Genomic diversity and genomic typing of Salmonella enterica serovar Typhimurium

Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the most frequently reported serovars in Australia. In the first study of this thesis, 21 S. Typhimurium genomes from Salmonella reference collection A (SARA) were sequenced. Together with 47 publicly available S. Typhimurium genomes to define S. Typhimurium core genes (STCG). The STCG consist of 3,846 genes, a set that is much larger than that of the 2,882 Salmonella core genes (SCG) found previously. STCG achieved 100% separation of all outbreaks compared to that of SCG typing, which failed to separate isolates from two outbreaks from background isolates. In the second study of this thesis, a set of 39 isolates was chosen for whole-genome sequencing by Illumina high-throughput methodology, which represents 15 repeat groups (RG) primarily determined by clustered regularly interspaced short palindromic repeats (CRISPR) typing. Nine Australian strains previously sequenced and 57 strains from publicly available sequenced strains isolated from different countries were included in the analysis. Phylogenetic analysis divided the 105 isolates into five clades, with the majority of the isolates belonging to clades 1 and 2. The genotype clusters defined primarily by composition of the CRISPR arrays correlated well with the sub-lineages and genotypes determined by SNP analysis. In the third study of this thesis, a total of 12,112 S. Typhimurium MLVA data from 2007 to 2014 in NSW were analyzed. The mid ranges of repeat units of 8 to 14 in VNTR locus STTR5, 6 to 13 in STTR6 and 9 to 12 in STTR10 were found to be always predominant in the population (>50%). in vitro passaging experiments using MLVA type carrying extreme length alleles found that the majority of long length alleles mutated to short ones and short length alleles mutated to longer ones. Sequencing of 28 isolates from a newly emerged MLVA type and its five single locus variants revealed that single nucleotide variation between isolates with up to two MLVA differences ranged from 0 to 12 SNPs. However there is no relationship between SNP and VNTR differences. Altogether, the studies performed in this thesis have advanced our understanding of evolution of S. Typhimurium.

Grantor dc:publisher

UNSW, Sydney

Year dc:date

2017

Author dc:creator

• Fu, Songzhe

Statement dc:rights

• open access
• CC BY-NC-ND 3.0
• free_to_read

Licence

• https://purl.org/coar/access_right/c_abf2
• https://creativecommons.org/licenses/by-nc-nd/3.0/au/

Language dc:language

EN

Identifier

https://doi.org/10.26190/unsworks/3149

OAI identifier oai:identifier

oai:unsworks.library.unsw.edu.au:1959.4/57448