A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa

Sandra Van Puyvelde (), Tessa de Block, Sushmita Sridhar, Matt Bawn, Robert A. Kingsley, Brecht Ingelbeen, Mathew A. Beale, Barbara Barbé, Hyon Jin Jeon, Lisette Mbuyi-Kalonji, Marie-France Phoba, Dadi Falay, Delphine Martiny, Olivier Vandenberg, Dissou Affolabi, Jean Pierre Rutanga, Pieter-Jan Ceyssens, Wesley Mattheus, Wim L. Cuypers, Marianne A. B. van der Sande, Se Eun Park, Simon Kariuki, Kephas Otieno, John P. A. Lusingu, Joyce R. Mbwana, Samuel Adjei, Anima Sarfo, Seth O. Agyei, Kwaku P. Asante, Walter Otieno, Lucas Otieno, Marc C. Tahita, Palpouguini Lompo, Irving F. Hoffman, Tisungane Mvalo, Chisomo Msefula, Fatimah Hassan-Hanga, Stephen Obaro, Grant Mackenzie, Stijn Deborggraeve, Nicholas Feasey, Florian Marks, Calman A. MacLennan, Nicholas R. Thomson, Jan Jacobs, Gordon Dougan, Samuel Kariuki and Octavie Lunguya
Additional contact information
Sandra Van Puyvelde: Cambridge Biomedical Campus
Tessa de Block: Institute of Tropical Medicine
Sushmita Sridhar: Cambridge Biomedical Campus
Matt Bawn: Quadram Institute Bioscience
Robert A. Kingsley: Quadram Institute Bioscience
Brecht Ingelbeen: Institute of Tropical Medicine
Mathew A. Beale: Wellcome Genome Campus
Barbara Barbé: Institute of Tropical Medicine
Hyon Jin Jeon: Cambridge Biomedical Campus
Lisette Mbuyi-Kalonji: University Teaching Hospital of Kinshasa
Marie-France Phoba: University Teaching Hospital of Kinshasa
Dadi Falay: University Hospital of Kisangani
Delphine Martiny: Université Libre de Bruxelles (ULB)
Olivier Vandenberg: Université Libre de Bruxelles (ULB)
Dissou Affolabi: Centre National Hospitalier Universitaire Hubert Koutoukou Maga
Jean Pierre Rutanga: Institute of Tropical Medicine
Pieter-Jan Ceyssens: National Reference Center for Salmonella, Unit of Human Bacterial Diseases, Sciensano
Wesley Mattheus: National Reference Center for Salmonella, Unit of Human Bacterial Diseases, Sciensano
Wim L. Cuypers: Institute of Tropical Medicine
Marianne A. B. van der Sande: Institute of Tropical Medicine
Se Eun Park: International Vaccine Institute
Simon Kariuki: Kenya Medical Research Institute/Centre for Global Health Research
Kephas Otieno: Kenya Medical Research Institute/Centre for Global Health Research
John P. A. Lusingu: National Institute for Medical Research
Joyce R. Mbwana: National Institute for Medical Research
Samuel Adjei: University of Health & Allied Sciences
Anima Sarfo: University of Health & Allied Sciences
Seth O. Agyei: University of Health & Allied Sciences
Kwaku P. Asante: Ghana Health Service, Kintampo North Municipality
Walter Otieno: KEMRI/Walter Reed Project
Lucas Otieno: KEMRI/Walter Reed Project
Marc C. Tahita: Direction Régionale du Centre-Ouest/ClinicalResearch Unit of Nanoro
Palpouguini Lompo: Direction Régionale du Centre-Ouest/ClinicalResearch Unit of Nanoro
Irving F. Hoffman: University of North Carolina Project
Tisungane Mvalo: University of North Carolina Project
Chisomo Msefula: Kamuzu University of Health Sciences
Fatimah Hassan-Hanga: Bayero University
Stephen Obaro: University of Nebraska Medical Center
Grant Mackenzie: Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine
Stijn Deborggraeve: Institute of Tropical Medicine
Nicholas Feasey: University of North Carolina Project
Florian Marks: Cambridge Biomedical Campus
Calman A. MacLennan: University of Oxford
Nicholas R. Thomson: Wellcome Genome Campus
Jan Jacobs: Institute of Tropical Medicine
Gordon Dougan: Cambridge Biomedical Campus
Samuel Kariuki: Kenya Medical Research Institute
Octavie Lunguya: University Teaching Hospital of Kinshasa

Nature Communications, 2023, vol. 14, issue 1, 1-17

Abstract: Abstract Invasive non-typhoidal Salmonella (iNTS) disease manifesting as bloodstream infection with high mortality is responsible for a huge public health burden in sub-Saharan Africa. Salmonella enterica serovar Typhimurium (S. Typhimurium) is the main cause of iNTS disease in Africa. By analysing whole genome sequence data from 1303 S. Typhimurium isolates originating from 19 African countries and isolated between 1979 and 2017, here we show a thorough scaled appraisal of the population structure of iNTS disease caused by S. Typhimurium across many of Africa’s most impacted countries. At least six invasive S. Typhimurium clades have already emerged, with ST313 lineage 2 or ST313-L2 driving the current pandemic. ST313-L2 likely emerged in the Democratic Republic of Congo around 1980 and further spread in the mid 1990s. We observed plasmid-borne as well as chromosomally encoded fluoroquinolone resistance underlying emergences of extensive-drug and pan-drug resistance. Our work provides an overview of the evolution of invasive S. Typhimurium disease, and can be exploited to target control measures.

Date: 2023
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DOI: 10.1038/s41467-023-41152-6

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