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 von 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 MayAmy 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 K Obaro, Silvia Argimon, David M. Aanensen, Andrew Page, Jacqueline A. Keane, Sebastian Duchene, Zoe Dyson, Kathryn E. Holt, Gordon Dougan, Florian Marks, Stephen Baker

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish (US)
Article number5094
JournalNature communications
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2018

Fingerprint

typhoid
fever
Phylogeography
Salmonella typhi
Africa South of the Sahara
Typhoid Fever
drugs
incidence
Incidence
Genotype
Pharmaceutical Preparations
organisms
Typhoid-Paratyphoid Vaccines
Eastern Africa
Conjugate Vaccines
Western Africa
Drug and Narcotic Control
Geographical distribution
vaccines
biological diversity

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Park, S. E., Pham, D. T., Boinett, C., Wong, V. K., Pak, G. D., Panzner, U., ... Baker, S. (2018). The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Nature communications, 9(1), [5094]. https://doi.org/10.1038/s41467-018-07370-z

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. / 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 K; Argimon, Silvia; Aanensen, David M.; Page, Andrew; Keane, Jacqueline A.; Duchene, Sebastian; Dyson, Zoe; Holt, Kathryn E.; Dougan, Gordon; Marks, Florian; Baker, Stephen.

In: Nature communications, Vol. 9, No. 1, 5094, 01.12.2018.

Research output: Contribution to journalArticle

Park, SE, Pham, DT, Boinett, C, Wong, VK, Pak, GD, Panzner, U, Espinoza, LMC, von Kalckreuth, V, Im, J, Schütt-Gerowitt, H, Crump, JA, Breiman, RF, Adu-Sarkodie, Y, Owusu-Dabo, E, Rakotozandrindrainy, R, Soura, AB, Aseffa, A, Gasmelseed, N, Keddy, KH, May, J, Sow, AG, Aaby, P, Biggs, HM, Hertz, JT, Montgomery, JM, Cosmas, L, Olack, B, Fields, B, Sarpong, N, Razafindrabe, TJL, Raminosoa, TM, Kabore, LP, Sampo, E, Teferi, M, Yeshitela, B, El Tayeb, MA, Sooka, A, Meyer, CG, Krumkamp, R, Dekker, DM, Jaeger, A, Poppert, S, Tall, A, Niang, A, Bjerregaard-Andersen, M, Løfberg, SV, Seo, HJ, Jeon, HJ, Deerin, JF, Park, J, Konings, F, Ali, M, Clemens, JD, Hughes, P, Sendagala, JN, Vudriko, T, Downing, R, Ikumapayi, UN, Mackenzie, GA, Obaro, SK, Argimon, S, Aanensen, DM, Page, A, Keane, JA, Duchene, S, Dyson, Z, Holt, KE, Dougan, G, Marks, F & Baker, S 2018, 'The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa', Nature communications, vol. 9, no. 1, 5094. https://doi.org/10.1038/s41467-018-07370-z
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 K ; Argimon, Silvia ; Aanensen, David M. ; Page, Andrew ; Keane, Jacqueline A. ; Duchene, Sebastian ; Dyson, Zoe ; Holt, Kathryn E. ; Dougan, Gordon ; Marks, Florian ; Baker, Stephen. / The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. In: Nature communications. 2018 ; Vol. 9, No. 1.
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AU - Pham, Duy Thanh

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AU - Espinoza, Ligia Maria Cruz

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AU - Tall, Adama

AU - Niang, Aissatou

AU - Bjerregaard-Andersen, Morten

AU - Løfberg, Sandra Valborg

AU - Seo, Hye Jin

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AU - Deerin, Jessica Fung

AU - Park, Jinkyung

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AU - Ali, Mohammad

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