Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa
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Curated by eLife
Evaluation Summary:
The paper "Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa" presents results from sequencing and analyzing 46 Vibrio cholerae whole genome sequence data. The paper presents findings from a region with little genomic surveillance, and as such these data are valuable. While the analysis doesn't provide much novelty in terms of understanding cholera transmission, the study was conducted in the context of a regional training, and as such adds value as a potential model for regionally coordinated genomic surveillance efforts in areas where surveillance is limited. However even though it seems that the authors aim to present this as a surveillance model, the current focus of the paper is on the somewhat limited inference made about transmission.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)
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Abstract
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.
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Reviewer #2 (Public Review):
Thank you for the opportunity to review the short report "Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa" by Ekeng and colleagues. The authors report an analysis of 46 new Vibrio cholerae genomes in context of 1280 published genomes. The goal of their analysis was to establish a recent snapshot of VC population genomics in West Africa and assess the occurrence importations of new lineages. From their analysis, they infer that the recent cases were endemic.
Overall, this report presents findings from a region with little genomic surveillance, and as such these data are valuable for the understanding of endemic cholera in the region. The authors' analysis is technically sound, and the figures are well constructed. However, the depth of the analysis is …
Reviewer #2 (Public Review):
Thank you for the opportunity to review the short report "Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa" by Ekeng and colleagues. The authors report an analysis of 46 new Vibrio cholerae genomes in context of 1280 published genomes. The goal of their analysis was to establish a recent snapshot of VC population genomics in West Africa and assess the occurrence importations of new lineages. From their analysis, they infer that the recent cases were endemic.
Overall, this report presents findings from a region with little genomic surveillance, and as such these data are valuable for the understanding of endemic cholera in the region. The authors' analysis is technically sound, and the figures are well constructed. However, the depth of the analysis is relatively shallow, even for a short report, and the conclusions drawn from the data appear more subjective then based on the analysis at hand. These weaknesses could be addressed by a more in-depth analysis and clarification of the points below. Last, I did appreciate that this study was conducted in the context of a regional training. This could be an effective model for future analyses of regional importance. I feel like that wasn't the main focus of the report. If they were to shift their focus, I would want to know:
Where did the isolates come from (e.g., cholera treatment centers, hospitals, or broader active surveillance)?
Do they conduct environmental sampling and could this be part of future efforts?
Who attended the training? Were they members from regional ministry of health labs, academic institutes etc?
Were the attendees laboratorians, bioinformaticians, clinicians etc?
Was there an effort to analyze the data, particularly the bioinformatics portion, locally or did the rely 100% on the collaborators at JHU? If the latter, then I don't think this is a good sustainable model for ongoing genomic epidemiology. If the prior, then were local or regional computing resources used?
Are they continuing to sequence isolates after the training?
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Reviewer #1 (Public Review):
Ekeng et al. have sequenced and analyzed 46 Vibrio cholerae whole genome sequence data. The authors demonstrated a predominant lineage (T12) where all isolates from 2018-2019 fall. Their analysis suggest continuous transmission through repeated reintroduction of the same lineage back into the population. The work is interesting and the conclusions of this paper are mostly well supported by data. The present study reinforce the need of more genome sequence data and a strong surveillance network to interpret the data.
This is a successful model of regional coordination to have genomic surveillance data from a region where surveillance data was inadequate. The manuscript should be modified to focus on strengthening of genomic surveillance further.
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Evaluation Summary:
The paper "Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa" presents results from sequencing and analyzing 46 Vibrio cholerae whole genome sequence data. The paper presents findings from a region with little genomic surveillance, and as such these data are valuable. While the analysis doesn't provide much novelty in terms of understanding cholera transmission, the study was conducted in the context of a regional training, and as such adds value as a potential model for regionally coordinated genomic surveillance efforts in areas where surveillance is limited. However even though it seems that the authors aim to present this as a surveillance model, the current focus of the paper is on the somewhat limited inference made about transmission.
(This preprint has …
Evaluation Summary:
The paper "Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa" presents results from sequencing and analyzing 46 Vibrio cholerae whole genome sequence data. The paper presents findings from a region with little genomic surveillance, and as such these data are valuable. While the analysis doesn't provide much novelty in terms of understanding cholera transmission, the study was conducted in the context of a regional training, and as such adds value as a potential model for regionally coordinated genomic surveillance efforts in areas where surveillance is limited. However even though it seems that the authors aim to present this as a surveillance model, the current focus of the paper is on the somewhat limited inference made about transmission.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)
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