Kotewicz Michael L, Jackson Scott A, LeClerc J Eugene, Cebula Thomas A
Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, MD 20708, USA.
Microbiology (Reading). 2007 Jun;153(Pt 6):1720-1733. doi: 10.1099/mic.0.2006/004507-0.
Optical maps of 11 Escherichia coli O157 : H7 strains have been generated by the assembly of contiguous sets of restriction fragments across their entire 5.3 to 5.6 Mbp chromosomes. Each strain showed a distinct, highly individual configuration of 500-700 BamHI fragments, yielding a map resembling a DNA 'bar code'. The accuracy of optical mapping was assessed by comparing directly the in silico restriction maps of two wholly sequenced reference genomes of E. coli O157 : H7, i.e. EDL933 and the Sakai isolate (RIMD 0509952), with the optical maps of the same strains. The optical maps of nine other E. coli O157 : H7 strains were compared similarly, using the sequence-based maps of the Sakai and EDL933 strains as references. A total of 91 changes at 28 loci were positioned and sized; these included complex chromosomal inversions, insertions, deletions, substitutions, as well as a number of simple RFLPs. The optical maps defined unique genome landmarks in each of the strains and demonstrated the ability of optical mapping to distinguish and differentiate, at the individual level, strains of this important pathogen.
通过组装跨越11株大肠杆菌O157 : H7整个530万至560万个碱基对染色体的连续限制性片段集，生成了这些菌株的光学图谱。每株菌株都显示出由500 - 700个BamHI片段组成的独特、高度个性化的构型，产生了一张类似DNA“条形码”的图谱。通过将两株全测序的大肠杆菌O157 : H7参考基因组（即EDL933和阪崎分离株（RIMD 0509952））的电子限制性图谱与相同菌株的光学图谱直接比较，评估了光学图谱的准确性。同样，以阪崎和EDL933菌株基于序列的图谱为参考，比较了另外9株大肠杆菌O157 : H7菌株的光学图谱。共定位并确定了28个位点的91处变化；这些变化包括复杂的染色体倒位、插入、缺失、替换，以及一些简单的限制性片段长度多态性。光学图谱定义了每株菌株中独特的基因组标记，并证明了光学图谱在个体水平上区分和鉴别这种重要病原体菌株的能力。
