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 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; Stephen Baker

doi:10.1038/s41467-018-07370-z

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 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 journal › Article › Research › peer-review

91 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 language	English
Article number	5094
Number of pages	10
Journal	Nature Communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-07370-z
Publication status	Published - 1 Dec 2018
Externally published	Yes

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1038/s41467-018-07370-zLicence: CC BY

269686986-oaFinal published version, 1.31 MBLicence: CC BY

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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., ... Baker, S. (2018). The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Nature Communications, 9(1), Article 5094. https://doi.org/10.1038/s41467-018-07370-z

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title = "The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa",

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.",

author = "Park, \{Se Eun\} and Pham, \{Duy Thanh\} and Christine Boinett and Wong, \{Vanessa K.\} and Pak, \{Gi Deok\} and Ursula Panzner and Espinoza, \{Ligia Maria Cruz\} and \{von Kalckreuth\}, Vera and Justin Im and Heidi Sch{\"u}tt-Gerowitt and Crump, \{John A.\} and Breiman, \{Robert F.\} and Yaw Adu-Sarkodie and Ellis Owusu-Dabo and Rapha{\"e}l Rakotozandrindrainy and Soura, \{Abdramane Bassiahi\} and Abraham Aseffa and Nagla Gasmelseed and Keddy, \{Karen H.\} and J{\"u}rgen May and Sow, \{Amy Gassama\} and Peter Aaby and Biggs, \{Holly M.\} and Hertz, \{Julian T.\} and Montgomery, \{Joel M.\} and Leonard Cosmas and Beatrice Olack and Barry Fields and Nimako Sarpong and Razafindrabe, \{Tsiriniaina Jean Luco\} and Raminosoa, \{Tiana Mirana\} and Kabore, \{Leon Parfait\} and Emmanuel Sampo and Mekonnen Teferi and Biruk Yeshitela and \{El Tayeb\}, \{Muna Ahmed\} and Arvinda Sooka and Meyer, \{Christian G.\} and Ralf Krumkamp and Dekker, \{Denise Myriam\} and Anna Jaeger and Sven Poppert and Adama Tall and Aissatou Niang and Morten Bjerregaard-Andersen and L{\o}fberg, \{Sandra Valborg\} and Seo, \{Hye Jin\} and Jeon, \{Hyon Jin\} and Deerin, \{Jessica Fung\} and Jinkyung Park and Frank Konings and Mohammad Ali and Clemens, \{John D.\} and Peter Hughes and Sendagala, \{Juliet Nsimire\} and Tobias Vudriko and Robert Downing and Ikumapayi, \{Usman N.\} and Mackenzie, \{Grant A.\} and Stephen Obaro and Silvia Argimon and Aanensen, \{David M.\} and Andrew Page and Keane, \{Jacqueline A.\} and Sebastian Duchene and Zoe Dyson and Holt, \{Kathryn E.\} and Gordon Dougan and Florian Marks and Stephen Baker",

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doi = "10.1038/s41467-018-07370-z",

language = "English",

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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, S, 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

TY - JOUR

T1 - The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

AU - Park, Se Eun

AU - Pham, Duy Thanh

AU - Boinett, Christine

AU - Wong, Vanessa K.

AU - Pak, Gi Deok

AU - Panzner, Ursula

AU - Espinoza, Ligia Maria Cruz

AU - von Kalckreuth, Vera

AU - Im, Justin

AU - Schütt-Gerowitt, Heidi

AU - Crump, John A.

AU - Breiman, Robert F.

AU - Adu-Sarkodie, Yaw

AU - Owusu-Dabo, Ellis

AU - Rakotozandrindrainy, Raphaël

AU - Soura, Abdramane Bassiahi

AU - Aseffa, Abraham

AU - Gasmelseed, Nagla

AU - Keddy, Karen H.

AU - May, Jürgen

AU - Sow, Amy Gassama

AU - Aaby, Peter

AU - Biggs, Holly M.

AU - Hertz, Julian T.

AU - Montgomery, Joel M.

AU - Cosmas, Leonard

AU - Olack, Beatrice

AU - Fields, Barry

AU - Sarpong, Nimako

AU - Razafindrabe, Tsiriniaina Jean Luco

AU - Raminosoa, Tiana Mirana

AU - Kabore, Leon Parfait

AU - Sampo, Emmanuel

AU - Teferi, Mekonnen

AU - Yeshitela, Biruk

AU - El Tayeb, Muna Ahmed

AU - Sooka, Arvinda

AU - Meyer, Christian G.

AU - Krumkamp, Ralf

AU - Dekker, Denise Myriam

AU - Jaeger, Anna

AU - Poppert, Sven

AU - Tall, Adama

AU - Niang, Aissatou

AU - Bjerregaard-Andersen, Morten

AU - Løfberg, Sandra Valborg

AU - Seo, Hye Jin

AU - Jeon, Hyon Jin

AU - Deerin, Jessica Fung

AU - Park, Jinkyung

AU - Konings, Frank

AU - Ali, Mohammad

AU - Clemens, John D.

AU - Hughes, Peter

AU - Sendagala, Juliet Nsimire

AU - Vudriko, Tobias

AU - Downing, Robert

AU - Ikumapayi, Usman N.

AU - Mackenzie, Grant A.

AU - Obaro, Stephen

AU - Argimon, Silvia

AU - Aanensen, David M.

AU - Page, Andrew

AU - Keane, Jacqueline A.

AU - Duchene, Sebastian

AU - Dyson, Zoe

AU - Holt, Kathryn E.

AU - Dougan, Gordon

AU - Marks, Florian

AU - Baker, Stephen

PY - 2018/12/1

Y1 - 2018/12/1

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85057585158

U2 - 10.1038/s41467-018-07370-z

DO - 10.1038/s41467-018-07370-z

M3 - Article

C2 - 30504848

AN - SCOPUS:85057585158

SN - 2041-1723

VL - 9

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 5094

ER -

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

Abstract

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