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Background  The 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.    Methods  We 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.    Results  We 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  bla   CTX-M-15 , demonstrating the continual evolution of this sequence type in Africa in response to widespread antibiotic usage.    Conclusions  The 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.    Electronic supplementary material  The online version of this article (doi:10.1186/s13073-017-0480-7) contains supplementary material, which is available to authorized users.

Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa