基于发夹引物实时 PCR 检测法对全球伤寒沙门氏菌血清型 Typhi 分离株进行单核苷酸多态性分型。
Single nucleotide polymorphism typing of global Salmonella enterica serovar Typhi isolates by use of a hairpin primer real-time PCR assay.
机构信息
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
出版信息
J Clin Microbiol. 2010 Oct;48(10):3504-9. doi: 10.1128/JCM.00709-10. Epub 2010 Jul 28.
Abstract
Salmonella enterica serovar Typhi is highly homogeneous. Single nucleotide polymorphisms (SNPs) have been shown to be valuable markers for molecular typing of S. enterica serovar Typhi. Here, we used a hairpin primer real-time PCR assay for SNP typing of S. enterica serovar Typhi isolates. Forty-two SNPs were selected from a comparison of 19 published S. enterica serovar Typhi genomes and sequences from other studies. The SNPs were used to type 71 global S. enterica serovar Typhi isolates and differentiated these S. enterica serovar Typhi isolates and the 19 genome sequenced strains into 25 SNP profiles. Phylogenetic analysis revealed that these SNP profiles were grouped into six major clusters. These clusters can be identified by using five SNPs, while the full differentiation of the 25 SNP profiles requires a minimum of 24 SNPs. This real-time PCR-based SNP typing method will be useful for global epidemiological analysis.
摘要
肠炎沙门氏菌血清型 Typhi 高度同质。单核苷酸多态性（SNP）已被证明是肠炎沙门氏菌血清型 Typhi 分子分型的有价值的标记物。在这里，我们使用发夹引物实时 PCR assay 对肠炎沙门氏菌血清型 Typhi 分离株进行 SNP 分型。从 19 个已发表的肠炎沙门氏菌血清型 Typhi 基因组和其他研究的序列比较中选择了 42 个 SNP。这些 SNP 用于对 71 个全球肠炎沙门氏菌血清型 Typhi 分离株进行分型，将这些肠炎沙门氏菌血清型 Typhi 分离株和 19 个测序的基因组菌株分为 25 个 SNP 图谱。系统发育分析表明，这些 SNP 图谱分为六个主要簇。可以使用五个 SNP 来识别这些簇，而 25 个 SNP 图谱的完全分化需要至少 24 个 SNP。这种基于实时 PCR 的 SNP 分型方法将有助于全球流行病学分析。
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