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Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

Vanessa Wong ^{1, 2, *} Stephen Baker ^{3, 4, 5} Derek Pickard ¹ Julian Parkhill ¹ Andrew Page ¹ Nicholas Feasey ⁶ Robert Kingsley ^{1, 7} Nicholas Thomson ^{1, 5} Jacqueline Keane ¹ François-Xavier Weill ⁸ David Edwards ⁹ Jane Hawkey ⁹ Simon Harris ¹ Alison Mather ¹ Amy Cain ¹ James Hadfield ¹ Peter Hart ¹⁰ Nga Tran Vu Thieu ³ Elizabeth E Klemm ¹ Dafni Glinos ¹ Robert Breiman ^{11, 12, 13} Conall Watson ⁵ Samuel Kariuki ^{1, 11} Melita A. Gordon ¹⁴ Robert S Heyderman ¹⁵ Chinyere Okoro ¹ Jan Jacobs ^{16, 17} Octavie Lunguya ^{18, 19} W John Edmunds ⁵ Chisomo Msefula ¹⁵ José A. Chabalgoity ²⁰ Mike Kama ²¹ Kylie Jenkins ²¹ Shanta Dutta ²² Florian Marks ²³ Josefina Campos ²⁴ Corinne Thompson ^{3, 4} Stephen Obaro ^{25, 26, 27} Calman Maclennan ^{1, 10, 28} Christiane Dolecek ⁴ Karen H Keddy ²⁹ Anthony Smith ²⁹ Christopher Parry ^{5, 30} Abhilasha Karkey ³ E Kim Mulholland ^{5, 31} James Campbell ^{3, 4} Sabina Dongol ³² Buddha Basnyat ³² Muriel Dufour ³³ Don Bandaranayake ³³ Take Toleafoa Naseri ³⁴ Shalini Pravin Singh ³⁵ Mochammad Hatta ³⁶ Paul Newton ^{37, 4} Robert Onsare ¹¹ Lupeoletalalei Isaia ³⁸ David Dance ^{37, 4} Viengmon Davong ³⁷ Guy E Thwaites ^{3, 4} Lalith Wijedoru ^{39, 40} John Crump ⁴¹ Elizabeth de Pinna ⁴² Satheesh Nair ⁴² Eric Nilles ³⁵ Duy Pham Thanh ³ Paul Turner ^{39, 4, 43} Sona Soeng ⁴³ Mary Valcanis ⁴⁴ Joan Powling ⁴⁴ Karolina Dimovski ⁴⁴ Geoff Hogg ⁴⁴ Jeremy Farrar ^{3, 4} Kathryn Holt ⁹ Gordon Dougan ¹

* Corresponding author

1 The Wellcome Trust Sanger Institute [Cambridge]

2 Addenbrooke's Hospital

3 OUCRU - Oxford University Clinical Research Unit [Ho Chi Minh City]

4 University of Oxford [Oxford]

5 LSHTM - London School of Hygiene and Tropical Medicine

6 LSTM - Liverpool School of Tropical Medicine

7 Institute of Food Research [Norwich]

8 BPE - Bactéries pathogènes entériques

9 University of Melbourne

10 University of Birmingham [Birmingham]

11 KEMRI - Kenya Medical Research Institute

12 CDC - Centers for Disease Control and Prevention [Atlanta]

13 EGHI - Emory Global Health Institute [Atlanta]

14 University of Liverpool

15 University of Malawi

16 ITM - Institute of Tropical Medicine [Antwerp]

17 KU Leuven - Catholic University of Leuven - Katholieke Universiteit Leuven

18 INRB - Institut National de Recherche Biomédicale [Kinshasa]

19 UNIKIN - University of Kinshasa

20 Universidad de Montevideo

21 Ministry of Health [Fiji]

22 National Institute of Cholera and Enteric Diseases

23 IVI - International Vaccine Institute

24 ANLIS - Administración Nacional de Laboratorios e Institutos de Salud ‘Carlos Malbran'

25 University of Nebraska Medical Center [Omaha, NE, USA]

26 University of Abuja

27 Bingham University

28 NVGH - Novartis Vaccines Institute for Global Health

29 WITS - University of the Witwatersrand [Johannesburg]

30 Nagasaki University

31 MCRI - Murdoch Children's Research Institute

32 Oxford University Clinical Research Unit [Kathmandu]

33 ESR - Institute of Environmental Science and Research

34 Ministry of Health [Samoa]

35 OMS / WHO - Organisation Mondiale de la Santé / World Health Organization Office

36 Unhas - Hasanuddin University

37 LOMWRU - Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit

38 TTM - Tupua Tamasese Meaole Hospital

39 Mahidol University [Bangkok]

40 Chelsea and Westminster Hospital

41 University of Otago [Dunedin, Nouvelle-Zélande]

42 Public Health England [London]

43 AHC - Angkor Hospital for Children

44 The Peter Doherty Institute for Infection and Immunity [Melbourne]

Abstract : The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.

Document type :

Journal articles

Domain :

Life Sciences [q-bio] / Microbiology and Parasitology / Bacteriology

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https://hal-pasteur.archives-ouvertes.fr/pasteur-02043698
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Submitted on : Thursday, February 21, 2019 - 10:54:15 AM
Last modification on : Thursday, April 7, 2022 - 10:10:25 AM