Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK

Bloomfield, Samuel J., Janecko, Nicol, Palau, Raphaёlle, Alikhan, Nabil-Fareed and Mather, Alison E. (2023) Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK. Microbial Genomics, 9 (7). ISSN 2057-5858

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Non-typhoidal Salmonella (NTS) is a major cause of bacterial gastroenteritis. Although many countries have implemented whole genome sequencing (WGS) of NTS, there is limited knowledge on NTS diversity on food and its contribution to human disease. In this study, the aim was to characterise the NTS genomes from retail foods in a particular region of the UK and assess the contribution to human NTS infections. Raw food samples were collected at retail in a repeated cross-sectional design in Norfolk, UK, including chicken (n=311), leafy green (n=311), pork (n=311), prawn (n=279) and salmon (n=157) samples. Up to eight presumptive NTS isolates per positive sample underwent WGS and were compared to publicly available NTS genomes from UK human cases. NTS was isolated from chicken (9.6 %), prawn (2.9 %) and pork (1.3 %) samples and included 14 serovars, of which Salmonella Infantis and Salmonella Enteritidis were the most common. The S. Enteritidis isolates were only isolated from imported chicken. No antimicrobial resistance determinants were found in prawn isolates, whilst 5.1 % of chicken and 0.64 % of pork samples contained multi-drug resistant NTS. The maximum number of pairwise core non-recombinant single nucleotide polymorphisms (SNPs) amongst isolates from the same sample was used to measure diversity and most samples had a median of two SNPs (range: 0–251). NTS isolates that were within five SNPs to clinical UK isolates belonged to specific serovars: S. Enteritidis and S. Infantis (chicken), and S. I 4,[5],12:i- (pork and chicken). Most NTS isolates that were closely related to human-derived isolates were obtained from imported chicken, but further epidemiological data are required to assess definitively the probable source of the human cases. Continued WGS surveillance of Salmonella on retail food involving multiple isolates from each sample is necessary to capture the diversity of Salmonella and determine the relative importance of different sources of human disease.

Item Type: Article
Additional Information: Funding information: This study was supported by the: Food Standards Agency (Award FS101185); Biotechnology and Biological Sciences Research Council (Awards BBS/E/F/000PR10348 and BB/R012504/1)
Uncontrolled Keywords: antimicrobial resistance,food,genomics,salmonella,genetics,molecular biology,epidemiology,microbiology,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1300/1311
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
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Depositing User: LivePure Connector
Date Deposited: 03 Aug 2023 15:33
Last Modified: 10 Aug 2023 08:31
DOI: 10.1099/mgen.0.001075


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