Genetic diversity and antimicrobial resistance in a global collection of the emerging human pathogen Salmonella Infantis

Mattock, Jennifer (2020) Genetic diversity and antimicrobial resistance in a global collection of the emerging human pathogen Salmonella Infantis. Doctoral thesis, University of East Anglia.

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High levels of Salmonella Infantis have been identified in poultry globally; for several years it has been the serovar most frequently found in broilers in Europe. It is also one of the most common serovars causing infection in humans, although responsible for lower numbers of cases than other Salmonella serovars.
Very little is known about the genetic diversity of S. Infantis, with previous research only comparing up to 264 genomes. In this project a collection of 4,670 S. Infantis genomes was amassed. The aims of this thesis were to determine: the global population structure of the serovar; the levels of antimicrobial resistance (AMR) and plasmids and whether genetic differences between human and poultry S. Infantis could explain the difference in incidence seen between these sources.
S. Infantis splits into two eBurstGroups (eBG), eBG31 and eBG297, the former comprising 96% of the global collection. However, the proportion of isolates belonging to either eBG varied geographically, with eBG297 strongly associated with isolation from Africa.
High levels of AMR were present in the eBG31 population; 39% of the isolates were multidrug resistant. This was associated with the presence of plasmid of emerging S. Infantis, which was identified in 34% of the eBG31 genomes, in particular from 69% of the poultry isolates.
Upon comparison of the eBG31 human and poultry genomes, a greater genetic diversity was observed amongst the human isolates. Furthermore, several thousand genes and intergenic regions were significantly associated with isolation source. This thesis concluded that the differences in the pathogenicity of S. Infantis between humans and poultry is due to either only a subgroup of poultry S. Infantis being capable of infecting humans; or that other sources are the cause of human infections. Public health teams worldwide will benefit from the increased understanding this work provides on this emerging pathogen.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
Depositing User: Chris White
Date Deposited: 05 Oct 2020 13:22
Last Modified: 05 Oct 2020 13:22


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