Genome evolution of Salmonella enterica serovar Typhimurium

Charity, Oliver (2021) Genome evolution of Salmonella enterica serovar Typhimurium. Doctoral thesis, University of East Anglia.

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Abstract

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a food-borne pathogen which accounts for ~25 % of non-typhoidal Salmonella infections, usually through faecal-oral transmission. To maintain food safety and avoid unnecessary human and animal disease, understanding how pathogens such as S. Typhimurium evolve and their requirements for persistence is paramount. This study investigated genomic evolution of S. Typhimurium. First, a recently acquired novel genomic island was characterised that initiated successful clonal expansion of pandemic monophasic S. Typhimurium ST34, Salmonella genomic island 4 (SGI-4). SGI-4 was discovered to be self-transferable and enhance resistance to heavy metals. This was consistent with the epidemiology of monophasic S. Typhimurium ST34 strains as they are most frequently isolated from pigs and copper is used as a growth promoter in pig farming. Next, the phage sensitivity of S. Typhimurium lineages was investigated through associating phage sensitivity with whole genome sequence (WGS). DT193 that is characterised by resistance to all Anderson typing scheme phage preparations was the most frequent majority phage type, consistent with selection for phage resistance occurring many times throughout S. Typhimurium. The monophasic S. Typhimurium ST34 population was then investigated using large-scale WGS-based statistical analyses. A novel prophage termed mTmII was associated with continuation of the monophasic ST34 lineage and acquisition was accompanied by an increase in phage resistance. How phage predation shapes the evolution and persistence of S. Typhimurium pathovars in host animal niches was then investigated and a novel phenomenon enabling rapid resistance to phage predation through polymorphic gene variation discovered, including a base-specific deletion of serogroup B1 O-antigen polymerase encoding wzy, coupled with recombination mediated reversion of the locus in a mixed population of a single strain.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	09 Mar 2022 14:42
Last Modified:	09 Mar 2022 14:42
URI:	https://ueaeprints.uea.ac.uk/id/eprint/83957
DOI:

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