Abstract
BackgroundThe ST313 sequence type of Salmonella Typhimurium causes invasive non-typhoidal salmonellosis and was thought to be confined to sub-Saharan Africa. Two distinct phylogenetic lineages of African ST313 have been identified.MethodsWe analysed the whole genome sequences of S. Typhimurium isolates from UK patients that were generated following the introduction of routine whole-genome sequencing (WGS) of Salmonella enterica by Public Health England in 2014.ResultsWe found that 2.7% (84/3147) of S. Typhimurium from patients in England and Wales were ST313 and were associated with gastrointestinal infection. Phylogenetic analysis revealed novel diversity of ST313 that distinguished UK-linked gastrointestinal isolates from African-associated extra-intestinal isolates. The majority of genome degradation of African ST313 lineage 2 was conserved in the UK-ST313, but the African lineages carried a characteristic prophage and antibiotic resistance gene repertoire. These findings suggest that a strong selection pressure exists for certain horizontally acquired genetic elements in the African setting. One UK-isolated lineage 2 strain that probably originated in Kenya carried a chromosomally located blaCTX-M-15, demonstrating the continual evolution of this sequence type in Africa in response to widespread antibiotic usage.ConclusionsThe discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in this important sequence type. This study highlights the power of routine WGS by public health agencies to make epidemiologically significant deductions that would be missed by conventional microbiological methods. We speculate that the niche specialisation of sub-Saharan African ST313 lineages is driven in part by the acquisition of accessory genome elements.
Highlights
The ST313 sequence type of Salmonella Typhimurium causes invasive non-typhoidal salmonellosis and was thought to be confined to sub-Saharan Africa
Typhimurium genomes sequenced by Public Health (PHE) within the timeframes stated above are listed in Additional file 1: Table S1
Typhimurium isolates from human, animal, food and environmental sources underwent whole-genome sequencing (WGS) by PHE, of which 79 (2.6%) were of multi-locus ST ST313
Summary
The ST313 sequence type of Salmonella Typhimurium causes invasive non-typhoidal salmonellosis and was thought to be confined to sub-Saharan Africa. Serovars of Salmonella enterica cause infections in a diverse range of hosts. Salmonella are responsible for a broad range of clinical presentations, from gastroenteritis to invasion of normally sterile compartments such as the bloodstream or brain. Salmonella Typhi and Salmonella Paratyphi A, are associated with both human-restricted and invasive disease. By inference, ‘non-typhoidal’ serovars have been considered to be non-invasive in immunocompetent individuals; this crude clinical distinction is misleading [1]. These ‘non-typhoidal’ Salmonella (NTS) serovars typically have a broad host-range and the majority of human cases
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