Fu Songzhe, Octavia Sophie, Tanaka Mark M, Sintchenko Vitali, Lan Ruiting
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia.
J Clin Microbiol. 2015 Aug;53(8):2530-8. doi: 10.1128/JCM.03407-14. Epub 2015 May 27.
Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing foodborne infections in Australia and many other countries. Twenty-one S. Typhimurium strains from Salmonella reference collection A (SARA) were analyzed using Illumina high-throughput genome sequencing. Single nucleotide polymorphisms (SNPs) in 21 SARA strains ranged from 46 to 11,916 SNPs, with an average of 1,577 SNPs per strain. Together with 47 strains selected from publicly available S. Typhimurium genomes, the S. Typhimurium core genes (STCG) were determined. 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. The STCG together with 1,576 core intergenic regions (IGRs) were defined as the S. Typhimurium core genome. Using 93 S. Typhimurium genomes from 13 epidemiologically confirmed community outbreaks, we demonstrated that typing based on the S. Typhimurium core genome (STCG plus core IGRs) provides superior resolution and higher discriminatory power than that based on SCG for outbreak investigation and molecular epidemiology of S. Typhimurium. STCG and STCG plus core IGR typing achieved 100% separation of all outbreaks compared to that of SCG typing, which failed to separate isolates from two outbreaks from background isolates. Defining the S. Typhimurium core genome allows standardization of genes/regions to be used for high-resolution epidemiological typing and genomic surveillance of S. Typhimurium.
肠炎沙门氏菌鼠伤寒血清型是澳大利亚和许多其他国家中引起食源性感染的最常见沙门氏菌血清型。使用Illumina高通量基因组测序对来自沙门氏菌参考菌株集A（SARA）的21株鼠伤寒沙门氏菌进行了分析。21株SARA菌株中的单核苷酸多态性（SNP）范围为46至11,916个SNP，平均每株1,577个SNP。结合从公开可用的鼠伤寒沙门氏菌基因组中选择的47株菌株，确定了鼠伤寒沙门氏菌核心基因（STCG）。STCG由3,846个基因组成，这一基因集比先前发现的2,882个沙门氏菌核心基因（SCG）大得多。STCG与1,576个核心基因间区域（IGR）一起被定义为鼠伤寒沙门氏菌核心基因组。利用来自13起经流行病学确认的社区暴发的93株鼠伤寒沙门氏菌基因组，我们证明基于鼠伤寒沙门氏菌核心基因组（STCG加核心IGR）的分型在鼠伤寒沙门氏菌的暴发调查和分子流行病学研究中比基于SCG的分型具有更高的分辨率和鉴别力。与SCG分型相比，STCG和STCG加核心IGR分型实现了所有暴发的100%分离，而SCG分型未能将来自两起暴发的分离株与背景分离株区分开。定义鼠伤寒沙门氏菌核心基因组可使用于鼠伤寒沙门氏菌高分辨率流行病学分型和基因组监测的基因/区域标准化。
