). Spillover between host and environment, as well as host colonization (17) or host-to-host transmission cycles (14), can cause bottlenecks that dramatically reduce the bacterial (population genetic measure) effective population size (N e ). Indeed, V. cholerae demographic history, inferred from the Bayesian time-scaled phylogeny (18), showed two population bottlenecks in mid-2012 and 2014 (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

Toxigenic Vibrio cholerae evolution and establishment of reservoirs in aquatic ecosystems

Mavian

Paisie

Alam

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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The spread of cholera in the midst of an epidemic is largely driven by direct transmission from person to person, although it is well-recognized thatVibrio choleraeis also capable of growth and long-term survival in aquatic ecosystems. While prior studies have shown that aquatic reservoirs are important in the persistence of the disease on the Indian subcontinent, an epidemiological view postulating that locally evolving environmentalV. choleraecontributes to outbreaks outside Asia remains debated. The single-source introduction of toxigenicV. choleraeO1 in Haiti, one of the largest outbreaks occurring this century, with 812,586 suspected cases and 9,606 deaths reported through July 2018, provided a unique opportunity to evaluate the role of aquatic reservoirs and assess bacterial transmission dynamics across environmental boundaries. To this end, we investigated the phylogeography of both clinical and aquatic toxigenicV. choleraeO1 isolates and show robust evidence of the establishment of aquatic reservoirs as well as ongoing evolution ofV. choleraeisolates from aquatic sites. Novel environmental lineages emerged from sequential population bottlenecks, carrying mutations potentially involved in adaptation to the aquatic ecosystem. Based on such empirical data, we developed a mixed-transmission dynamic model ofV. cholerae, where aquatic reservoirs actively contribute to genetic diversification and epidemic emergence, which underscores the complexity of transmission pathways in epidemics and endemic settings and the need for long-term investments in cholera control at both human and environmental levels.

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Population Analysis of Vibrio cholerae in Aquatic Reservoirs Reveals a Novel Sister Species ( Vibrio paracholerae sp. nov.) with a History of Association with Humans

Islam

Nasreen

Kirchberger

et al. 2021

Appl Environ Microbiol

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Most efforts to understand the biology of Vibrio cholerae have focused on a single group, the pandemic-generating lineage harbouring the strains responsible for all known cholera pandemics. Consequently, little is known about the diversity of this species in its native aquatic environment. To understand the differences in the V. cholerae populations inhabiting regions with a history of cholera cases and those lacking such a history, a comparative analysis of population composition was performed. Little overlap was found in lineage compositions between those in Dhaka (cholera endemic) located in the Ganges delta, and of Falmouth (no known history of cholera), a small coastal town on the United States east coast. The most striking difference was the presence of a group of related lineages at high abundance in Dhaka which was completely absent from Falmouth. Phylogenomic analysis revealed that these lineages form a cluster at the base of the phylogeny for the V. cholerae species, sufficiently differentiated genetically and phenotypically to form a novel species. A retrospective search revealed that strains from this species have been anecdotally found from around the world and were isolated as early as 1916 from a British soldier in Egypt suffering from choleraic diarrhoea. In 1935 Gardner and Venkatraman unofficially referred to a member of this group as Vibrio paracholerae . In recognition of this earlier designation, we propose the name Vibrio paracholerae sp. nov. for this bacterium. Genomic analysis suggests a link with human populations for this novel species and substantial interaction with its better-known sister species. Importance Cholera continues to remain a major public health threat around the globe. Understanding the ecology, evolution, and environmental adaptation of the causative agent Vibrio cholerae and tracking the emergence of novel lineages with pathogenic potential are essential to combat the problem. In this study, we investigated the population dynamics of Vibrio cholerae in an inland locality which is known as endemic for cholera and compared with that of a cholera free coastal location. We found the consistent presence of the pandemic generating V. cholerae in cholera-endemic Dhaka and an exclusive presence of a lineage phylogenetically distinct from other V. cholerae . Our study suggests that this lineage represents a novel species having pathogenic potential and a human link to its environmental abundance. The possible association with human population, co-existence and interaction with toxigenic V. cholerae in the natural environment make this potential human pathogen an important subject for future studies.

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Vibrio choleraegenomic diversity within and between patients

Cited by 5 publications

References 84 publications

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

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

Toxigenic Vibrio cholerae evolution and establishment of reservoirs in aquatic ecosystems

Population Analysis of Vibrio cholerae in Aquatic Reservoirs Reveals a Novel Sister Species ( Vibrio paracholerae sp. nov.) with a History of Association with Humans

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