The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

Se Eun Park, Duy Thanh Pham, Christine Boinett, Vanessa K. Wong, Gi Deok Pak, Ursula Panzner, Ligia Maria Cruz Espinoza, Vera Kalckreuth, Justin Im, Heidi Schütt-Gerowitt, John A. Crump, Robert F. Breiman, Yaw Adu-Sarkodie, Ellis Owusu-Dabo, Raphaël Rakotozandrindrainy, Abdramane Bassiahi Soura, Abraham Aseffa, Nagla Gasmelseed, Karen H. Keddy, Jürgen May, Amy Gassama Sow, Peter Aaby, Holly M. Biggs, Julian T. Hertz, Joel M. Montgomery, Leonard Cosmas, Beatrice Olack, Barry Fields, Nimako Sarpong, Tsiriniaina Jean Luco Razafindrabe, Tiana Mirana Raminosoa, Leon Parfait Kabore, Emmanuel Sampo, Mekonnen Teferi, Biruk Yeshitela, Muna Ahmed El Tayeb, Arvinda Sooka, Christian G. Meyer, Ralf Krumkamp, Denise Myriam Dekker, Anna Jaeger, Sven Poppert, Adama Tall, Aissatou Niang, Morten Bjerregaard-Andersen, Sandra Valborg Løfberg, Hye Jin Seo, Hyon Jin Jeon, Jessica Fung Deerin, Jinkyung Park, Frank Konings, Mohammad Ali, John D. Clemens, Peter Hughes, Juliet Nsimire Sendagala, Tobias Vudriko, Robert Downing, Usman N. Ikumapayi, Grant A. Mackenzie, Stephen Obaro, Silvia Argimon, David M. Aanensen, Andrew Page, Jacqueline A. Keane, Sebastian Duchene, Zoe Dyson, Kathryn E. Holt, Gordon Dougan, Florian Marks () and Stephen Baker
Additional contact information
Se Eun Park: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Duy Thanh Pham: Oxford University Clinical Research Unit
Christine Boinett: Oxford University Clinical Research Unit
Vanessa K. Wong: Wellcome Genome Campus, Hinxton
Gi Deok Pak: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Ursula Panzner: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Ligia Maria Cruz Espinoza: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Vera Kalckreuth: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Justin Im: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Heidi Schütt-Gerowitt: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
John A. Crump: Kilimanjaro Christian Medical Centre
Robert F. Breiman: Centers for Disease Control and Prevention
Yaw Adu-Sarkodie: Kwame Nkrumah University of Science and Technology
Ellis Owusu-Dabo: Kwame Nkrumah University of Science and Technology
Raphaël Rakotozandrindrainy: University of Antananarivo
Abdramane Bassiahi Soura: University of Ouagadougou
Abraham Aseffa: Armauer Hansen Research Institute
Nagla Gasmelseed: Faculty of Medicine, University of Gezira
Karen H. Keddy: National Institute for Communicable Diseases
Jürgen May: Bernhard Nocht Institute for Tropical Medicine
Amy Gassama Sow: Institute Pasteur de Dakar
Peter Aaby: Bandim Health Project, Apartado
Holly M. Biggs: Kilimanjaro Christian Medical Centre
Julian T. Hertz: Kilimanjaro Christian Medical Centre
Joel M. Montgomery: Centers for Disease Control and Prevention
Leonard Cosmas: Centers for Disease Control and Prevention
Beatrice Olack: Kenya Medical Research Institute
Barry Fields: Centers for Disease Control and Prevention
Nimako Sarpong: Kwame Nkrumah University of Science and Technology
Tsiriniaina Jean Luco Razafindrabe: University of Antananarivo
Tiana Mirana Raminosoa: University of Antananarivo
Leon Parfait Kabore: Schiphra Hospital
Emmanuel Sampo: Schiphra Hospital
Mekonnen Teferi: Armauer Hansen Research Institute
Biruk Yeshitela: Armauer Hansen Research Institute
Muna Ahmed El Tayeb: Faculty of Medicine, University of Gezira
Arvinda Sooka: National Institute for Communicable Diseases
Christian G. Meyer: Eberhard-Karls University Tübingen, Geschwister-Scholl-Platz
Ralf Krumkamp: Bernhard Nocht Institute for Tropical Medicine
Denise Myriam Dekker: Bernhard Nocht Institute for Tropical Medicine
Anna Jaeger: Bernhard Nocht Institute for Tropical Medicine
Sven Poppert: University of Basel
Adama Tall: Université Cheikh Anta Diop de Dakar
Aissatou Niang: Université Cheikh Anta Diop de Dakar
Morten Bjerregaard-Andersen: Bandim Health Project, Apartado
Sandra Valborg Løfberg: Bandim Health Project, Apartado
Hye Jin Seo: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Hyon Jin Jeon: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Jessica Fung Deerin: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Jinkyung Park: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Frank Konings: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Mohammad Ali: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
John D. Clemens: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Peter Hughes: Medical Research Center (MRC)/Uganda Virus Research Institute (UVRI) & London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit
Juliet Nsimire Sendagala: Medical Research Center (MRC)/Uganda Virus Research Institute (UVRI) & London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit
Tobias Vudriko: Medical Research Center (MRC)/Uganda Virus Research Institute (UVRI) & London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit
Robert Downing: Uganda Virus Research Institute (UVRI)
Usman N. Ikumapayi: Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara
Grant A. Mackenzie: Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara
Stephen Obaro: University of Nebraska Medical Center, 42nd and Emile
Silvia Argimon: Wellcome Genome Campus, Hinxton
David M. Aanensen: Wellcome Genome Campus, Hinxton
Andrew Page: Wellcome Genome Campus, Hinxton
Jacqueline A. Keane: Wellcome Genome Campus, Hinxton
Sebastian Duchene: University of Melbourne
Zoe Dyson: University of Melbourne
Kathryn E. Holt: University of Melbourne
Gordon Dougan: Wellcome Genome Campus, Hinxton
Florian Marks: SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
Stephen Baker: Oxford University Clinical Research Unit

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4.3.1 (H58) (99/249; 40%), 3.1.1 (97/249; 39%), and 2.3.2 (29/249; 12%). Genotypes 4.3.1 and 3.1.1 are confined within East and West Africa, respectively. MDR phenotype is found in over 50% of organisms restricted within these dominant genotypes. High incidences of MDR S. Typhi are calculated in locations with a high burden of typhoid, specifically in children aged

Date: 2018
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DOI: 10.1038/s41467-018-07370-z

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