Abdel-Rhman Shaymaa H, Rizk Dina E
Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.
Department of Pharmaceutics and Pharmaceutical Biotechnology, Faculty of Pharmacy, Taibah University, AlMadinah Al Munawwarah, Saudi Arabia.
Infect Drug Resist. 2021 Mar 17;14:1019-1035. doi: 10.2147/IDR.S298838. eCollection 2021.
is one of the important causes of nosocomial infections. Analyzing the diversity of these isolates is important to control the diseases caused by them. Studies of molecular epidemiology depend on the application of typing methods.
This study aims to assess the performance of PCR- based typing techniques (RAPD, ribotyping, tDNA, and ERIC) in determining the genetic diversity of 44 urinary isolates.
Performance parameters were analyzed for each of the tested methods. The banding pattern was assessed by calculating polymorphism, genotypic gene diversity and the effective multiplex ratio. Moreover, strain diversity, typeability, and discriminatory power were used to measure the efficiency of typing methods. The congruence among typing methods was calculated by Rand's and Wallace coefficients.
P-640 among RAPD primers and Ribo-2 among ribotyping primers were more informative as they gave high strain diversity, the highest number of clusters, and highest discriminatory power (ISD=70.45%, 29 clusters at 70% cutoff, DI=0.97 and ISD=75%, 25 clusters at 70% cutoff DI=0.969, respectively). Comparison of typing methods showed that RAPD-PCR gave the highest mean percent polymorphism per assay (76.85%) followed by ERIC-PCR. ERIC-PCR outperformed in most marker parameters; highest mean number of alleles, number of monomorphic bands per assay unit, mean genotypic gene diversity, effective multiplex ratio, and assay efficiency index. Calculated congruence revealed that individual methods demonstrate moderate to poor predictive power. Interestingly, this power increased by combining data obtained from another method.
RAPD primer (P-640) had more discrimination power followed by ribo-2 and ERIC. The performance and predictive power of typing methods can be improved by combining data obtained from different methods as ERIC+OPA-02 and ERIC+P-640 combinations gave complete typeability and discrimination of isolates. ERIC, ERIC+OPA-02, and ERIC+P-640 combinations can provide finer discrimination and classification of strains than the other tested methods.
是医院感染的重要原因之一。分析这些分离株的多样性对于控制由它们引起的疾病很重要。分子流行病学研究依赖于分型方法的应用。
本研究旨在评估基于PCR的分型技术（随机扩增多态性DNA分析、核糖体分型、tDNA分型和肠杆菌基因间重复共有序列分析）在确定44株尿液分离株遗传多样性方面的性能。
对每种测试方法的性能参数进行分析。通过计算多态性、基因型基因多样性和有效多重率来评估条带模式。此外，菌株多样性、分型能力和鉴别力用于衡量分型方法的效率。通过兰德系数和华莱士系数计算分型方法之间的一致性。
随机扩增多态性DNA分析引物中的P-640和核糖体分型引物中的Ribo-2提供的信息更多，因为它们具有较高的菌株多样性、最多的聚类数和最高的鉴别力（ISD分别为70.45%，在70%截断值时为29个聚类，DI = 0.97；ISD为75%，在70%截断值时为25个聚类，DI = 0.969）。分型方法比较表明，随机扩增多态性DNA分析PCR每次检测的平均多态性百分比最高（76.85%），其次是肠杆菌基因间重复共有序列分析PCR。肠杆菌基因间重复共有序列分析PCR在大多数标记参数方面表现出色；平均等位基因数最多、每个检测单位的单态性条带数、平均基因型基因多样性、有效多重率和检测效率指数最高。计算得出的一致性表明，单个方法的预测能力中等至较差。有趣的是，通过合并从另一种方法获得的数据，这种能力会提高。
随机扩增多态性DNA分析引物（P-640）的鉴别力更强，其次是Ribo-2和肠杆菌基因间重复共有序列分析。通过合并从不同方法获得的数据可以提高分型方法的性能和预测能力，因为肠杆菌基因间重复共有序列分析+OPA-02和肠杆菌基因间重复共有序列分析+P-640组合能够实现对分离株的完全分型和鉴别。与其他测试方法相比，肠杆菌基因间重复共有序列分析、肠杆菌基因间重复共有序列分析+OPA-02和肠杆菌基因间重复共有序列分析+P-640组合能够对菌株提供更精细的鉴别和分类。
