Comparative genomics of Australian and international isolates of Salmonella Typhimurium: correlation of core genome evolution with CRISPR and prophage profiles

Abstract

Salmonella enterica subsp enterica serovar Typhimurium (S. Typhimurium) is a serovar with broad host range. To determine the genomic diversity of S. Typhimurium, we sequenced 39 isolates (37 Australian and 2 UK isolates) representing 14 Repeats Groups (RGs) determined primarily by clustered regularly interspaced short palindromic repeats (CRISPR). Analysis of single nucleotide polymorphisms (SNPs) among the 39 isolates yielded an average of 1,232 SNPs per isolate, ranging from 128 SNPs to 11,339 SNPs relative to the reference strain LT2. Phylogenetic analysis of the 39 isolates together with 66 publicly available genomes divided the 105 isolates into five clades and 19 lineages, with the majority of the isolates belonging to clades I and II. The composition of CRISPR profiles correlated well with the lineages, showing progressive deletion and occasional duplication of spacers. Prophage genes contributed nearly a quarter of the S. Typhimurium accessory genome. Prophage profiles were found to be correlated with lineages and CRISPR profiles. Three new variants of HP2-like P2 prophage, several new variants of P22 prophage and a plasmid-like genomic island StmGI_0323 were found. This study presents evidence of horizontal transfer from other serovars or species and provides a broader understanding of the global genomic diversity of S. Typhimurium.

Genomic comparison of diverse Salmonella serovars isolated from swine

“…The inter serovars core genome size (3, 224 core genes) within the 35 Salmonella subsp. enterica was lower while the intra serovar core genome size (3, 836 core genes) for S. Typhimurium was higher compared to our analysis [76,77]. Low number of unique genes was directly related to the reduced genomes size, where HGT events were less and S. Bovismorbificans well correlated in this context with lowest numbers of unique genes and lower genome size.…”

CRISPR-cas3 of Salmonella Upregulates Bacterial Biofilm Formation and Virulence to Host Cells by Targeting Quorum-Sensing Systems

“…Furthermore, CRISPR-multi-virulence-locus sequence typing (MVLST) has been frequently used to subtype Salmonella serovars [10,11]. The conserved genetic organization of the cas genes in some Salmonella serovars is consistent with its biological function in these bacteria [12][13][14]. In addition, some reports found that in S. Typhi, this system consists of five transcriptional units, including two messenger ribonucleic acids (CRISPR-cas and cas3), one sense ribonucleic acid (scse2), and two antisense RNAs (ascse2-1 and ascas2-1) [15].…”

Genetic characterisation of variants of the virulence plasmid, pSLT, in Salmonella enterica serovar Typhimurium provides evidence of a variety of evolutionary directions consistent with vertical rather than horizontal transmission

“…Typhimurium isolates by a combination of variable-number tandem repeats (VNTRs) and clustered regularly interspaced short palindromic repeats (CRISPR) profiling called Repeats Typing has been used by Hiley et al 2014 [11] to recognise at least fifteen distinct genotypes. Whole genome sequencing (WGS) followed by core-genome single-nucleotide-polymorphism (SNP) analysis has supported the separation of strains into the same genotypes and determined the likely relationships between genotypes [12]. Genotyping has shown that there is a distinct divide between genotypes likely to have pSLT and those unlikely to have it.…”