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Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types.

Authors :
Pang, Stanley
Octavia, Sophie
Lu Feng
Bin Liu
Reeves, Peter R.
Lan, Ruiting
Lei Wang
Source :
BMC Genomics; 2013, Vol. 14 Issue 1, p1-29, 29p
Publication Year :
2013

Abstract

Background Salmonella enterica serovar Typhimurium (or simply Typhimurium) is the most common serovar in both human infections and farm animals in Australia and many other countries. Typhimurium is a broad host range serovar but has also evolved into host-adapted variants (ie. isolated from a particular host such as pigeons). Six Typhimurium strains of different phage types (defined by patterns of susceptibility to lysis by a set of bacteriophages) were analysed using Illumina high-throughput genome sequencing. Results Variations between strains were mainly due to single nucleotide polymorphisms (SNPs) with an average of 611 SNPs per strain, ranging from 391 SNPs to 922 SNPs. There were seven insertions/deletions (indels) involving whole or partial gene deletions, four inactivation events due to IS200 insertion and 15 pseudogenes due to early termination. Four of these inactivated or deleted genes may be virulence related. Nine prophage or prophage remnants were identified in the six strains. Gifsy-1, Gifsy-2 and the sopE2 and sspH2 phage remnants were present in all six genomes while Fels-1, Fels-2, ST64B, ST104 and CP4-57 were variably present. Four strains carried the 90-kb plasmid pSLT which contains several known virulence genes. However, two strains were found to lack the plasmid. In addition, one strain had a novel plasmid similar to Typhi strain CT18 plasmid pHCM2. Conclusion The genome data suggest that variations between strains were mainly due to accumulation of SNPs, some of which resulted in gene inactivation. Unique genetic elements that were common between host-adapted phage types were not found. This study advanced our understanding on the evolution and adaptation of Typhimurium at genomic level. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
14712164
Volume :
14
Issue :
1
Database :
Complementary Index
Journal :
BMC Genomics
Publication Type :
Academic Journal
Accession number :
91879816
Full Text :
https://doi.org/10.1186/1471-2164-14-718