Laing Chad, Pegg Crystal, Yawney Davis, Ziebell Kim, Steele Marina, Johnson Roger, Thomas James E, Taboada Eduardo N, Zhang Yongxiang, Gannon Victor P J
Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
Appl Environ Microbiol. 2008 Nov;74(21):6606-15. doi: 10.1128/AEM.00985-08. Epub 2008 Sep 12.
In this study, variably absent or present (VAP) regions discovered through comparative genomics experiments were targeted for the development of a rapid, PCR-based method to subtype and fingerprint Escherichia coli O157:H7. Forty-four VAP loci were analyzed for discriminatory power among 79 E. coli O157:H7 strains of 13 phage types (PT). Twenty-three loci were found to maximize resolution among strains, generating 54 separate fingerprints, each of which contained strains of unique PT. Strains from the three previously identified major E. coli O157:H7 lineages, LSPA6-LI, LSPA6-LI/II, and LSPA6-LII, formed distinct branches on a dendrogram obtained by hierarchical clustering of comparative genomic fingerprinting (CGF) data. By contrast, pulsed-field gel electrophoresis (PFGE) typing generated 52 XbaI digestion profiles that were not unique to PT and did not cluster according to O157:H7 lineage. Our analysis identified a subpopulation comprised of 25 strains from a closed herd of cattle, all of which were of PT87 and formed a cluster distinct from all other E. coli O157:H7 strains examined. CGF found five related but unique fingerprints among the highly clonal herd strains, with two dominant subtypes characterized by a shift from the presence of locus fprn33 to its absence. CGF had equal resolution to PFGE typing but with greater specificity, generating fingerprints that were unique among phenotypically related E. coli O157:H7 lineages and PT. As a comparative genomics typing method that is amenable for use in high-throughput platforms, CGF may be a valuable tool in outbreak investigations and strain characterization.
在本研究中，通过比较基因组学实验发现的可变缺失或存在（VAP）区域被用于开发一种基于PCR的快速方法，以对大肠杆菌O157:H7进行亚型分析和指纹识别。对44个VAP位点在13种噬菌体类型（PT）的79株大肠杆菌O157:H7菌株中的鉴别能力进行了分析。发现23个位点可使菌株间的分辨率最大化，产生54个独立的指纹图谱，每个指纹图谱都包含独特PT的菌株。来自先前确定的三个主要大肠杆菌O157:H7谱系LSPA6-LI、LSPA6-LI/II和LSPA6-LII的菌株，在通过比较基因组指纹图谱（CGF）数据进行层次聚类得到的树状图上形成了不同的分支。相比之下，脉冲场凝胶电泳（PFGE）分型产生了52个XbaI消化图谱，这些图谱并非PT所特有，也未根据O157:H7谱系聚类。我们的分析确定了一个由来自一个封闭牛群的25株菌株组成的亚群，所有这些菌株均为PT87，并且形成了一个与所有其他检测的大肠杆菌O157:H7菌株不同的簇。CGF在高度克隆的牛群菌株中发现了五个相关但独特的指纹图谱，其中两个主要亚型的特征是从存在fprn33位点转变为不存在该位点。CGF与PFGE分型具有相同的分辨率，但特异性更高，产生的指纹图谱在表型相关的大肠杆菌O157:H7谱系和PT中是独特的。作为一种适用于高通量平台的比较基因组学分型方法，CGF可能成为疫情调查和菌株特征分析的有价值工具。
