Nature Communications (Oct 2023)
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,
- Octavie Lunguya
Affiliations
- Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus
- Tessa de Block
- Institute of Tropical Medicine
- Sushmita Sridhar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus
- Matt Bawn
- Quadram Institute Bioscience
- Robert A. Kingsley
- Quadram Institute Bioscience
- Brecht Ingelbeen
- Institute of Tropical Medicine
- Mathew A. Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus
- Barbara Barbé
- Institute of Tropical Medicine
- Hyon Jin Jeon
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus
- Lisette Mbuyi-Kalonji
- Department of Medical Biology, University Teaching Hospital of Kinshasa
- Marie-France Phoba
- Department of Medical Biology, University Teaching Hospital of Kinshasa
- Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani
- Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles-Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB)
- Olivier Vandenberg
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles-Universitair Laboratorium Brussel (LHUB-ULB), 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
- Kintampo Health Research Centre, Research and Development Division, Ghana Health Service, Kintampo North Municipality
- Walter Otieno
- KEMRI/Walter Reed Project
- Lucas Otieno
- KEMRI/Walter Reed Project
- Marc C. Tahita
- Institut de Recherche en Science de la Santé, Direction Régionale du Centre-Ouest/ClinicalResearch Unit of Nanoro
- Palpouguini Lompo
- Institut de Recherche en Science de la Santé, 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
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences
- Fatimah Hassan-Hanga
- Department of Paediatrics, 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 Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus
- Calman A. MacLennan
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford
- Nicholas R. Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus
- Jan Jacobs
- Institute of Tropical Medicine
- Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus
- Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute
- Octavie Lunguya
- Department of Medical Biology, University Teaching Hospital of Kinshasa
- DOI
- https://doi.org/10.1038/s41467-023-41152-6
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 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.
