Evidence map›Paper›PMID 30504848›Full record

ArticleNature communications2018

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 and 60 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
82citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

82 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Trial
  3. Trial
  4. Trial
  5. Article
  6. Article
  7. Genomic analysis ofMicrobial genomics · 2026
    Article
  8. Article
  9. Article
  10. Article
  11. Comparative genomics ofVirulence · 2025
    Article
  12. Article
  13. A contemporary genomic snapshot ofMicrobial genomics · 2025
    Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. medRxiv : the preprint server for health sciences · 2024
    Article
  20. Article

22 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

70 authors.

Se Eun ParkInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.ORCID http://orcid.org/0000-0002-1632-3045
Duy Thanh PhamThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quant 5, Ho Chi Minh City, Vietnam.
Christine BoinettThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quant 5, Ho Chi Minh City, Vietnam.
Vanessa K WongCentre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Gi Deok PakInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Ursula PanznerInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Ligia Maria Cruz EspinozaInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Vera von KalckreuthInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Justin ImInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Heidi Schütt-GerowittInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
John A CrumpKilimanjaro Christian Medical Centre, P.O. Box 3010, Moshi, Tanzania.
Robert F BreimanCenters for Disease Control and Prevention, KEMRI Complex, Mbagathi Road off Mbagathi Way, P.O. Box 606-00621 Village Market, Nairobi, Kenya.
Yaw Adu-SarkodieKwame Nkrumah University of Science and Technology, P.O. Box PMB KNUST, Kumasi, Ghana.
Ellis Owusu-DaboKwame Nkrumah University of Science and Technology, P.O. Box PMB KNUST, Kumasi, Ghana.
Raphaël RakotozandrindrainyUniversity of Antananarivo, BP 566, Antananarivo 101, Madagascar.
Abdramane Bassiahi SouraInstitut Supérieur des Sciences de la Population, University of Ouagadougou, 03 B.P. 7118, Ouagadougou 03, Burkina Faso.
Abraham AseffaArmauer Hansen Research Institute, Jimma Road, ALERT Compound, P.O. Box 1005, Addis Ababa, Ethiopia.ORCID http://orcid.org/0000-0002-8028-1150
Nagla GasmelseedFaculty of Medicine, University of Gezira, P.O. Box 20, Wad Medani, Sudan.
Karen H KeddyNational Institute for Communicable Diseases, Private Bag X4, Sandringham, 2131 Johannesburg, South Africa.
Jürgen MayBernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.ORCID http://orcid.org/0000-0001-7831-8420
Amy Gassama SowInstitute Pasteur de Dakar, 36 Avenue Pasteur, B.P. 220, Dakar, Senegal.
Peter AabyBandim Health Project, Apartado, 8611004, Bissau codex, Bissau, Guinea-Bissau.
Holly M BiggsKilimanjaro Christian Medical Centre, P.O. Box 3010, Moshi, Tanzania.
Julian T HertzKilimanjaro Christian Medical Centre, P.O. Box 3010, Moshi, Tanzania.
Joel M MontgomeryCenters for Disease Control and Prevention, KEMRI Complex, Mbagathi Road off Mbagathi Way, P.O. Box 606-00621 Village Market, Nairobi, Kenya.
Leonard CosmasCenters for Disease Control and Prevention, KEMRI Complex, Mbagathi Road off Mbagathi Way, P.O. Box 606-00621 Village Market, Nairobi, Kenya.
Beatrice OlackKenya Medical Research Institute, Mbagathi Rd. P.O. BOX 54840-00200, Nairobi, Kenya.
Barry FieldsCenters for Disease Control and Prevention, KEMRI Complex, Mbagathi Road off Mbagathi Way, P.O. Box 606-00621 Village Market, Nairobi, Kenya.
Nimako SarpongKwame Nkrumah University of Science and Technology, P.O. Box PMB KNUST, Kumasi, Ghana.
Tsiriniaina Jean Luco RazafindrabeUniversity of Antananarivo, BP 566, Antananarivo 101, Madagascar.
Tiana Mirana RaminosoaUniversity of Antananarivo, BP 566, Antananarivo 101, Madagascar.
Leon Parfait KaboreSchiphra Hospital, Ouagadougou 01, 01 B.P. 121, Burkina Faso.
Emmanuel SampoSchiphra Hospital, Ouagadougou 01, 01 B.P. 121, Burkina Faso.
Mekonnen TeferiArmauer Hansen Research Institute, Jimma Road, ALERT Compound, P.O. Box 1005, Addis Ababa, Ethiopia.
Biruk YeshitelaArmauer Hansen Research Institute, Jimma Road, ALERT Compound, P.O. Box 1005, Addis Ababa, Ethiopia.
Muna Ahmed El TayebFaculty of Medicine, University of Gezira, P.O. Box 20, Wad Medani, Sudan.
Arvinda SookaNational Institute for Communicable Diseases, Private Bag X4, Sandringham, 2131 Johannesburg, South Africa.
Christian G MeyerInstitute of Tropical Medicine, Eberhard-Karls University Tübingen, Geschwister-Scholl-Platz, 72074, Tübingen, Germany.
Ralf KrumkampBernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.
Denise Myriam DekkerBernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.
Anna JaegerBernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.
Sven PoppertSwiss Tropical and Public Health Institute, University of Basel, Socinstrasse 57, Postfach, CH-4002, Basel, Switzerland.
Adama TallUniversité Cheikh Anta Diop de Dakar, Dakar, B.P. 5005, Senegal.
Aissatou NiangUniversité Cheikh Anta Diop de Dakar, Dakar, B.P. 5005, Senegal.
Morten Bjerregaard-AndersenBandim Health Project, Apartado, 8611004, Bissau codex, Bissau, Guinea-Bissau.
Sandra Valborg LøfbergBandim Health Project, Apartado, 8611004, Bissau codex, Bissau, Guinea-Bissau.
Hye Jin SeoInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Hyon Jin JeonInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Jessica Fung DeerinInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Jinkyung ParkInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Frank KoningsInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Mohammad AliInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.ORCID http://orcid.org/0000-0003-1410-388X
John D ClemensInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea.
Peter HughesMedical Research Center (MRC)/Uganda Virus Research Institute (UVRI) & London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Plot 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda.
Juliet Nsimire SendagalaMedical Research Center (MRC)/Uganda Virus Research Institute (UVRI) & London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Plot 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda.
Tobias VudrikoMedical Research Center (MRC)/Uganda Virus Research Institute (UVRI) & London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Plot 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda.
Robert DowningUganda Virus Research Institute (UVRI), Plot 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda.
Usman N IkumapayiMedical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia.
Grant A MackenzieMedical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia.
Stephen ObaroDivision of Pediatric Infectious Diseases, University of Nebraska Medical Center, 42nd and Emile, Omaha, Nebraska, 68198, USA.
Silvia ArgimonCentre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
David M AanensenCentre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Andrew PageCentre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Jacqueline A KeaneCentre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Sebastian DucheneDepartment of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia.
Zoe DysonDepartment of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia.ORCID http://orcid.org/0000-0002-8887-3492
Kathryn E HoltDepartment of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia.ORCID http://orcid.org/0000-0003-3949-2471
Gordon DouganCentre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Florian MarksInternational Vaccine Institute, SNU Research Park, 1 Gwanak-ro, 1 Gwanak-gu, Seoul, 08826, Republic of Korea. fmarks@ivi.int.ORCID http://orcid.org/0000-0002-6043-7170
Stephen BakerThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quant 5, Ho Chi Minh City, Vietnam.

Funding

Social and Behavioral Sciences CoreP30AI064518 · NIAID · DUKE UNIVERSITY · PI Nwora Lance Okeke · 2005 to 2026
$50.5M
Fogarty International Clinical Research Scholars Support Center @ Vanderbilt-AAMCR24TW007988 · FIC · VANDERBILT UNIVERSITY · PI VERMUND, STEN H. · 2007 to 2011
$27.6M
Viral and Host Determinants of HIV-1 TransmissionU01AI067854 · NIAID · DUKE UNIVERSITY · PI HAYNES, BARTON F · 2005 to 2005
$14.9M
HIV/AIDS Clinical Trials UnitU01AI069484 · NIAID · DUKE UNIVERSITY · PI BARTLETT, JOHN A · 2007 to 2011
$14.6M
International Clinical Trials UnitU01AI062563 · NIAID · DUKE UNIVERSITY · PI BARTLETT, JOHN A · 2004 to 2007
$4.0M
The Impact and Society Ecology of Bacterial Zoonoses in Northern Tanzania: UnderR01TW009237 · FIC · DUKE UNIVERSITY · PI CRUMP, JOHN ANDREW · 2011 to 2014
$1.7M
FIC NIH HHS R01 TW009237FIC NIH HHS R24 TW007988NIAID NIH HHS P30 AI064518NIAID NIH HHS U01 AI062563NIAID NIH HHS U01 AI067854NIAID NIH HHS U01 AI069484Wellcome Trust
6 · The paper itself

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.

Indexed as

Africa South of the SaharaAnti-Bacterial AgentsDrug Resistance, Multiple, BacterialGenetic VariationGenotypeHumansIncidencePhylogenyPhylogeographySalmonella InfectionsSalmonella typhiTyphoid FeverAnti-Bacterial Agents

Identifiers

PMID30504848
PMCPMC6269545

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.