|Identification of Genes to Differentiate Closely Related Salmonella Lineages|
|Zou, Qing-Hua1; Li, Ren-Qing2; Wang, Ye-Jun3; Liu, Shu-Lin1,3,4|
|WOS标题词||Science & Technology|
|研究领域[WOS]||Science & Technology - Other Topics|
|关键词[WOS]||GENOMIC CLEAVAGE MAP ; ENTERICA SEROVAR TYPHIMURIUM ; PATHOGENICITY ISLANDS ; TYPHI ; PARATYPHI ; EVOLUTION ; SEQUENCE ; REARRANGEMENTS ; RECOMBINATION ; CONVERGENCE|
Background: Salmonella are important human and animal pathogens. Though highly related, the Salmonella lineages may be strictly adapted to different hosts or cause different diseases, from mild local illness like gastroenteritis to fatal systemic infections like typhoid. Therefore, rapid and accurate identification of Salmonella is essential for timely and correct diagnosis of Salmonella infections. The current identification methods such as 16S rRNA sequencing and multilocus sequence typing are expensive and time consuming. Additionally, these methods often do not have sufficient distinguishing resolution among the Salmonella lineages.
Methodologies/Principal Findings: We compared 27 completely sequenced Salmonella genomes to identify possible genomic features that could be used for differentiation of individual lineages. We concatenated 2372 core genes in each of the 27 genomes and constructed a neighbor-joining tree. On the tree, strains of each serotype were clustered tightly together and different serotypes were unambiguously separated with clear genetic distances, demonstrating systematic genomic divergence among the Salmonella lineages. We made detailed comparisons among the 27 genomes and identified distinct sets of genomic differences, including nucleotide variations and genomic islands (GIs), among the Salmonella lineages. Two core genes STM4261 and entF together could unambiguously distinguish all Salmonella lineages compared in this study. Additionally, strains of a lineage have a common set of GIs and closely related lineages have similar sets of GIs.
Conclusions: Salmonella lineages have accumulated distinct sets of mutations and laterally acquired DNA (e.g., GIs) in evolution. Two genes entF and STM4261 have diverged sufficiently among the Salmonella lineages to be used for their differentiation. Further investigation of the distinct sets of mutations and GIs will lead to novel insights into genomic evolution of Salmonella and greatly facilitate the elucidation of pathogeneses of Salmonella infections.
|资助机构||National Natural Science Foundation of China|
|作者单位||1.Peking Univ, Hlth Sci Ctr, Sch Basic Med Sci, Dept Microbiol, Beijing 100871, Peoples R China|
2.Beijing Ctr Dis Control & Prevent, Inst Immunol, Beijing, Peoples R China
3.Harbin Med Univ, Genom Res Ctr, State Prov Key Labs Biomed Pharmaceut China, Harbin, Peoples R China
4.Univ Calgary, Dept Microbiol & Infect Dis, Calgary, AB, Canada
|Zou, Qing-Hua,Li, Ren-Qing,Wang, Ye-Jun,et al. Identification of Genes to Differentiate Closely Related Salmonella Lineages[J]. PLOS ONE,2013,8(2).|
|APA||Zou, Qing-Hua,Li, Ren-Qing,Wang, Ye-Jun,&Liu, Shu-Lin.(2013).Identification of Genes to Differentiate Closely Related Salmonella Lineages.PLOS ONE,8(2).|
|MLA||Zou, Qing-Hua,et al."Identification of Genes to Differentiate Closely Related Salmonella Lineages".PLOS ONE 8.2(2013).|
|Identification of Ge（802KB）||期刊论文||出版稿||开放获取||CC BY-NC-SA||浏览 请求全文|