Origins of the current seventh cholera pandemic

Hu, Dalong; Liu, Bin; Feng, Lu; Ding, Peng; Guo, Xi; Wang, Min; Cao, Bihua; Reeves, Peter R.; Wang, Lei

doi:10.1073/pnas.1608732113

Cited by 171 publications

(150 citation statements)

References 54 publications

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“…S, VSP-II with VC0495-VC0498 deletion; T, typical VSP-II; V, novel variant identified in this study; À, no genomic island was found at the site between VC0489 and VC0517. and additional mutations before it became the seventh pandemic in 1961 (6). The typical VSP-II was found to be dominant in wave 1 and 2 strains, but was not found in all 96 strains of wave 3.…”

Section: Discussionmentioning

confidence: 95%

Analysis of Vibrio seventh pandemic island II and novel genomic islands in relation to attachment sequences among a wide variety of Vibrio cholerae strains

Nguyen

Pham

Higa

et al. 2018

Microbiology and Immunology

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Vibrio cholerae O1 El Tor, the pathogen responsible for the current cholera pandemic, became pathogenic by acquiring virulent factors including Vibrio seventh pandemic islands (VSP)‐I and −II. Diversity of VSP‐II is well recognized; however, studies addressing attachment sequence left (attL) sequences of VSP‐II are few. In this report, a wide variety of V. cholerae strains were analyzed for the structure and distribution of VSP‐II in relation to their attachment sequences. Of 188 V. cholerae strains analyzed, 81% (153/188) strains carried VSP‐II; of these, typical VSP‐II, and a short variant was found in 36% (55/153), and 63% (96/153), respectively. A novel VSP‐II was found in two V. cholerae non‐O1/non‐O139 strains. In addition to the typical 14‐bp attL, six new attL‐like sequences were identified. The 14‐bp attL was associated with VSP‐II in 91% (139/153), whereas the remaining six types were found in 9.2% (14/153) of V. cholerae strains. Of note, six distinct types of the attL‐like sequence were found in the seventh pandemic wave 1 strains; however, only one or two types were found in the wave 2 or 3 strains. Interestingly, 86% (24/28) of V. cholerae seventh pandemic strains harboring a 13‐bp attL‐like sequence were devoid of VSP‐II. Six novel genomic islands using two unique insertion sites to those of VSP‐II were identified in 11 V. cholerae strains in this study. Four of those shared similar gene clusters with VSP‐II, except integrase gene.

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Section: Discussionmentioning

confidence: 95%

Analysis of Vibrio seventh pandemic island II and novel genomic islands in relation to attachment sequences among a wide variety of Vibrio cholerae strains

Nguyen

Pham

Higa

et al. 2018

Microbiology and Immunology

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“…During the current seventh cholera pandemic El Tor (7PET), at least three independent but temporally overlapping waves of global transmission have been identified by phylogenetic analyses in Africa [10–13], with at least 13 re-introduction events (T1-13) causing epidemics, each genetic lineage probably representing an independent introduction event to that location [4, 14]. Recent phylogenetic analysis of isolates associated with cholera outbreaks in DRC between 2006 and 2014 showed that all of them belonged to the 7PET, wave 3, T10 east African sub-lineage [4].…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis of pathogenic isolates ofVibrio choleraefrom eastern Democratic Republic of the Congo (2014-2017)

Irenge

Ambroise

Mitangala³

et al. 2019

Preprint

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AbstractBackgroundOver the past recent years, Vibrio cholerae has been associated with outbreaks in Sub Saharan Africa, notably in Democratic Republic of the Congo (DRC). This study aimed to determine the genetic relatedness of isolates responsible for cholera outbreaks in eastern DRC between 2014 and 2017, and their potential spread to bordering countries.Methods/Principal findingsPhenotypic analysis and whole genome sequencing (WGS) were carried out on 78 clinical isolates of V. cholerae associated with cholera in eastern provinces of DRC between 2014 and 2017. SNP-based phylogenomic data show that most isolates (73/78) were V. cholerae O1 biotype El Tor with CTX-3 type prophage. They fell within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and were contained in the introduction event (T)10 in East Africa. These isolates clustered in two sub-clades corresponding to Multiple Locus Sequence Types (MLST) profiles ST69 and the newly assigned ST515, the latter displaying a higher genetic diversity. Both sub-clades showed a distinct geographic clustering, with ST69 isolates mostly restricted to Lake Tanganyika basin and phylogenetically related to V. cholerae isolates associated with cholera outbreaks in western Tanzania, whereas ST515 isolates were disseminated along the Albertine Rift and closely related to isolates in South Sudan, Uganda, Tanzania and Zambia. Other V. cholerae isolates (5/78) were non-O1/non-O139 without any CTX prophage and no phylogenetic relationship with already characterized non-O1/non-O139 isolates.Conclusions/SignificanceCurrent data confirm the association of both DRC O1 7PET (T)10 sub-clades ST69 and ST515 with recurrent outbreaks in eastern DRC and at regional level over the past 10 years. Interestingly, while ST69 is predominantly a locally endemic sequence type, ST515 became adaptable enough to expand across DRC neighboring countries.Author’s summaryCholera is a severe diarrheal disease caused by the Gram-negative bacterium Vibrio cholerae. After originating in Asia, the disease spread across sub-Saharan Africa, notably Democratic Republic of the Congo. The aim of our study was to assess the transmission pattern of V. cholerae strains prevailing in eastern DRC, and determine their genetic relatedness to strains from other African countries and other parts of the world. Between 2014 and 2017, we isolated V. cholerae from fecal samples of patients with acute diarrhea in eastern DRC, and subsequently examined the DNA of the bacteria. The results show that they all clustered in two genetic groups (ST69 and ST515) falling within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and T10 introduction event in East Africa. The genetic signature of ST515 may be involved in its adaptation to environmental conditions found in eastern DRC, and contribute to its extended geographic distribution. Indeed, unlike the locally endemic ST69, ST515 is spreading extensively through DRC cross-border countries such as South Sudan, Tanzania, Uganda and Zambia. This plainly justifies a regional strategy to strengthen the fight against cholera in eastern Africa.

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“…However, V. cholerae strains carrying group ET‐5, ET‐6 or ET‐7, which have been circulating in Indonesia and the Philippines, are devoid of RS1. One report found one V. cholerae El Tor wave 1 strain isolated in Indonesia in 1961 to lack RS1 , but this phenomenon is rare. Hassan et al .…”

Section: Discussionmentioning

confidence: 99%

“…It is well recognized that recombination events have rarely occurred in the V. cholerae seventh pandemic strains since 1961, when they emerged (33,36); however, recombination seems to have occurred frequently in preseventh pandemic strains (33). In this study, however, we found that a panel of CTX prophage regions with distinct structures is carried by a variety of pathogenic V. cholerae strains isolated from geographically diverse area, possibly indicating that CTX prophage region specific recombination events occurred at much higher frequencies than expected among pathogenic V. cholerae strains in the early wave 1 period.…”

Section: Discussionmentioning

confidence: 99%

Comparative analyses of CTX prophage region of Vibrio cholerae seventh pandemic wave 1 strains isolated in Asia

Pham

Nguyen

Iwashita

et al. 2018

Microbiology and Immunology

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Vibrio cholerae O1 causes cholera, and cholera toxin, the principal mediator of massive diarrhea, is encoded by ctxAB in the cholera toxin (CTX) prophage. In this study, the structures of the CTX prophage region of V. cholerae strains isolated during the seventh pandemic wave 1 in Asian countries were determined and compared. Eighteen strains were categorized into eight groups by CTX prophage region‐specific restriction fragment length polymorphism and PCR profiles and the structure of the region of a representative strain from each group was determined by DNA sequencing. Eight representative strains revealed eight distinct CTX prophage regions with various combinations of CTX‐1, RS1 and a novel genomic island on chromosome I. CTX prophage regions carried by the wave 1 strains were diverse in structure. V. cholerae strains with an area specific CTX prophage region are believed to circulate in South‐East Asian countries; additionally, multiple strains with distinct types of CTX prophage region are co‐circulating in the area. Analysis of a phylogenetic tree generated by single nucleotide polymorphism differences across 2483 core genes revealed that V. cholerae strains categorized in the same group based on CTX prophage region structure were segregated in closer clusters. CTX prophage region‐specific recombination events or gain and loss of genomic elements within the region may have occurred at much higher frequencies and contributed to producing a panel of CTX prophage regions with distinct structures among V. cholerae pathogenic strains in lineages with close genetic backgrounds in the early wave 1 period of the seventh cholera pandemic.

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Origins of the current seventh cholera pandemic

Cited by 171 publications

References 54 publications

Analysis of Vibrio seventh pandemic island II and novel genomic islands in relation to attachment sequences among a wide variety of Vibrio cholerae strains

Analysis of Vibrio seventh pandemic island II and novel genomic islands in relation to attachment sequences among a wide variety of Vibrio cholerae strains

Genomic analysis of pathogenic isolates ofVibrio choleraefrom eastern Democratic Republic of the Congo (2014-2017)

Comparative analyses of CTX prophage region of Vibrio cholerae seventh pandemic wave 1 strains isolated in Asia

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