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

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 bla CTX-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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-017-0480-7) contains supplementary material, which is available to authorized users.

Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?

“…A recent study based on public health surveillance in the UK highlighted that S. enterica Typhimurium causing invasive non‐typhoidal salmonellosis in Africa carried a specific prophage as well as antibiotic resistance genes that are not found in the UK version of this lineage (Kintz et al ., ; Owen et al ., ; Ashton et al ., ). As a consequence stably integrated prophages are useful tools as epidemiology markers in addition to CRISPR‐Cas typing.…”

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

“…The ability to select a subset of the displayed nodes facilitates focused attention on individual groups of related genotypes. For example, we re-investigated the global relationships of recently described isolates of Salmonella serovar Typhimurium of legacy MLST ST313 and ST302 from Africa and the UK (Ashton et al 2017) (yellow polygon in Supplemental Fig S1A). Legacy MLST STs were used as metadata to identify and select these genomes among 19,670 Typhimurium genomes in a GrapeTree based on cgMLST STs.…”

A window into lysogeny: Revealing temperate phage biology with transcriptomics

“…The majority of bacterial taxa contain prophages (Roux et al, 2015; Touchon et al, 2016), and prophages are very frequently the main sources of genetic diversity between closely-related bacterial strains or pathovariants (Ashton et al, 2017; Mottawea et al, 2018). Given that more genome sequences exist for bacteria than for any other domain of life, and bacteria frequently harbour multiple prophages, it has been argued that temperate phage may be the most deeply sequenced organisms on the planet (Owen et al, 2018).…”