A Study on the Geophylogeny of Clinical and Environmental Vibrio cholerae in Kenya

Kiiru, John; Mutreja, Ankur; Mohamed, Ahmed Abade; Kimani, R.; Mwituria, Joyce; Sanaya, Robert Onsare; Muyodi, Jane; Revathi, Gunturu; Parkhill, Julian; Thomson, Nicholas R.; Dougan, Gordon; Kariuki, Samuel

doi:10.1371/journal.pone.0074829

Cited by 34 publications

(35 citation statements)

References 32 publications

(45 reference statements)

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“…The average G+C content was determined to be 47.5 %. All DRC O1 isolates (n=73) were ompW+, RfbV+ , wbfZ-, tcpA El Tor , rstR El Tor , rtxC and VC2346+, which characterize 7PET O1 V. cholerae [11]. Five isolates were omp W+, Rfb V -, wbf Z - , tcpA-, rst R-, rstx C-, corresponding to V. cholerae non-O1/non-O139.…”

Section: Resultsmentioning

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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Section: Resultsmentioning

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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“…Previous large-scale genomic studies on the 7P (3, 4) analyzed only 28 African isolates and provided a preliminary view of overall disease transmission on the continent. Other genomic studies dealing with epidemics in Africa have been published, but these studies focused on the disease exclusively at national or regional levels (14)(15)(16)(17).…”

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confidence: 99%

Genomic history of the seventh pandemic of cholera in Africa

Weill

Domman

Njamkepo

et al. 2017

Science

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274

363

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The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa

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“…According to recent comparative genomics of African V. cholerae O1 El Tor, a third wave of global transmission of the cholera seventh pandemic reached Africa between 1989 and 1997 [16,23]. However, V. cholerae O1 isolations in Mozambique up to 2005 showed the second-wave genotype reference strain as the prevalent causative agent of epidemic cholera [6].…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, current cholera outbreaks in north central Mozambique are caused by a V. cholerae O1 no longer related to V. cholerae O1 B33, but genetically closer to third pandemic wave V. cholerae O1 CIRS 101. The latter was responsible for the 2010 Haiti epidemic and is currently the prevalent causative agent of cholera epidemics in the Indian subcontinent and worldwide [16,20,23].…”

Section: Discussionmentioning

confidence: 99%

Epidemic waves of cholera in the last two decades in Mozambique

Langa

Semá

Deus

et al. 2015

J Infect Dev Ctries

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Introduction: Africa is increasingly affected by cholera. In Mozambique, cholera appeared in the early 1970s when the seventh pandemic entered Africa from the Indian subcontinent. In the following decades, several epidemics were registered in the country, the 1997-1999 epidemic being the most extended. Since then, Mozambique has been considered an endemic area for cholera, characterized by yearly outbreaks occurring with a seasonal pattern.. At least three pandemic variants are thought to have originated in the Indian subcontinent and spread worldwide at different times. To understand the epidemiology of cholera in Mozambique, whether the disease re-emerges periodically or is imported by different routes of transmission, we investigated clinical V. cholerae O1 isolated during 1997-1999 and 2012-2014 epidemics. Methodology: By detecting and characterizing seven genetic elements, the mobilome profile of each isolate was obtained. By comparing it to known seventh pandemic reference strains, it was possible to discern among different V. cholerae O1 variants active in the country. Results: During 1997-1999, epidemic strains showed two different genetic profiles, both related to a pandemic clone that originated from India and was reported in other African countries in the 1990s. Isolates from 2012-2014 outbreaks showed a genetic background related to the pandemic strains currently active as the prevalent causative agent of cholera worldwide. Conclusions: Despite cholera being endemic in Mozambique, the epidemiology of the disease in the past 20 years has been strongly influenced by the cholera seventh pandemic waves that originated in the Indian subcontinent.

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A Study on the Geophylogeny of Clinical and Environmental Vibrio cholerae in Kenya

Cited by 34 publications

References 32 publications

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

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

Genomic history of the seventh pandemic of cholera in Africa

Epidemic waves of cholera in the last two decades in Mozambique

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