计算预测和新型标记物的实验验证用于检测 STEC O157:H7。
Computational prediction and experimental validation of novel markers for detection of STEC O157:H7.
机构信息
Department of Pathogenobiology, Norman Bethune Medical College of Jilin University, Changchun 130000, Jilin Province, China.
出版信息
World J Gastroenterol. 2011 Apr 14;17(14):1910-4. doi: 10.3748/wjg.v17.i14.1910.
AIM
To identify and assess the novel makers for detection of Shiga toxin producing Escherichia coli (STEC) O157:H7 with an integrated computational and experimental approach.
METHODS
High-throughput NCBI blast (E-value cutoff e-5) was used to search homologous genes among all sequenced prokaryotic genomes of each gene encoded in each of the three strains of STEC O157:H7 with complete genomes, aiming to find unique genes in O157:H7 as its potential markers. To ensure that the identified markers from the three strains of STEC O157:H7 can serve as general markers for all the STEC O157:H7 strains, a genomic barcode approach was used to select the markers to minimize the possibility of choosing a marker gene as part of a transposable element. Effectiveness of the markers predicted was then validated by running polymerase chain reaction (PCR) on 18 strains of O157:H7 with 5 additional genomes used as negative controls.
RESULTS
The blast search identified 20, 16 and 20 genes, respectively, in the three sequenced strains of STEC O157:H7, which had no homologs in any of the other prokaryotic genomes. Three genes, wzy, Z0372 and Z0344, common to the three gene lists, were selected based on the genomic barcode approach. PCR showed an identification accuracy of 100% on the 18 tested strains and the 5 controls.
CONCLUSION
The three identified novel markers, wzy, Z0372 and Z0344, are highly promising for the detection of STEC O157:H7, in complementary to the known markers.
目的
采用集成计算和实验方法，鉴定和评估用于检测产志贺毒素大肠杆菌（STEC）O157：H7 的新型标记物。
方法
利用高通量 NCBI blast（E 值截止值 e-5），在具有完整基因组的三种 STEC O157：H7 菌株的每个基因中搜索所有已测序原核基因组中的同源基因，旨在寻找 O157：H7 中的特有基因作为其潜在的标记物。为确保从三种 STEC O157：H7 菌株中鉴定出的标记物可以作为所有 STEC O157：H7 菌株的通用标记物，采用基因组条码方法选择标记物，以最大程度地减少选择标记基因作为转座元件一部分的可能性。然后通过对 18 株 O157：H7 菌株进行聚合酶链反应（PCR）来验证预测标记物的有效性，另外 5 个基因组用作阴性对照。
结果
在三种 STEC O157：H7 测序菌株中，通过 Blast 搜索分别鉴定出 20、16 和 20 个基因，它们在任何其他原核基因组中均没有同源物。基于基因组条码方法，从三个基因列表中选择了三个共同的基因，wzy、Z0372 和 Z0344。PCR 显示在 18 株测试菌株和 5 株对照菌株上的鉴定准确率为 100%。
结论
鉴定出的三个新型标记物 wzy、Z0372 和 Z0344 对 STEC O157：H7 的检测具有很高的应用前景，可与已知标记物互补。
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