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Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
- Source :
- Nature Microbiology, Pulford, C V, Perez-Sepulveda, B M, Canals, R, Bevington, J A, Bengtsson, R J, Wenner, N, Rodwell, E V, Kumwenda, B, Zhu, X, Bennett, R J, Stenhouse, G E, Malaka De Silva, P, Webster, H J, Bengoechea, J A, Dumigan, A, Tran-Dien, A, Prakash, R, Banda, H C, Alufandika, L, Mautanga, M P, Bowers-Barnard, A, Beliavskaia, A Y, Predeus, A V, Rowe, W P M, Darby, A C, Hall, N, Weill, F X, Gordon, M A, Feasey, N A, Baker, K S & Hinton, J C D 2021, ' Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa ', Nature Microbiology, vol. 6, no. 3, pp. 327-338 . https://doi.org/10.1038/s41564-020-00836-1
- Publication Year :
- 2020
- Publisher :
- Springer Science and Business Media LLC, 2020.
-
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.<br />Stepwise evolution of invasive Salmonella Typhimurium in Africa is defined using genotypic and phenotypic analyses of isolates collected over a 50-yr period.
- Subjects :
- Salmonella typhimurium
Salmonella
Lineage (evolution)
Bacteremia
Genome informatics
medicine.disease_cause
Applied Microbiology and Biotechnology
Genome
Genotype
Phylogeny
Genetics
0303 health sciences
Virulence
Phylogenetic tree
Phylogenetics
Phenotype
Salmonella enterica
Salmonella Infections
Pseudogenes
Plasmids
Microbiology (medical)
Immunology
Biology
Microbiology
Article
Evolution, Molecular
03 medical and health sciences
Antibiotic resistance
SDG 3 - Good Health and Well-being
Sepsis
Drug Resistance, Bacterial
medicine
Humans
030304 developmental biology
030306 microbiology
Genetic Variation
Cell Biology
biology.organism_classification
Computational biology and bioinformatics
Africa
Molecular evolution
Genome, Bacterial
Subjects
Details
- ISSN :
- 20585276
- Volume :
- 6
- Database :
- OpenAIRE
- Journal :
- Nature Microbiology
- Accession number :
- edsair.doi.dedup.....7a49e6ff039ac94bfb81b219ce79cab4