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

BMC Genomics

Research Article

Sophie Octavia¹  Ruiting Lan¹  Stanley Pang¹  Peter R Reeves²  Lei Wang³  Bin Liu³  Lu Feng³ 

[1] School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052, Sydney, New South Wales, Australia;School of Molecular Bioscience, University of Sydney, 2006, Sydney, New South Wales, Australia;TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China;

关键词: Typhimurium;    Genome;    Next generation sequencing;    Phage type;    Evolution;    Single nucleotide polymorphism;   

DOI  :  10.1186/1471-2164-14-718

 received in 2012-11-21, accepted in 2013-10-11,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundSalmonella 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 (i.e. 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.ResultsVariations 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.ConclusionThe 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.

【 授权许可】

Unknown   
© Pang et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.