Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan.
Infect Genet Evol. 2011 Jan;11(1):78-82. doi: 10.1016/j.meegid.2010.10.007. Epub 2010 Oct 28.
The distribution of insertion sequence (IS) 629 among strains of enterohemorrhagic Escherichia coli serovar O157 (O157) was investigated and compared with the strain lineages defined by lineage specific polymorphism assay-6 (LSPA-6) to demonstrate the effectiveness of IS629 analysis for population genetics analysis. Using pulsed-field gel electrophoresis and variable-number tandem repeat typing, 140 strains producing both VT1 and VT2 and 98 strains producing only VT2 were selected from a total of 592 strains isolated from patients and asymptomatic carriers in Chiba Prefecture, Japan, during 2003-2008. By LSPA-6 analysis, six strains had atypical amplicon sizes in their Z5935 loci and five strains had atypical amplicon sizes in their arp-iclR intergenic regions. Sequence analyses of PCR amplified DNAs showed that five of the six loci used for LSPA-6 analysis had tandem repeats and the allele changes were due to changes in the number of tandem repeats. Subculturing and long-term incubation was found to have no detectable effect on the lineages defined by LSPA-6 analysis, demonstrating the robustness of LSPA-6 analysis. Minimum spanning tree analysis reconstruction revealed that strains in lineage I, I/II, and II clustered on separate branches, indicating that the distribution of IS629 was biased among O157 strains in different lineages. Strains with LSPA-6 codes 231111, 211113, and 211114 had atypical amplicon sizes and were clustered in lineage I/II branch, and strains with LSPA-6 codes 212114, 221123, 221223, 222123, 222224, 242123, 252123, and 242222 had atypical amplicon sizes and clustered in lineage II branches. Linkage disequilibrium was observed in strains in every lineage when the standardized index of association was calculated using IS629 distribution data. Therefore, the distribution analysis of IS629 may be effective for population genetics analysis of O157 due to the biased IS629 distribution among strains in the three O157 lineages.
我们调查了肠出血性大肠杆菌血清型 O157（O157）菌株中插入序列（IS）629 的分布，并将其与谱系特异性多态性检测-6（LSPA-6）定义的菌株谱系进行比较，以证明 IS629 分析在群体遗传学分析中的有效性。使用脉冲场凝胶电泳和可变数串联重复分型，从 2003 年至 2008 年在日本千叶县从患者和无症状携带者中分离的总共 592 株产生 VT1 和 VT2 的菌株和 98 株仅产生 VT2 的菌株中选择了 140 株。通过 LSPA-6 分析，在 Z5935 基因座中，有 6 株的典型扩增子大小异常，在 arp-iclR 基因间隔区有 5 株的典型扩增子大小异常。PCR 扩增 DNA 的序列分析表明，LSPA-6 分析中使用的 6 个基因座中的 5 个具有串联重复，等位基因的变化是由于串联重复数目的变化。发现继代培养和长期孵育对 LSPA-6 分析定义的谱系没有可检测的影响，表明 LSPA-6 分析的稳健性。最小生成树分析重建显示，谱系 I、I/II 和 II 中的菌株聚集在不同的分支上，表明 IS629 的分布在不同谱系的 O157 菌株中存在偏倚。LSPA-6 代码为 231111、211113 和 211114 的菌株具有异常的扩增子大小，并聚集在 I/II 分支中，而 LSPA-6 代码为 212114、221123、221223、222123、222224、242123、252123 和 242222 的菌株具有异常的扩增子大小，并聚集在 II 分支中。当使用 IS629 分布数据计算标准化关联指数时，在每个谱系中的菌株中观察到连锁不平衡。因此，由于三个 O157 谱系中的菌株之间的 IS629 分布存在偏倚，因此 IS629 的分布分析可能对 O157 的群体遗传学分析有效。
