Genetic Characterization of Vibrio cholerae O1 isolates from outbreaks between 2011 and 2015 in Tanzania

Kachwamba, Yazid; Mohammed, A. A.; Lukupulo, Haji; Urio, Loveness John; Majigo, Mtebe; Mosha, Fausta; Matonya, M.; Kishimba, Rogath; Mghamba, Janneth; Lusekelo, J.; Nyanga, Salum Kassim; Almeida, Mathieu; Li, S.; Domman, Daryl; Massele, S.Y.; Stine, O. Colin

doi:10.1186/s12879-017-2252-9

Cited by 23 publications

(34 citation statements)

References 17 publications

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“…The V. cholerae O1 global phylogeny including data from Uganda [15], Tanzania [49], DRC, Central African Republic, and Zambia [5] confirms that the ST515 sub-clade has now spread to several regions of Central and Eastern Africa, including western provinces of DRC up to the Atlantic coast. Whereas the reason why only the ST515 expands so widely, and not the ST69 sub-clade, remains unknown, the hypothesis is that the higher genetic diversity among ST515 isolates results from a high mutation frequency, which favors their adaptation to changing environmental conditions.…”

Section: Discussionmentioning

confidence: 92%

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: Discussionmentioning

confidence: 92%

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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“…Genomic DNA was extracted from 38 isolates using published phenol-chloroform extraction methods [ 23 ]. Genome sequencing was performed as previously published on an Illumina HiSeq2500 (Illumina, San Diego, CA, USA) [ 24 , 25 ].…”

Section: Methodsmentioning

confidence: 99%

“…We choose the wave 3 isolate genome, S002604, as the reference, in order to minimize the number of variable sites that were different between the reference genome and all the genomes in our sample since those variable sites do not contribute to the analysis. PARSNP (v1.2) [ 28 ] was used to extract and align the variable nucleotides using previously published options [ 24 , 25 ]. The ‘.ggr’ file was loaded in Gingr (v1.2) [ 28 ] to visualize the alignments.…”

Section: Methodsmentioning

confidence: 99%

Genetic relatedness of Vibrio cholerae isolates within and between households during outbreaks in Dhaka, Bangladesh

et al. 2017

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BackgroundHousehold contacts of cholera patients have a 100 times higher risk of developing a cholera infection than the general population. To compare the genetic relatedness of clinical and water source Vibrio cholerae isolates from cholera patients’ households across three outbreaks, we analyzed these isolates using whole-genome-sequencing (WGS) and multilocus variable-number tandem-repeat analysis (MLVA).ResultsThe WGS analyses revealed that 80% of households had source water isolates that were more closely related to clinical isolates from the same household than to any other isolates. While in another 20% of households an isolate from a person was more closely related to clinical isolates from another household than to source water isolates from their own household. The mean pairwise differences in single nucleotide-variant (SNV) counts for isolates from the same household were significantly lower than those for different households (2.4 vs. 7.7 p < 0.0001), and isolates from the same outbreak had significantly fewer mean pairwise differences compared to isolates from different outbreaks (mean: 6.2 vs. 8.0, p < 0.0001). Based on MLVA in outbreak 1, we observed that the majority of households had clinical isolates with MLVA genotypes related to other clinical isolates and unrelated to water source isolates from the same household. While in outbreak 3, there were different MLVA genotypes between households, however within the majority of households, the clinical and water source isolates had the same MLVA genotypes. The beginning of outbreak 2 resembled outbreak 1 and the latter part resembled outbreak 3. We validated our use of MLVA by comparing it to WGS. Isolates with the identical MLVA genotype had significantly fewer mean pairwise SNV differences than those isolates with different MLVA genotypes (mean: 4.8 vs. 7.7, p < 0.0001). Furthermore, consistent with WGS results, the number of pairwise differences in the five MLVA loci for isolates within the same household was significantly lower than isolates from different households (mean: 1.6 vs. 3.0, p < 0.0001).ConclusionThese results suggest that transmission patterns for cholera are a combination of person-to-person and water-to-person cholera transmission with the proportions of the two modes varying within and between outbreaks.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4254-9) contains supplementary material, which is available to authorized users.

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“…Whereas random sampling is ideal, it is difficult to implement during epidemics because of competing priorities. Furthermore, although studies have shown that 6-locus MLVA can be highly discriminative for identifying a closely related pandemic strain isolated in a small timeframe and geographic area ( 12 , 13 ), our lack of knowledge of MLVA limitations makes it more difficult to draw inferences about strain relatedness and phylogenetic history, especially compared with whole-genome sequencing ( 14 ). …”

Section: The Studymentioning

confidence: 99%

Cholera Epidemic in South Sudan and Uganda and Need for International Collaboration in Cholera Control

Abubakar

Bwire²,

Azman³

et al. 2018

Emerg. Infect. Dis.

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Genetic Characterization of Vibrio cholerae O1 isolates from outbreaks between 2011 and 2015 in Tanzania

Cited by 23 publications

References 17 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)

Genetic relatedness of Vibrio cholerae isolates within and between households during outbreaks in Dhaka, Bangladesh

Cholera Epidemic in South Sudan and Uganda and Need for International Collaboration in Cholera Control

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