Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa

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Pulford, Caisey, Perez-Sepulveda, Blanca M, Canals, Rocio, Bevington, Jessica A, Bengtsson, Rebecca J, Wenner, Nicolas, Rodwell, Ella V, Kumwenda, Benjamin, Zhu, Xioajun, Bennett, Rebecca J ORCID: 0000-0001-5290-5109 et al (show 21 more authors) , Stenhouse, George E, De Silva, Malaka ORCID: 0000-0002-0579-0131, Webster, Hermione J ORCID: 0000-0001-8655-911X, Bengoechea, Jose A, Dumigan, Amy, Tran-Dien, ALicia, Prakash, Reenesh, Banda, Happy C, Alufandika, Lovemore, Mautanga, Mike P, Bowers-Barnard, Arthuer, Beliavskaia, Alexendra Y ORCID: 0000-0002-1194-5689, Predeus, Alexander V ORCID: 0000-0002-2750-1599, Rowe, Will PM, Darby, Alister C ORCID: 0000-0002-3786-6209, Nall, Neil, Weill, Francois-Xavier, Gordon, Melita A ORCID: 0000-0002-0629-0884, Feasey, Nicholas A, Baker, Kate S ORCID: 0000-0001-5850-1949 and Hinton, Jay ORCID: 0000-0003-2671-6026 (2020) Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nature Microbiology, 6 (3). 327-+.

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Abstract

Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear. Here, to define the evolutionary dynamics of ST313, we sub-sampled from two comprehensive collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, which had not occurred in other ST313 lineages. Despite arising only recently in the clinic, ST313 L3 is a phylogenetic intermediate between ST313 L1 and L2, with a characteristic accessory genome. Our in-depth genotypic and phenotypic characterization identifies the crucial loss-of-function genetic events that occurred during the stepwise evolution of invasive S. Typhimurium across Africa.

Item Type:	Article
Additional Information:	Nature Microbiology have agreed to publish this paper Open Access - because of its focus on global health issues of importance to developing countries. The Editor tells me that there will be no APC charge, but I have not heard this "officially".
Uncontrolled Keywords:	Humans, Salmonella typhimurium, Salmonella Infections, Sepsis, Evolution, Molecular, Phylogeny, Drug Resistance, Bacterial, Virulence, Genotype, Phenotype, Genome, Bacterial, Pseudogenes, Plasmids, Africa, Genetic Variation
Depositing User:	Symplectic Admin
Date Deposited:	13 Jan 2021 11:45
Last Modified:	18 Jan 2023 23:05
DOI:	10.1038/s41564-020-00836-1
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3111141

Available Versions of this Item

• Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. (deposited 17 Nov 2020 08:50)
  • Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. (deposited 13 Jan 2021 11:45) [Currently Displayed]