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 SandeSe 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

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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.

Original languageEnglish
Article number6392
JournalNature Communications
Number of pages17
Publication statusPublished - 2023


  • Humans
  • Salmonella typhimurium/genetics
  • Salmonella Infections/epidemiology
  • Africa South of the Sahara/epidemiology
  • Genomics
  • Drug Resistance, Microbial


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