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. 2021 Jun 18:10:e65159.
doi: 10.7554/eLife.65159.

Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa

Eme Ekeng #  1 , Serges Tchatchouang #  2 , Blaise Akenji  3 , Bassira Boubacar Issaka  4 , Ifeoluwa Akintayo  5 , Christopher Chukwu  1 , Ibrahim Dan Dano  4 , Sylvie Melingui  3 , Sani Ousmane  4 , Michael Oladotun Popoola  1 , Ariane Nzouankeu  2 , Yap Boum  6 , Francisco Luquero  6 , Anthony Ahumibe  1 , Dhamari Naidoo  7 , Andrew Azman  8 , Justin Lessler  8 , Shirlee Wohl  8
Affiliations

Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa

Eme Ekeng et al. Elife. .

Abstract

Background: Despite recent insights into cholera transmission patterns in Africa, regional and local dynamics in West Africa-where cholera outbreaks occur every few years-are still poorly understood. Coordinated genomic surveillance of Vibrio cholerae in the areas most affected may reveal transmission patterns important for cholera control.

Methods: During a regional sequencing workshop in Nigeria, we sequenced 46 recent V. cholerae isolates from Cameroon, Niger, and Nigeria (37 from 2018 to 2019) to better understand the relationship between the V. cholerae bacterium circulating in these three countries.

Results: From these isolates, we generated 44 whole Vibrio cholerae O1 sequences and analyzed them in the context of 1280 published V. cholerae O1 genomes. All sequences belonged to the T12 V. cholerae seventh pandemic lineage.

Conclusions: Phylogenetic analysis of newly generated and previously published V. cholerae genomes suggested that the T12 lineage has been continuously transmitted within West Africa since it was first observed in the region in 2009, despite lack of reported cholera in the intervening years. The results from this regional sequencing effort provide a model for future regionally coordinated surveillance efforts.

Funding: Funding for this project was provided by Bill and Melinda Gates Foundation OPP1195157.

Keywords: Vibrio cholerae; West Africa; antimicrobial resistance; epidemiology; genetics; genomics; global health; transmission.

PubMed Disclaimer

Conflict of interest statement

EE, ST, BA, BI, IA, CC, ID, SM, SO, MP, AN, YB, FL, AA, DN, AA, JL, SW No competing interests declared

Figures

Figure 1.
Figure 1.. Cholera cases and sequenced isolates.
(A) Weekly suspected cholera cases for Cameroon (orange), Niger (blue), and Nigeria (green) from 2010 through 2019 (‘Regional Cholera Platform in West and Central Africa,’ n.d.) (Figure 1—source data 1). Suspected cases are defined as recommended by the World Health Organization (Global Task Force on Cholera Control Surveillance Working Group, 2017). Red points: weeks with no more than five suspected cases reported across all three countries. Arrows: collection dates of isolates sequenced. Collection dates provided as year only (n=2) are plotted on January 1 of their given year. (B) Map of Cameroon, Niger, and Nigeria. Colors are as in (A). White points: location of sequenced isolates collected in 2018 and 2019 (Figure 1—source data 2). Black crosses: location of sequenced isolates collected prior to 2018. One isolate with unknown sub-country location is not shown.
Figure 2.
Figure 2.. Phylogenetic tree of V. cholerae O1 sequences.
Left: maximum likelihood tree of global V. cholerae isolates. Samples generated in this study are shown in blue (see also, Figure 2—source data 1). Right: zoom view of a portion of the T12 lineage containing V. cholerae genomes generated in this study. Country codes: TGO, Togo; NER, Niger; GHA, Ghana; CMR, Cameroon; NGA, Nigeria; TCD, Chad. Scale bar unit: nucleotide substitutions per site.
Figure 2—figure supplement 1.
Figure 2—figure supplement 1.. Proportion of reported cholera cases and V. cholerae sequences by continent.
For each decade, the proportion of cholera cases reported to the World Health Organization from each continent (blue bars) and proportion of V. cholerae sequences included in this study from each continent (gray bars).
Figure 2—figure supplement 2.
Figure 2—figure supplement 2.. Proportion of reported cholera cases and V. cholerae sequences by African region.
For each decade, the proportion of cholera cases reported to the World Health Organization from each African subregion (blue bars) and proportion of V. cholerae sequences included in this study from each African subregion (gray bars).
See this image and copyright information in PMC

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