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



Ashton, Philip M, Owen, Sian V ORCID: 0000-0001-5330-3177, Kaindama, Lukeki, Rowe, Will PM ORCID: 0000-0003-0384-4463, Lane, Chris R, Larkin, Lesley, Nair, Satheesh, Jenkins, Claire, de Pinna, Elizabeth M, Feasey, Nicholas A
et al (show 2 more authors) (2017) Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa. GENOME MEDICINE, 9.

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Abstract

Background:The ST313 sequence type ofSalmonellaTyphimurium causes invasive non-typhoidal salmonellosis and wasthought to be confined to sub-Saharan Africa. Two distinct phylogenetic lineages of African ST313 have been identified.Methods:We analysed the whole genome sequences ofS. Typhimurium isolates from UK patients that weregenerated following the introduction of routine whole-genome sequencing (WGS) ofSalmonella entericabyPublic Health England in 2014.Results:We found that 2.7% (84/3147) ofS. Typhimurium from patients in England and Wales were ST313 and wereassociated with gastrointestinal infection. Phylogenetic analysis revealed novel diversity of ST313 that distinguishedUK-linked gastrointestinal isolates from African-associated extra-intestinal isolates. The majority of genome degradationof African ST313 lineage 2 was conserved in the UK-ST313, but the African lineages carried a characteristic prophageand antibiotic resistance gene repertoire. These findings suggest that a strong selection pressure exists for certainhorizontally acquired genetic elements in the African setting. One UK-isolated lineage 2 strain that probably originatedin Kenya carried a chromosomally locatedblaCTX-M-15, demonstrating the continual evolution of this sequence type inAfrica in response to widespread antibiotic usage.Conclusions:The discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in thisimportant sequence type. This study highlights thepower of routine WGS by public health agencies to makeepidemiologically significant deductions that would be missed by conventional microbiological methods. Wespeculate that the niche specialisation of sub-Saharan African ST313 lineages is driven in part by the acquisitionof accessory genome elements.

Item Type: Article
Depositing User: Symplectic Admin
Date Deposited: 07 Nov 2017 07:50
Last Modified: 17 Jun 2021 21:10
DOI: 10.1186/s13073-017-0480-7
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3011652