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Science. 2017 Nov 10;358(6364):785-789. doi: 10.1126/science.aad5901.

Genomic history of the seventh pandemic of cholera in Africa.

Author information

1
Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France.
2
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
3
Centers for Disease Control and Prevention, Escherichia and Shigella Reference Unit, Atlanta, GA 30333, USA.
4
Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg 2131, South Africa.
5
Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.
6
Institut Pasteur, Mathematical Modelling of Infectious Diseases, Paris, 75015, France.
7
Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
8
Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, 13385, France.
9
National Institute of Cholera and Enteric Diseases (NICED), Kolkata, West Bengal 700010, India.
10
Institut Pasteur de Bangui, BP 923, Bangui, Central African Republic.
11
Institut Pasteur de Dakar, BP 220, Dakar, Senegal.
12
Epicentre, Paris, 75011, France.
13
Centre Pasteur du Cameroun, BP 1274, Yaoundé, Cameroon.
14
Bacteriology and Virology Department, Institut Pasteur, Abidjan, Côte d'Ivoire.
15
Rostov-on-Don Research Institute for Plague Control, Rostov-on-Don, 344022, Russia.
16
Institut Pasteur, Plate-forme Génomique (PF1), Paris, 75015, France.
17
University of Bari "A. Moro", Department of Biology, Bari, 70126, Italy.
18
Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0SP, UK.
19
Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India.
20
Robert Koch Institute, 13353 Berlin, Germany.
21
Centre de Recherche Medicale et Sanitaire (CERMES), BP 10887, Niamey, Niger.
22
Médecins Sans Frontières (MSF), Paris, 75011, France.
23
Cantacuzino National Institute of Research-Development for Microbiology and Immunology, Bucharest, Romania.
24
Agence de Médecine Préventive (AMP), Paris, 75015, France.
25
Université de Versailles Saint-Quentin-en-Yvelines, UFR des sciences de la santé Simone Veil, Montigny-le-Bretonneux, 78180, France.
26
Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, 75005, France.
27
Laboratoire Microbiologie Santé et Environnement (LMSE), EDST-FSP, Université Libanaise, Tripoli, Lebanon.
28
Médecins Sans Frontières, Brussels, B 1050, Belgium.
29
Centre Hospitalier des Armées Bouffard, Djibouti, Republic of Djibouti.
30
Institut Pasteur, Unité du Choléra et des Vibrions, Paris, 75015, France.
31
Institut Pasteur, Unité Biodiversité des Bactéries Pathogènes Emergentes, Paris, 75015, France.
32
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
33
London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.

Abstract

The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa.

PMID:
29123067
DOI:
10.1126/science.aad5901
[Indexed for MEDLINE]

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