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

Author

Listed:
  • Se Eun Park

    (SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
    Oxford University Clinical Research Unit)

  • Duy Thanh Pham

    (Oxford University Clinical Research Unit)

  • Christine Boinett

    (Oxford University Clinical Research Unit
    University of Oxford, Old Road campus)

  • Vanessa K. Wong

    (Wellcome Genome Campus, Hinxton
    Cambridge Biomedical Campus, Hills Road)

  • 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
    University of Cologne)

  • John A. Crump

    (Kilimanjaro Christian Medical Centre
    Duke University Medical Center
    Duke University
    University of Otago)

  • Robert F. Breiman

    (Centers for Disease Control and Prevention
    Emory University, 1599 Clifton Road, NE)

  • Yaw Adu-Sarkodie

    (Kwame Nkrumah University of Science and Technology
    Kwame Nkrumah University of Science and Technology, KCCR, UPO, PMB, KNUST)

  • Ellis Owusu-Dabo

    (Kwame Nkrumah University of Science and Technology
    Kwame Nkrumah University of Science and Technology, KCCR, UPO, PMB, KNUST)

  • 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
    University of Hafr Al Batin, Al Jamiah)

  • Karen H. Keddy

    (National Institute for Communicable Diseases
    University of the Witwatersrand)

  • Jürgen May

    (Bernhard Nocht Institute for Tropical Medicine
    Hamburg-Borstel-Lübeck)

  • Amy Gassama Sow

    (Institute Pasteur de Dakar
    Université Cheikh Anta Diop de Dakar)

  • Peter Aaby

    (Bandim Health Project, Apartado
    Bandim Health Project, Statens Serum Institut)

  • Holly M. Biggs

    (Kilimanjaro Christian Medical Centre
    Duke University Medical Center)

  • Julian T. Hertz

    (Kilimanjaro Christian Medical Centre
    Duke University Medical Center)

  • 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
    Hamburg-Borstel-Lübeck)

  • 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
    Duy Tan University, 254 Nguyen Van Linh)

  • Ralf Krumkamp

    (Bernhard Nocht Institute for Tropical Medicine)

  • Denise Myriam Dekker

    (Bernhard Nocht Institute for Tropical Medicine
    Hamburg-Borstel-Lübeck)

  • 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
    Bandim Health Project, Statens Serum Institut)

  • Sandra Valborg Løfberg

    (Bandim Health Project, Apartado
    Bandim Health Project, Statens Serum Institut)

  • 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
    Johns Hopkins Bloomberg School of Public Health)

  • John D. Clemens

    (SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
    International Centre for Diarrheal Disease Research, Bangladesh (ICDDR,B)
    University of California, Fielding School of Public Health)

  • 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)
    Public Health Emergency Operations Centre)

  • 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
    Murdoch Children’s Research Institute
    Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formations (IRESSEF), Arrondissement 4 Rue 2D1, BP 7325)

  • Stephen Obaro

    (University of Nebraska Medical Center, 42nd and Emile
    University of Abuja Teaching Hospital
    Bingham University, P.M.B 005, KM 26 Abuja-Keffi Expressway Kodope)

  • Silvia Argimon

    (Wellcome Genome Campus, Hinxton)

  • David M. Aanensen

    (Wellcome Genome Campus, Hinxton
    University of Oxford, Old Road Campus)

  • 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
    The University of Cambridge)

  • Florian Marks

    (SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu
    The University of Cambridge)

  • Stephen Baker

    (Oxford University Clinical Research Unit
    University of Oxford, Old Road campus
    The University of Cambridge)

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

Suggested Citation

  • 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 & Ro, 2018. "The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-07370-z
    DOI: 10.1038/s41467-018-07370-z
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    Cited by:

    1. Joseph Walker & Chrispin Chaguza & Nathan D. Grubaugh & Megan Carey & Stephen Baker & Kamran Khan & Isaac I. Bogoch & Virginia E. Pitzer, 2023. "Assessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella Typhi," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

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