Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing

Garrine, Marcelino; Mandomando, Inácio; Vubil, Delfino; Nhampossa, Tacilta; Acácio, Sozinho; Li, Shan; Paulson, Joseph N.; Almeida, Mathieu; Domman, Daryl; Thomson, Nicholas R.; Alonso, Pedro L.; Stine, O. Colin

doi:10.1371/journal.pntd.0005671

Cited by 26 publications

(24 citation statements)

References 36 publications

(59 reference statements)

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“…As also reported in other countries [33,50,51], two V. cholerae non-O1/non-O139 lineages were also identified and characterized from cholera-like diarrhea cases in eastern DRC, and were assigned to two novel sequence types, ST612 and ST613. Recent cholera outbreaks affecting the Kasai provinces highlight the urgent need to better understand the factors favoring the endemicity and epidemicity of cholera among the exposed populations.…”

Section: Discussionsupporting

confidence: 71%

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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: Discussionsupporting

confidence: 71%

“…ST 612 and ST 613, by the curator of the V. cholerae MLST database (https://pubmlst.org/vcholerae/). Whereas ST612 isolates (n = 4) were closely related between them and to some extent to isolates characterized in Mozambique [33] and Haiti [34], the ST613 DRC isolate could not be related to any characterized V. cholerae isolate.…”

Section: Resultsmentioning

confidence: 94%

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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“…To date, more than 30 complete and numerous draft genome sequences for V. cholerae strains are available in the Gen-Bank database (http://www.ncbi.nlm.nih.gov/genom e/) or online (http://www.genom esonl ine.org). Many comparative analyses of these V. cholerae genomes have been reported (e.g., Banerjee et al 2014;Dutilh et al 2014;Okada et al 2014;Garrine et al 2017;Imamura et al 2017). In the present study, we determined the complete genome sequence of V. cholerae CHN108B (non-O1/O139 serogroup, ct − tcp − ), which was recently isolated from surface water from the Yangtze River Estuary, China (Song et al 2013), to address the lack of complete genome data regarding this bacterium originating from an estuary environment in China (Yi et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics for non-O1/O139 Vibrio cholerae isolates recovered from the Yangtze River Estuary versus V. cholerae representative isolates from serogroup O1

et al. 2018

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Vibrio cholerae, which is autochthonous to estuaries worldwide, can cause human cholera that is still pandemic in developing countries. A number of V. cholerae isolates of clinical and environmental origin worldwide have been subjected to genome sequencing to address their phylogenesis and bacterial pathogenesis, however, little genome information is available for V. cholerae isolates derived from estuaries, particularly in China. In this study, we determined the complete genome sequence of V. cholerae CHN108B (non-O1/O139 serogroup) isolated from the Yangtze River Estuary, China and performed comparative genome analysis between CHN108B and other eight representative V. cholerae isolates. The 4,168,545-bp V. cholerae CHN108B genome (47.2% G+C) consists of two circular chromosomes with 3,691 predicted protein-encoding genes. It has 110 strain-specific genes, the highest number among the eight representative V. cholerae whole genomes from serogroup O1: there are seven clinical isolates linked to cholera pandemics (1937-2010) and one environmental isolate from Brazil. Various mobile genetic elements (such as insertion sequences, prophages, integrative and conjugative elements, and superintegrons) were identified in the nine V. cholerae genomes of clinical and environmental origin, indicating that the bacterium undergoes extensive genetic recombination via lateral gene transfer. Comparative genomics also revealed different virulence and antimicrobial resistance gene patterns among the V. cholerae isolates, suggesting some potential virulence factors and the rising development of resistance among pathogenic V. cholerae. Additionally, draft genome sequences of multiple V. cholerae isolates recovered from the Yangtze River Estuary were also determined, and comparative genomics revealed many genes involved in specific metabolism pathways, which are likely shaped by the unique estuary environment. These results provide additional evidence of V. cholerae genome plasticity and will facilitate better understanding of the genome evolution and pathogenesis of this severe water-borne pathogen worldwide.

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Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing

Cited by 26 publications

References 36 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

Comparative genomics for non-O1/O139 Vibrio cholerae isolates recovered from the Yangtze River Estuary versus V. cholerae representative isolates from serogroup O1

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