Genomic history of the seventh pandemic of cholera in Africa

François-Xavier Weill (1, 2) , Daryl Domman (2) , Elisabeth Njamkepo (1) , Cheryl Tarr (3) , Jean Rauzier (1) , Nizar Fawal (1) , Karen H. Keddy (4, 5) , Henrik Salje (6, 7) , Sandra Moore (8, 9) , Asish Mukhopadhyay (9, 8) , Raymond Bercion (10, 11) , Francisco J. Luquero (12) , Antoinette Ngandjio (13) , Mireille Dosso (14) , Elena Monakhova (15) , Benoit Garin (11) , Christiane Bouchier (16) , Carlo Pazzani (17) , Ankur Mutreja (18, 19) , Roland Grunow (20) , Fati Sidikou (21) , Laurence Bonte (12) , Sebastien Breurec (10) , Maria Damian (22) , Berthe-Marie Njanpop-Lafourcade (23) , Guillaume Sapriel (24, 25) , Anne-Laure Page (12) , Monzer Hamze (26) , Myriam Henkens (27) , Goutam Chowdhury (28) , Martin Mengel (23) , Jean-Louis Koeck (29) , Jean-Michel Fournier (30) , Gordon W Dougan (2, 18) , Patrick A. D. Grimont (31) , Julian Parkhill (2) , Kathryn E. Holt (32) , Renaud Piarroux (8, 9) , Thandavarayan Ramamurthy (19) , Marie Laure Quilici (30) , Nicholas R Thomson (2, 33)

1 BPE - Bactéries pathogènes entériques
2 The Wellcome Trust Sanger Institute [Cambridge]
3 CDC - Centers for Disease Control and Prevention [Atlanta]
4 NICD - National Institute for Communicable Diseases [Johannesburg]
5 WITS - University of the Witwatersrand [Johannesburg]
6 Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases
7 Johns Hopkins Bloomberg School of Public Health [Baltimore]
8 TIMONE - Hôpital de la Timone [CHU - APHM]
9 Université de la Méditerranée - Aix-Marseille 2
10 IPB - Institut Pasteur de Bangui
11 Institut Pasteur de Dakar
12 Epicentre [Paris] [Médecins Sans Frontières]
13 Centre Pasteur du Cameroun
14 Institut Pasteur de Côte d'Ivoire
15 Rostov-on-Don Research Institute for Plague Control
16 Génomique (Plate-Forme) - Genomics Platform
17 UNIBA - Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro
18 CAM - University of Cambridge [UK]
19 THSTI - Translational Health Science and Technology Institute [Faridabad]
20 RKI - Robert Koch Institute [Berlin]
21 CERMES - Centre de Recherche Médicale et Sanitaire [Niamey, Niger]
22 Institut Cantacuzène - Cantacuzino Institute [Bucarest, Roumania]
23 Agence de Médecine Préventive
24 UVSQ - Université de Versailles Saint-Quentin-en-Yvelines
25 ISYEB - Institut de Systématique, Evolution, Biodiversité
26 LU / ULB - الجامعة اللبنانية [بيروت] = Lebanese University [Beirut] = Université libanaise [Beyrouth]
27 Médecins Sans Frontières Belgique
28 National Institute of Cholera and Enteric Diseases
29 Hôpital Bouffard - Centre Hospitalier des Armées Bouffard [Djibouti]
30 CNR - Centre National de Référence des Vibrions et du Choléra - National Reference Center Vibrios and Cholera
31 Biodiversité des Bactéries Pathogènes Émergentes
32 University of Melbourne
33 LSHTM - London School of Hygiene and Tropical Medicine

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.

Domaines: Santé publique et épidémiologie

François-Xavier Weill, Daryl Domman, Elisabeth Njamkepo, Cheryl Tarr, Jean Rauzier, et al.. Genomic history of the seventh pandemic of cholera in Africa. Science, 2017, 358 (6364), pp.785-789. ⟨10.1126/science.aad5901⟩. ⟨pasteur-02045755⟩