Genomic insights into the 2016–2017 cholera epidemic in Yemen

François-Xavier Weill (), Daryl Domman, Elisabeth Njamkepo, Abdullrahman A. Almesbahi, Mona Naji, Samar Saeed Nasher, Ankur Rakesh, Abdullah M. Assiri, Naresh Chand Sharma, Samuel Kariuki, Mohammad Reza Pourshafie, Jean Rauzier, Abdinasir Abubakar, Jane Y. Carter, Joseph F. Wamala, Caroline Seguin, Christiane Bouchier, Thérèse Malliavin, Bita Bakhshi, Hayder H. N. Abulmaali, Dhirendra Kumar, Samuel M. Njoroge, Mamunur Rahman Malik, John Kiiru, Francisco J. Luquero, Andrew S. Azman, Thandavarayan Ramamurthy, Nicholas R. Thomson and Marie-Laure Quilici
Additional contact information
François-Xavier Weill: Unité des Bactéries Pathogènes Entériques
Daryl Domman: Wellcome Sanger Institute
Elisabeth Njamkepo: Unité des Bactéries Pathogènes Entériques
Abdullrahman A. Almesbahi: National Centre of Public Health Laboratories (NCPHL)
Mona Naji: National Centre of Public Health Laboratories (NCPHL)
Samar Saeed Nasher: National Centre of Public Health Laboratories (NCPHL)
Ankur Rakesh: Epicentre
Abdullah M. Assiri: Ministry of Health
Naresh Chand Sharma: Maharishi Valmiki Infectious Diseases Hospital
Samuel Kariuki: Kenya Medical Research Institute
Mohammad Reza Pourshafie: Pasteur Institute of Iran, Department of Bacteriology
Jean Rauzier: Unité des Bactéries Pathogènes Entériques
Abdinasir Abubakar: WHO Regional Office for the Eastern Mediterranean (EMRO)
Jane Y. Carter: Amref Health Africa
Joseph F. Wamala: WHO
Caroline Seguin: Médecins Sans Frontières (MSF)
Christiane Bouchier: Institut Pasteur, Plate-forme Génomique (PF1)
Thérèse Malliavin: Unité de Bioinformatique Structurale, UMR 3528, CNRS; C3BI, USR 3756, Institut Pasteur
Bita Bakhshi: Tarbiat Modares University
Hayder H. N. Abulmaali: Central Public Health Laboratory (CPHL)
Dhirendra Kumar: Maharishi Valmiki Infectious Diseases Hospital
Samuel M. Njoroge: Kenya Medical Research Institute
Mamunur Rahman Malik: WHO Regional Office for the Eastern Mediterranean (EMRO)
John Kiiru: Kenya Medical Research Institute
Francisco J. Luquero: Epicentre
Andrew S. Azman: Johns Hopkins Bloomberg School of Public Health
Thandavarayan Ramamurthy: Translational Health Science and Technology Institute (THSTI)
Nicholas R. Thomson: Wellcome Sanger Institute
Marie-Laure Quilici: Unité des Bactéries Pathogènes Entériques

Nature, 2019, vol. 565, issue 7738, 230-233

Abstract: Abstract 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 Tor2–4. 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.

Date: 2019
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DOI: 10.1038/s41586-018-0818-3

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