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Cited by 120Salmonella and Campylobacter epidemiologyAntibiotic Resistance in BacteriaAntibiotic Use and Resistance

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

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Park, Se Eun, Pham, Duy Thanh, Boinett, Christine, Wong, Vanessa K., Pak, Gi Deok, Panzner, Ursula, Espinoza, Ligia Maria Cruz, von Kalckreuth, Vera, Im, Justin, Schütt-Gerowitt, Heidi, Crump, John A., Breiman, Robert F., Adu-Sarkodie, Yaw, Owusu-Dabo, Ellis, Rakotozandrindrainy, Raphaël, Soura, Abdramane Bassiahi, Aseffa, Abraham, Gasmelseed, Nagla, Keddy, Karen H., May, Jürgen, Sow, Amy Gassama, Aaby, Peter, Biggs, Holly M., Hertz, Julian T., Montgomery, Joel M., Cosmas, Leonard, Olack, Beatrice, Fields, Barry, Sarpong, Nimako, Razafindrabe, Tsiriniaina Jean Luco, Raminosoa, Tiana Mirana, Kabore, Leon Parfait, Sampo, Emmanuel, Teferi, Mekonnen, Yeshitela, Biruk, El Tayeb, Muna Ahmed, Sooka, Arvinda, Meyer, Christian G., Krumkamp, Ralf, Dekker, Denise Myriam, Jaeger, Anna, Poppert, Sven, Tall, Adama, Niang, Aissatou, Bjerregaard-Andersen, Morten, Løfberg, Sandra Valborg, Seo, Hye Jin, Jeon, Hyon Jin, Deerin, Jessica Fung, Park, Jinkyung, Konings, Frank, Ali, Mohammad, Clemens, John D., Hughes, Peter, Sendagala, Juliet Nsimire, Vudriko, Tobias, Downing, Robert, Ikumapayi, Usman N., Mackenzie, Grant A., Obaro, Stephen, Argimon, Silvia, Aanensen, David M., Page, Andrew, Keane, Jacqueline A., Duchene, Sebastian, Dyson, Zoe, Holt, Kathryn E., Dougan, Gordon, Marks, Florian, Baker, Stephen·2018·Nature Communications
DOI 10.1038/s41467-018-07370-zPMC PMC6269545
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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 <15 years. Antimicrobial stewardship, MDR surveillance, and the introduction of typhoid conjugate vaccines will be critical for the control of MDR typhoid in Africa.

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  • In the past two decades, multidrug-resistant Salmonella Typhi has emerged and spread throughout the sub-Saharan Africa region.

    “in the past two decades, multidrug-resistant (defined as resistance to ampicillin, trimethoprim-sulfamethoxazole, and chloramphenicol) S. Typhi has emerged and spread throughout the region.”

    From Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now? (2022) · cites this paper as [68]

    The Discussion (page unavailable) reports that MDR S. Typhi can arise locally and spread through population movements in East and West Africa. The Results (page unavailable) use the stated three-drug definition, but identify MDR isolates in only four of the eleven sampled countries. The paper does not establish spread throughout sub-Saharan Africa over the claimed two-decade period. (LLM, conf=0.87)

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Cited by

Sorted by citations

Authors
Park, S. E., Pham, D. T., Boinett, C., Wong, V. K., Pak, G. D., Panzner, U., Espinoza, L. M. C., von Kalckreuth, V., Im, J., Schütt-Gerowitt, H., Crump, J. A., Breiman, R. F., Adu-Sarkodie, Y., Owusu-Dabo, E., Rakotozandrindrainy, R., Soura, A. B., Aseffa, A., Gasmelseed, N., Keddy, K. H., May, J., Sow, A. G., Aaby, P., Biggs, H. M., Hertz, J. T., Montgomery, J. M., Cosmas, L., Olack, B., Fields, B., Sarpong, N., Razafindrabe, T. J. L., Raminosoa, T. M., Kabore, L. P., Sampo, E., Teferi, M., Yeshitela, B., El Tayeb, M. A., Sooka, A., Meyer, C. G., Krumkamp, R., Dekker, D. M., Jaeger, A., Poppert, S., Tall, A., Niang, A., Bjerregaard-Andersen, M., Løfberg, S. V., Seo, H. J., Jeon, H. J., Deerin, J. F., Park, J., Konings, F., Ali, M., Clemens, J. D., Hughes, P., Sendagala, J. N., Vudriko, T., Downing, R., Ikumapayi, U. N., Mackenzie, G. A., Obaro, S., Argimon, S., Aanensen, D. M., Page, A., Keane, J. A., Duchene, S., Dyson, Z., Holt, K. E., Dougan, G., Marks, F., & Baker, S.
Affiliations
  • International Vaccine Institute (KR)
  • University of Oxford (GB)
  • Cambridge University Hospitals NHS Foundation Trust (GB)
  • Duke University (US)
  • Emory University (US)
  • University of Antananarivo (MG)
  • Université Joseph Ki-Zerbo (BF)
  • All Africa Leprosy Tuberculosis and Rehabilitation Training Centre (ET)
  • University of Hafr Al-Batin (SA)
  • University of the Witwatersrand (ZA)
  • German Center for Infection Research (DE)
  • Institut Pasteur de Dakar (SN)
  • Statens Serum Institut (DK)
  • Kenya Medical Research Institute (KE)
  • Kwame Nkrumah University of Science and Technology (GH)
  • National Institute for Communicable Diseases (ZA)
  • Duy Tan University (VN)
  • Bernhard Nocht Institute for Tropical Medicine (DE)
  • Swiss Tropical and Public Health Institute (CH)
  • Cheikh Anta Diop University (SN)
  • London School of Hygiene & Tropical Medicine (GB)
  • Uganda Virus Research Institute (UG)
  • MRC Unit the Gambia (GM)
  • Bingham University (NG)
  • The University of Melbourne (AU)
  • University of Cambridge (GB)
Corresponding author
Marks, Florian
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2018-11-30
Volume
9
Issue
1
Pages
5094-5094
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-018-07370-z
PMC
PMC6269545
OpenAlex
W2902905086
Cited by
120
References
2
Citations by year
2026: 6 · 2025: 12 · 2024: 17 · 2023: 15 · 2022: 22 · 2021: 19 · 2020: 18 · 2019: 11
FWCI
11.24
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
  • edoc (University of Basel) (acceptedVersion)
  • LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Apollo (cc-by)
Funders
  • Bill and Melinda Gates Foundation (OPPGH5231)
  • Styrelsen för Internationellt Utvecklingssamarbete
  • Wellcome Trust (106158, 100087/Z/12/Z, 100087, 106158/Z/14/Z)
  • National Institute for Health and Care Research (CL-2015-14-006)
  • Royal Society (100087/Z/12/Z)
  • National Institutes of Health (PA-03-018, D43 PA-03-018, AI069484, AI067854, AI064518)
  • Centers for Disease Control and Prevention (R24 TW007988)
  • Directorate for Biological Sciences
  • Medical Research Council
  • Biotechnology and Biological Sciences Research Council (BBS/E/F/000PR10352)
  • NIHR Cambridge Biomedical Research Centre
  • National Institute of Allergy and Infectious Diseases (U01AI062563, U01AI069484, U01AI067854, P30AI064518)
  • Fogarty International Center (R01TW009237, R24TW007988)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Food Science › Salmonella and Campylobacter epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
  • Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Antibiotic Use and Resistance
Keywords
typhoid fever, phylogeography, whole genome sequencing, genotypes, antimicrobial resistance, sub-Saharan Africa, antimicrobial stewardship, typhoid conjugate vaccine, disease incidence, children
MeSH terms
Anti-Bacterial Agents, Genotype, Humans, Phylogeny, Salmonella Infections, Salmonella typhi, Typhoid Fever, Genetic Variation, Incidence, Africa South of the Sahara, Drug Resistance, Multiple, Bacterial, Phylogeography

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