Genomic insights into the 2016–2017 cholera epidemic in Yemen
[2];
more »
- Inst. Pasteur, Unité des Bactéries Pathogènes Entériques, Paris (France)
- Wellcome Sanger Inst., Hinxton (United Kingdom); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- National Centre of Public Health Laboratories (NCPHL), Sana’a (Yemen)
- Epicentre, Paris (France)
- Ministry of Health, Riyadh (Saudi Arabia)
- Maharishi Valmiki Infectious Diseases Hospital, Delhi (India)
- Kenya Medical Research Inst., Nairobi (Kenya). Centre for Microbiology Research
- Pasteur Institute of Iran, Tehran (Iran). Dept. of Bacteriology
- WHO Regional Office for the Eastern Mediterranean (EMRO), Cairo (Egypt)
- Amref Health Africa, Nairobi (Kenya)
- WHO, Juba (South Sudan)
- Médecins Sans Frontières (MSF), Dubai (United Arab Emirates)
- Inst. Pasteur, Plate-forme Génomique (PF1), Paris (France)
- Inst. Pasteur, Paris (France)
- Tarbiat Modares Univ., Tehran (Iran). Dept. of Bacteriology, Faculty of Medical Sciences
- Central Public Health Lab. (CPHL), Baghdad (Iraq)
- Maharishi Valmiki Infectious Diseases Hospital, Delhi (India); Johns Hopkins Univ., Baltimore, MD (United States). Bloomberg School of Public Health, Dept. of Epidemiology
- Translational Health Science and Technology Inst.(THSTI), Faridabad, Haryana (India)
- Johns Hopkins Univ., Baltimore, MD (United States). Bloomberg School of Public Health, Dept. of Epidemiology
- Wellcome Sanger Inst., Hinxton (United Kingdom)
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 reported. Here in this paper 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 Tor. 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.
- Research Organization:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Organization:
- Wellcome Trust; France Génomique consortium; USDOE
- Grant/Contract Number:
- 89233218CNA000001; ANR-10-LABX-62-IBEID
- OSTI ID:
- 1492674
- Report Number(s):
- LA-UR-18-28662
- Journal Information:
- Nature (London), Vol. 565, Issue 7738; ISSN 0028-0836
- Publisher:
- Nature Publishing GroupCopyright Statement
- Country of Publication:
- United States
- Language:
- English
Web of Science
Similar Records
Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae
Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity