Genetic and resistance phenotypic subtyping of Salmonella Saintpaul isolates from various food sources and humans: Phylogenetic concordance in combinatory analyses
Genetic and resistance phenotypic subtyping of Salmonella Saintpaul isolates from various food sources and humans: Phylogenetic concordance in combinatory analyses
复制标题
DOI：
10.1016/j.meegid.2015.08.022
复制
发表时间：
2015-12-01
影响因子：
3.2
通讯作者：
Elkins, Christopher A.
中科院分区：
文献类型：
--
作者：
Hayford, Alice E.;Brown, Eric W.;Elkins, Christopher A.
用于食源性暴发公共卫生追溯的细菌病原体亚型越来越多地产生了许多不同分辨率的不同分子技术。在这里，我们跨越三种方法弥合分子鸿沟，转换数据类型进行交叉比较，并测试系统发育一致性。将单核苷酸多态性（SNP）发现与脉冲场凝胶电泳（PFGE）和抗菌药敏谱相结合，对来自零售肉类、农产品相关暴发和临床来源的183株密切相关的肠沙门氏菌血清型圣保罗分离株进行了鉴定和区分。通过比较基因组分析，鉴定出30个不同基因中的56个snp。这些snp将一般的、单系的圣保罗菌株特异性特征分层为信息丰富的菌株特异性标记。该SNP面板产生了17种不同的基因型，与标准PFGE分析相一致，当数据转换为交叉可比的二进制格式时，在克隆群分离物中产生了额外的歧视性力量。在有限数量的病例中，抗菌药物敏感性谱（ASP）在类似组合时为某些菌株提供了额外的属性。然而，正如预期的那样，抗性和易感群体在大多数克隆复合体中产生了一些相互冲突的信号，但它们在很大程度上不破坏一般的一致性。将三个数据集（snp、PFGE、ASP）结合在一起，得出了156个独立的系统发育特征的矩阵，经过统计评估，发现这些特征在很大程度上是一致的，从而得到了一个结构一致、非同质的系统发育信号和树状拓扑结构。Elsevier B.V.出版
Bacterial pathogen subtyping for public health traceback of foodborne outbreaks has increasingly produced a number of disparate molecular techniques of varying resolution. Here, we bridge the molecular divide across three methodologies, transform data types for cross-comparison, and test phylogenetic concordance. Single nucleotide polymorphism(SNP) discovery was combined with pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility profiles for identifying and differentiating 183 strains of closely related Salmonella enterica serovar Saintpaul isolates from retail meats, produce-associated outbreaks, and clinical sources. Fifty-six SNPs across 30 different genes were identified by comparative genomic analysis. These SNPs stratified general, monophyletic S. Saintpaul serovar specific signatures down to informative strain-specific markers. This SNP panel resulted in 17 distinct genotypes that, in concert with standard PFGE profiling, generated additional discriminatory power among clonal swarms of isolates when the data were transformed into a cross-comparable binary format. In a limited number of cases, antimicrobial susceptibility profiles (ASP) provided additional attributes for some strains when combined similarly. However, as expected from presumably acquired elements, resistant and susceptible populations produced some conflicting signals in most clonal complexes but they remained largely undisruptive to the general concordance. Taken in concert together, the three datasets (SNPs, PFGE, ASP) yielded a matrix of 156 independent phylogenetic characters that were statistically evaluated and found to be largely congruent, resulting in a consistently structured, non-homoplastic, phylogenetic signal and tree topology. Published by Elsevier B.V.