Abstract
The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.
Original language | English (US) |
---|---|
Article number | 12827 |
Journal | Nature communications |
Volume | 7 |
DOIs | |
State | Published - 2016 |
ASJC Scopus subject areas
- Chemistry(all)
- Biochemistry, Genetics and Molecular Biology(all)
- Physics and Astronomy(all)
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An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. / Wong, Vanessa K.; Baker, Stephen; Connor, Thomas R.; Pickard, Derek; Page, Andrew J.; Dave, Jayshree; Murphy, Niamh; Holliman, Richard; Sefton, Armine; Millar, Michael; Dyson, Zoe A.; Dougan, Gordon; Holt, Kathryn E.; Parkhill, Julian; Kingsley, Robert A.; Thomson, Nicholas R.; Keane, Jacqueline A.; Hadfield, James; Klemm, Elizabeth J.; Harris, Simon R.; Cain, Amy K.; Kariuki, Samuel; Okoro, Chinyere; MacLennan, Calman A.; Vu Thieu, Nga Tran; Thanh, Duy Pham; Thompson, Corinne; Dolecek, Christiane; Campbell, James I.; Thwaites, Guy; Farrar, Jeremy; Newton, Paul N.; Dance, David; Turner, Paul; Mulholland, E. Kim; Hawkey, Jane; Edwards, David J.; Feasey, Nicholas A.; Weill, François Xavier; Le Hello, Simon; Hart, Peter J.; Breiman, Robert F.; Onsare, Robert S.; Watson, Conall H.; Edmunds, W. John; Gordon, Melita A.; Heyderman, Robert S.; Msefula, Chisomo; Jacobs, Jan; Lunguya, Octavie; Chabalgoity, Jose A.; Kama, Mike; Jenkins, Kylie; Dutta, Shanta; Marks, Florian; Campos, Josefina; Obaro, Stephen; Keddy, Karen H.; Smith, Anthony M.; Parry, Christopher M.; Karkey, Abhilasha; Dongol, Sabina; Basnyat, Buddha; Arjyal, Amit; Dufour, Muriel; Bandaranayake, Don; Toleafoa, Take N.; Singh, Shalini Pravin; Hatta, Mochammad; Davong, Viengmon; Isaia, Lupeoletalalelei; Wijedoru, Lalith; Crump, John A.; De Pinna, Elizabeth; Nair, Satheesh; Nilles, Eric J.; Soeng, Sona; Valcanis, Mary; Powling, Joan; Dimovski, Karolina; Hogg, Geoff; Mather, Alison E.; Amos, Ben.
In: Nature communications, Vol. 7, 12827, 2016.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid
AU - Wong, Vanessa K.
AU - Baker, Stephen
AU - Connor, Thomas R.
AU - Pickard, Derek
AU - Page, Andrew J.
AU - Dave, Jayshree
AU - Murphy, Niamh
AU - Holliman, Richard
AU - Sefton, Armine
AU - Millar, Michael
AU - Dyson, Zoe A.
AU - Dougan, Gordon
AU - Holt, Kathryn E.
AU - Parkhill, Julian
AU - Kingsley, Robert A.
AU - Thomson, Nicholas R.
AU - Keane, Jacqueline A.
AU - Hadfield, James
AU - Klemm, Elizabeth J.
AU - Harris, Simon R.
AU - Cain, Amy K.
AU - Kariuki, Samuel
AU - Okoro, Chinyere
AU - MacLennan, Calman A.
AU - Vu Thieu, Nga Tran
AU - Thanh, Duy Pham
AU - Thompson, Corinne
AU - Dolecek, Christiane
AU - Campbell, James I.
AU - Thwaites, Guy
AU - Farrar, Jeremy
AU - Newton, Paul N.
AU - Dance, David
AU - Turner, Paul
AU - Mulholland, E. Kim
AU - Hawkey, Jane
AU - Edwards, David J.
AU - Feasey, Nicholas A.
AU - Weill, François Xavier
AU - Le Hello, Simon
AU - Hart, Peter J.
AU - Breiman, Robert F.
AU - Onsare, Robert S.
AU - Watson, Conall H.
AU - Edmunds, W. John
AU - Gordon, Melita A.
AU - Heyderman, Robert S.
AU - Msefula, Chisomo
AU - Jacobs, Jan
AU - Lunguya, Octavie
AU - Chabalgoity, Jose A.
AU - Kama, Mike
AU - Jenkins, Kylie
AU - Dutta, Shanta
AU - Marks, Florian
AU - Campos, Josefina
AU - Obaro, Stephen
AU - Keddy, Karen H.
AU - Smith, Anthony M.
AU - Parry, Christopher M.
AU - Karkey, Abhilasha
AU - Dongol, Sabina
AU - Basnyat, Buddha
AU - Arjyal, Amit
AU - Dufour, Muriel
AU - Bandaranayake, Don
AU - Toleafoa, Take N.
AU - Singh, Shalini Pravin
AU - Hatta, Mochammad
AU - Davong, Viengmon
AU - Isaia, Lupeoletalalelei
AU - Wijedoru, Lalith
AU - Crump, John A.
AU - De Pinna, Elizabeth
AU - Nair, Satheesh
AU - Nilles, Eric J.
AU - Soeng, Sona
AU - Valcanis, Mary
AU - Powling, Joan
AU - Dimovski, Karolina
AU - Hogg, Geoff
AU - Mather, Alison E.
AU - Amos, Ben
N1 - Funding Information: This work was supported by a number of organizations. The Wellcome Trust Sanger Institute authors were funded by Wellcome Trust Award #098051. V.K.W. was supported by the Wellcome Trust (#098051) and the National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre (BRC). N.F. was supported by the Wellcome Trust Research Fellowship #WT092152MA. N.F., R.S.H. and this work were supported by a strategic award from the Wellcome Trust for the MLW Clinical Research Programme (#101113/Z/13/Z). C.P. was funded by The Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme, supported by the Wellcome Trust of Great Britain (Major Overseas Programmes?Thailand Unit Core Grant), the European Society for Paediatric Infectious Diseases and University of Oxford-Li Ka Shing Global Health Foundation. D.D., P.N. and V.D. were supported by the Wellcome Trust (core grant #089275/H/09/Z). Z.A.D. was supported by the Wellcome Trust (Strategic award #106158). K.E.H. was supported by the NHMRC of Australia (fellowship #1061409) and the Victorian Life Sciences Computation Initiative (VLSCI; grant #VR0082). C.A.M. was supported by a Clinical Research Fellowship from GlaxoSmithKline and PJH by a UK Medical Research Council PhD studentship. This work forms part of an EU FP7 Marie Curie Actions Industry Academia Partnerships and Pathways (IAPP) Consortium Programme, entitled GENDRIVAX (Genome-driven vaccine development for bacterial infections), involving the Wellcome Trust Sanger Institute, KEMRI Nairobi and Novartis Vaccines Institute for Global Health. The Institut Pasteur (IP) authors were funded by the IP, the Institut de Veille Sanitaire and by the French Government ?Investissement d?Avenir? programme (Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence, grant #ANR-10-LABX-62-IBEID). C.H.W. was supported by the UK Medical Research Council (MRC; #MR/J003999/1). C.O. was supported by Society in Science, The Branco Weiss Fellowship, administered by the ETH Zurich. A.K.C. was supported by the MRC (#G1100100/1). J.J. was supported by the antibiotic resistance surveillance project in DR Congo, funded by Project 2.01 of the Third Framework Agreement between the Belgian Directorate General of Development Cooperation and the Institute of Tropical Medicine, Antwerp, Belgium. F.M. was supported by a research grant from the Bill and Melinda Gates Foundation. J.A.C. was supported by the joint US National Institutes of Health-National Science Foundation Ecology and Evolution of Infectious Disease program (#R01 TW009237) and the UK Biotechnology and Biological Sciences Research Council (BBSRC; #BB/J010367/1), and by UK BBSRC Zoonoses in Emerging Livestock Systems awards #BB/L017679, #BB/L018926 and #BB/L018845. S.K. was supported by the NIH Grant Number R01 AI099525-02. S.B. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (#100087/Z/12/Z). S.O. was supported by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health (#R01AI097493). C.D. was supported by the University of Oxford-Li Ka Shing Global Health Programme. A.E.M. was supported by a Biotechnology and Biological Sciences Research Council award (#BB/M014088/1). P.T. was supported by the Wellcome Trust of Great Britain (Major Overseas Programmes?Thailand Unit Core Grant) and University of Oxford-Li Ka Shing Global Health Foundation.
PY - 2016
Y1 - 2016
N2 - The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.
AB - The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.
UR - http://www.scopus.com/inward/record.url?scp=84991011519&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84991011519&partnerID=8YFLogxK
U2 - 10.1038/ncomms12827
DO - 10.1038/ncomms12827
M3 - Article
C2 - 27703135
AN - SCOPUS:84991011519
VL - 7
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
M1 - 12827
ER -