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Nature. 2019 Jan;565(7738):230-233. doi: 10.1038/s41586-018-0818-3. Epub 2019 Jan 2.

Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Author information

1
Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France. francois-xavier.weill@pasteur.fr.
2
Wellcome Sanger Institute, Hinxton, UK.
3
Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
4
Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France.
5
National Centre of Public Health Laboratories (NCPHL), Sana'a, Yemen.
6
Epicentre, Paris, France.
7
Ministry of Health, Riyadh, Saudi Arabia.
8
Maharishi Valmiki Infectious Diseases Hospital, Delhi, India.
9
Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.
10
Pasteur Institute of Iran, Department of Bacteriology, Tehran, Iran.
11
WHO Regional Office for the Eastern Mediterranean (EMRO), Cairo, Egypt.
12
Amref Health Africa, Nairobi, Kenya.
13
WHO, Juba, South Sudan.
14
Médecins Sans Frontières (MSF), Dubai, United Arab Emirates.
15
Institut Pasteur, Plate-forme Génomique (PF1), Paris, France.
16
Unité de Bioinformatique Structurale, UMR 3528, CNRS; C3BI, USR 3756, Institut Pasteur, Paris, France.
17
Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
18
Central Public Health Laboratory (CPHL), Baghdad, Iraq.
19
Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India.
20
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
21
London School of Hygiene and Tropical Medicine, London, UK.

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.

Comment in

PMID:
30602788
PMCID:
PMC6420076
DOI:
10.1038/s41586-018-0818-3
[Indexed for MEDLINE]
Free PMC Article

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