Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2,3,4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1—the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)—are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
The whole-genome alignment for the 1,203 genomes and other files that support the findings of this study have been deposited in FigShare: https://figshare.com/s/b70a9efac9cf2625480e. Short-read sequence data were submitted to the ENA, under study accession numbers PRJEB24611 and ERP021285 and the genome accession numbers are provided in Supplementary Table 1. Phylogeny and metadata can be viewed interactively at https://microreact.org/project/globalcholera.
Camacho, A. et al. Cholera epidemic in Yemen, 2016–18: an analysis of surveillance data. Lancet Glob. Health 6, e680–e690 (2018).
Weill, F. X. et al. Genomic history of the seventh pandemic of cholera in Africa. Science 358, 785–789 (2017).
Kachwamba, Y. et al. Genetic characterization of Vibrio cholerae O1 isolates from outbreaks between 2011 and 2015 in Tanzania. BMC Infect. Dis. 17, 157 (2017).
Bwire, G. et al. Molecular characterization of Vibrio cholerae responsible for cholera epidemics in Uganda by PCR, MLVA and WGS. PLoS Negl. Trop. Dis. 12, e0006492 (2018).
Mutreja, A. et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477, 462–465 (2011).
Naha, A. et al. Development and evaluation of a PCR assay for tracking the emergence and dissemination of Haitian variant ctxB in Vibrio cholerae O1 strains isolated from Kolkata, India. J. Clin. Microbiol. 50, 1733–1736 (2012).
Chin, C. S. et al. The origin of the Haitian cholera outbreak strain. N. Engl. J. Med. 364, 33–42 (2011).
Domman, D. et al. Integrated view of Vibrio cholerae in the Americas. Science 358, 789–793 (2017).
Katz, L. S. et al. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. mBio 4, e00398-13 (2013).
Ghosh Dastidar, P., Sinha, A. M., Ghosh, S. & Chatterjee, G. C. Biochemical mechanism of nitrofurantoin resistance in Vibrio el tor. Folia Microbiol. (Praha) 24, 487–494 (1979).
Sandegren, L., Lindqvist, A., Kahlmeter, G. & Andersson, D. I. Nitrofurantoin resistance mechanism and fitness cost in Escherichia coli. J. Antimicrob. Chemother. 62, 495–503 (2008).
Herrera, C. M. et al. The Vibrio cholerae VprA–VprB two-component system controls virulence through endotoxin modification. mBio 5, e02283-14 (2014).
Matson, J. S., Livny, J. & DiRita, V. J. A putative Vibrio cholerae two-component system controls a conserved periplasmic protein in response to the antimicrobial peptide polymyxin B. PLoS ONE 12, e0186199 (2017).
Devault, A. M. et al. Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849. N. Engl. J. Med. 370, 334–340 (2014).
Samanta, P., Ghosh, P., Chowdhury, G., Ramamurthy, T. & Mukhopadhyay, A. K. Sensitivity to polymyxin B in El Tor Vibrio cholerae O1 strain, Kolkata, India. Emerg. Infect. Dis. 21, 2100–2102 (2015).
Hasan, N. A. et al. Genomic diversity of 2010 Haitian cholera outbreak strains. Proc. Natl Acad. Sci. USA 109, E2010–E2017 (2012).
Zarocostas, J. Cholera outbreak in Haiti-from 2010 to today. Lancet 389, 2274–2275 (2017).
UN Office for the Coordination of Humanitarian Affairs. Humanitarian needs overview, Yemen. http://www.unocha.org/sites/unocha/files/dms/yemen_humanitarian_needs_overview_hno_2018_20171204.pdf (2017).
International Organization for Migration. Irregular migration in Horn of Africa increases in 2015. https://www.iom.int/news/irregular-migration-horn-africa-increases-2015 (2016).
Danish Refugee Council. Mixed migration in the Horn of Africa & Yemen region. RMMS https://reliefweb.int/sites/reliefweb.int/files/resources/RMMS%20Mixed%20Migration%20Monthly%20Summary%20September%202016_0.pdf (2016).
Dodin, A. & Fournier, J. M. Laboratory Methods for the Diagnosis of Cholera Vibrio and Other Vibrios 59–82 (Institut Pasteur Paris, Paris 1992).
CA-SFM & EUCAST. Comité de l’Antibiogramme de la Société Française de Microbiologie Recommandations 2017. http://www.sfm-microbiologie.org/UserFiles/files/casfm/CASFMV1_0_MARS_2017.pdf (2017).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15 (2015).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).
Rambaut, A., Lam, T. T., Max Carvalho, L. & Pybus, O. G. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2, vew007 (2016).
Rieux, A. & Khatchikian, C. E. tipdatingbeast: an R package to assist the implementation of phylogenetic tip-dating tests using beast. Mol. Ecol. Resour. 17, 608–613 (2017).
This study was supported by the Institut Pasteur, Santé publique France, the French government’s Investissement d’Avenir programme, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), the Wellcome Trust through grant 098051 to the Sanger Institute and the Department of Biotechnology of India. The Institut Pasteur Genomics Platform is a member of the France Génomique consortium (ANR10-INBS-09-08). We thank D. Legros, A. Fadaq, A. Alsomine, F. Bazel and H. A. Jokhdar for their support; M. Musoke and S. Vernadat for technical assistance; Z. M. Eisa for providing isolates; L. Ma, C. Fund, S. Sjunnebo and the sequencing teams at the Institut Pasteur and Wellcome Sanger Institute for sequencing the samples. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Nature thanks J. Mekalanos, C. Stine, M. Waldor and the other anonymous reviewer(s) for their contribution to the peer review of this work.
The authors declare no competing interests.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data figures and tables
Extended Data Fig. 1 Geographic location of the sequenced V. cholerae O1 El Tor isolates and number of reported cholera cases.
a, Geographic location of the 116 V. cholerae O1 El Tor isolates sequenced. The number of isolates collected per country is indicated. The three isolates collected in Jizan, Saudi Arabia (denoted by an asterisk) were from Yemeni refugees originating from Hajjah District. The map is a cropped version of the one available at https://commons.wikimedia.org/wiki/File:BlankMap-World.png. b, Number of cholera cases per country reported to the WHO (World Health Organisation) between 2014 and 2016. The total number of cholera cases reported to the WHO by the countries was 268,337. The maps were created using Paintmaps, a free online map generating tool (http://www.paintmaps.com/).
a, Linear regression of the root-to-tip distance against sampling time obtained with TempEst29 using a maximum-likelihood phylogeny of 81 representative seventh pandemic V. cholerae O1 isolates (that is, those used for the BEAST analysis). Bars on nodes indicate the precision of the isolation date (for example, if only the year of isolation is known, the bar spans the entire year). b, Comparison of the ucld.mean parameter estimated from 20 date-randomization BEAST experiments and the original dataset. The rate for the correctly dated tree is shown in red. The median and 95% Bayesian credible interval for the ucld.mean parameter are provided.
Maximum clade credibility tree produced with BEAST28 for a subset of 81 representative isolates of the distal part of the genomic wave 3 (that is, those with the ctxB7 allele). The nodes supported by posterior probability values ≥0.5 are indicated.
Extended Data Fig. 4 Visualization of the posterior distribution of trees from the BEAST Markov chain Monte Carlo analysis.
The opacity of the branches is scaled according to the number of times a clade is seen in the distribution. There is high support for the East Africa/Yemen clade. The uncertainty in the placement of the node for the Indian/East African isolates is the reason for the low posterior support value for this node in Extended Data Fig. 3.
Extended Data Fig. 5 Multiple sequence alignment of VprA (VC1320) with two-component response regulators.
A non-synonymous mutation at position 89 of VC1320 that resulted in a D-to-N amino acid change was associated with a phenotype of polymyxin B susceptibility.
About this article
Cite this article
Weill, F., Domman, D., Njamkepo, E. et al. Genomic insights into the 2016–2017 cholera epidemic in Yemen. Nature 565, 230–233 (2019). https://doi.org/10.1038/s41586-018-0818-3
A Point Mutation in carR Is Involved in the Emergence of Polymyxin B-Sensitive Vibrio cholerae O1 El Tor Biotype by Influencing Gene Transcription
Infection and Immunity (2020)
Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017)
PLOS Neglected Tropical Diseases (2020)
Journal of microbiology, epidemiology and immunobiology (2020)
Culture‐independent tracking of Vibrio cholerae lineages reveals complex spatiotemporal dynamics in a natural population
Environmental Microbiology (2020)