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 › peer-review

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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.

Original language	English (US)
Article number	5094
Journal	Nature communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-07370-z
State	Published - Dec 1 2018

ASJC Scopus subject areas

General Physics and Astronomy
General Chemistry
General Biochemistry, Genetics and Molecular Biology

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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

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

@article{d1f7e9bd20fe4b0aa05e3d7282b52e4b,

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",

note = "Funding Information: This study was supported by the Bill & Melinda Gates Foundation (grant: OPPGH5231). The findings and conclusions contained within are our own and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation or the US Centers for Disease Control and Prevention, the International Vaccine Institute. The International Vaccine Institute acknowledges its donors, including the Government of the Republic of Korea and the Swedish International Development Cooperation Agency (SIDA). Research infrastructure at the Moshi site was supported by the US National Institutes of Health (R01TW009237; U01 AI062563; R24 TW007988; D43 PA-03-018; U01 AI069484; U01 AI067854; P30 AI064518), and by the UK Biotechnology and Biological Sciences Research Council (BB/J010367). SB is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (100087/Z/12/Z). KEH is supported by a Senior Medical Research Fellowship from the Viertel Foundation of Australia. Z.A.D. was supported by strategic award #106158 from the Wellcome Trust of Great Britain (106158/Z/14/Z). V.K.W. is supported by NIHR and NIHR Cambridge BRC. We thank staff at the TSAP network countries, the Medical Research Council Unit The Gambia, and the Uganda Public Health Emergency Operations Centre, Kampala, Uganda. We are grateful to Soo-Young Kwon for her invaluable administrative support of the project. Publisher Copyright: {\textcopyright} 2018, The Author(s).",

year = "2018",

month = dec,

day = "1",

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

language = "English (US)",

volume = "9",

journal = "Nature communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

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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

N1 - Funding Information: This study was supported by the Bill & Melinda Gates Foundation (grant: OPPGH5231). The findings and conclusions contained within are our own and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation or the US Centers for Disease Control and Prevention, the International Vaccine Institute. The International Vaccine Institute acknowledges its donors, including the Government of the Republic of Korea and the Swedish International Development Cooperation Agency (SIDA). Research infrastructure at the Moshi site was supported by the US National Institutes of Health (R01TW009237; U01 AI062563; R24 TW007988; D43 PA-03-018; U01 AI069484; U01 AI067854; P30 AI064518), and by the UK Biotechnology and Biological Sciences Research Council (BB/J010367). SB is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (100087/Z/12/Z). KEH is supported by a Senior Medical Research Fellowship from the Viertel Foundation of Australia. Z.A.D. was supported by strategic award #106158 from the Wellcome Trust of Great Britain (106158/Z/14/Z). V.K.W. is supported by NIHR and NIHR Cambridge BRC. We thank staff at the TSAP network countries, the Medical Research Council Unit The Gambia, and the Uganda Public Health Emergency Operations Centre, Kampala, Uganda. We are grateful to Soo-Young Kwon for her invaluable administrative support of the project. Publisher Copyright: © 2018, The Author(s).

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.

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U2 - 10.1038/s41467-018-07370-z

DO - 10.1038/s41467-018-07370-z

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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

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