Dataset Information

New Vibrio cholerae sequences from Eastern and Southern Africa alter our understanding of regional cholera transmission.

ABSTRACT: Despite ongoing containment and vaccination efforts, cholera remains prevalent in many countries in sub-Saharan Africa. Part of the difficulty in containing cholera comes from our lack of understanding of how it circulates throughout the region. To better characterize regional transmission, we generated and analyzed 118 Vibrio cholerae genomes collected between 2007-2019 from five different countries in Southern and Eastern Africa. We showed that V. cholerae sequencing can be successful from a variety of sample types and filled in spatial and temporal gaps in our understanding of circulating lineages, including providing some of the first sequences from the 2018-2019 outbreaks in Uganda, Kenya, Tanzania, Zambia, and Malawi. Our results present a complex picture of cholera transmission in the region, with multiple lineages found to be co-circulating within several countries. We also find evidence that previously identified sporadic cases may be from larger, undersampled outbreaks, highlighting the need for careful examination of sampling biases and underscoring the need for continued and expanded cholera surveillance across the African continent.

SUBMITTER: Xiao S

PROVIDER: S-EPMC10996759 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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Whole genome sequencing and transmission analysis of <i>Vibrio cholerae</i> isolates from Eastern and Southern Africa: a genomic epidemiology study.

Xiao Shaoming S Abade Ahmed A Boru Waqo W Kasambara Watipaso W Mwaba John J Ongole Francis F Mmanywa Mariam M Trovão Nídia Sequeira NS Chilengi Roma R Kwenda Geoffrey G Orach Christopher Garimoi CG Chibwe Innocent I Bwire Godfrey G Stine O Colin OC Milstone Aaron M AM Lessler Justin J Azman Andrew S AS Luo Wensheng W Murt Kelsey K Sack David A DA Debes Amanda K AK Wohl Shirlee S

medRxiv : the preprint server for health sciences 20250403

<h4>Background</h4>Despite ongoing containment and vaccination efforts, cholera remains prevalent in many countries in sub-Saharan Africa. Part of the difficulty in containing cholera comes from our lack of understanding of how it circulates throughout the region, so this study uses genomic epidemiology to identify disease transmission patterns in Southern and Eastern Africa.<h4>Methods</h4>To better characterize regional transmission, we performed whole genome sequencing on 142 <i>Vibrio choler ...[more]

PMID: 38585829

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Project description:Cholera remains a major global public health threat and continuous emergence of new Vibrio cholerae strains is of major concern. We conducted a molecular epidemiological study to detect virulence markers and antimicrobial resistance patterns of V. cholerae isolates obtained from the 2012-2015 cholera outbreaks in Ghana. Archived clinical isolates obtained from the 2012, 2014 and 2015 cholera outbreaks in Ghana were revived by culture and subjected to microscopy, biochemical identification, serotyping, antibiotic susceptibility testing, molecular detection of distinct virulence factors and Multi-Locus Variable-Number of Tandem-Repeat Analysis (MLVA). Of 277 isolates analysed, 168 (60.6%) were confirmed to be V. cholerae and 109 (39.4%) isolates constituted other bacteria (Escherichia coli, Aeromonas sobria, Pseudomonas aeruginosa, Enterobacter cloacae and Enterococci faecalis). Serotyping the V. cholerae isolates identified 151 (89.9%) as Ogawa, 3 (1.8%) as Inaba and 14 (8.3%) as non-O1/O139 serogroup. The O1 serogroup isolates (154/168, 91.7%) carried the cholera toxin ctxB gene as detected by PCR. Additional virulence genes detected include zot, tcpA, ace, rtxC, toxR, rtxA, tcpP, hlyA and tagA. The most common and rare virulence factors detected among the isolates were rtxC (165 isolates) and tcpP (50 isolates) respectively. All isolates from 2014 and 2015 were multidrug resistant against the selected antibiotics. MLVA differentiated the isolates into 2 large unique clones A and B, with each predominating in a particular year. Spatial analysis showed clustering of most isolates at Ablekuma sub-district. Identification of several virulence genes among the two different genotypes of V. cholerae isolates and resistance to first- and second-line antibiotics, calls for scaleup of preventive strategies to reduce transmission, and strengthening of public health laboratories for rapid antimicrobial susceptibility testing to guide accurate treatment. Our findings support the current WHO licensed cholera vaccines which include both O1 Inaba and Ogawa serotypes.

Project description:BackgroundVirulence determinants are crucial to the risk assessment of pathogens in an environment. This study investigated the presence of eleven key virulence-associated genes in Vibrio cholerae (n = 111) and Vibrio mimicus (n = 22) and eight virulence determinants in Vibrio alginolyticus (n = 65) and Vibrio parahaemolyticus (n = 17) isolated from six important water resources in Eastern Cape, South Africa, using PCR techniques. The multiple virulence gene indexes (MVGI) for sampling sites and isolates as well as hotspots for potential vibriosis outbreaks among sampling sites were determined statistically based on the comparison of MVGI.ResultThe PCR assay showed that all the V. cholerae isolates belong to non-O1/non-O139 serogroups. Of the isolates, Vibrio Cholera (84%), V. mimicus (73%), V. alginolyticus (91%) and V. parahaemolyticus (100%) isolates harboured at least one of the virulence-associated genes investigated. The virulence gene combinations detected in isolates varied at sampling site and across sites. Typical virulence-associated determinants of V. cholerae were detected in V. mimicus while that of V. parahaemolyticus were detected in V. alginolyticus. The isolates with the highest MVGI were recovered from three estuaries (Sunday river, Swartkopps river, buffalo river) and a freshwater resource (Lashinton river). The cumulative MVGI for V. cholerae, V. mimicus, V. alginolyticus and V. parahaemolyticus isolates were 0.34, 0.20, 0.45, and 0.40 respectively. The targeted Vibrio spp. in increasing order of the public health risk posed in our study areas based on the MVGI is V. alginolyticus > V. parahaemolyticus > V. cholerae > V. mimicus. Five (sites SR, PA5, PA6, EL4 and EL6) out of the seventeen sampling sites were detected as the hotspots for potential cholera-like infection and vibriosis outbreaks.ConclusionsOur findings suggest that humans having contact with water resources in our study areas are exposed to potential public health risks owing to the detection of virulent determinants in human pathogenic Vibrio spp. recovered from the water resources. The study affirms the relevancy of environmental Vibrio species to the epidemiology of vibriosis, cholera and cholera-like infections. Hence we suggest a monitoring program for human pathogenic Vibrio spp. in the environment most especially surface water that humans have contact with regularly.

Dataset Information

New Vibrio cholerae sequences from Eastern and Southern Africa alter our understanding of regional cholera transmission.

Publications

Whole genome sequencing and transmission analysis of <i>Vibrio cholerae</i> isolates from Eastern and Southern Africa: a genomic epidemiology study.

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

New Vibrio cholerae sequences from Eastern and Southern Africa alter our understanding of regional cholera transmission.

Publications

Whole genome sequencing and transmission analysis of &lt;i&gt;Vibrio cholerae&lt;/i&gt; isolates from Eastern and Southern Africa: a genomic epidemiology study.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Whole genome sequencing and transmission analysis of <i>Vibrio cholerae</i> isolates from Eastern and Southern Africa: a genomic epidemiology study.