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首页> 外文期刊>BMC Microbiology >Multilocus variable-number tandem repeat analysis for molecular typing and phylogenetic analysis of Shigella flexneri
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Multilocus variable-number tandem repeat analysis for molecular typing and phylogenetic analysis of Shigella flexneri

机译：多位点可变数目串联重复分析用于弗氏志贺氏菌的分子分型和系统发育分析

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Background Shigella flexneri is one of the causative agents of shigellosis, a major cause of childhood mortality in developing countries. Multilocus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyping method to resolve closely related bacterial isolates for investigation of disease outbreaks and provide information for establishing phylogenetic patterns among isolates. The present study aimed to develop an MLVA method for S. flexneri and the VNTR loci identified were tested on 242 S. flexneri isolates to evaluate their variability in various serotypes. The isolates were also analyzed by pulsed-field gel electrophoresis (PFGE) to compare the discriminatory power and to evaluate the usefulness of MLVA as a tool for phylogenetic analysis of S. flexneri. Results Thirty-six VNTR loci were identified by exploring the repeat sequence loci in genomic sequences of Shigella species and by testing the loci on nine isolates of different subserotypes. The VNTR loci in different serotype groups differed greatly in their variability. The discriminatory power of an MLVA assay based on four most variable VNTR loci was higher, though not significantly, than PFGE for the total isolates, a panel of 2a isolates, which were relatively diverse, and a panel of 4a/Y isolates, which were closely-related. Phylogenetic groupings based on PFGE patterns and MLVA profiles were considerably concordant. The genetic relationships among the isolates were correlated with serotypes. The phylogenetic trees constructed using PFGE patterns and MLVA profiles presented two distinct clusters for the isolates of serotype 3 and one distinct cluster for each of the serotype groups, 1a/1b/NT, 2a/2b/X/NT, 4a/Y, and 6. Isolates that had different serotypes but had closer genetic relatedness than those with the same serotype were observed between serotype Y and subserotype 4a, serotype X and subserotype 2b, subserotype 1a and 1b, and subserotype 3a and 3b. Conclusions The 36 VNTR loci identified exhibited considerably different degrees of variability among S. flexneri serotype groups. VNTR locus could be highly variable in a serotype but invariable in others. MLVA assay based on four highly variable loci could display a comparable resolving power to PFGE in discriminating isolates. MLVA is also a prominent molecular tool for phylogenetic analysis of S. flexneri; the resulting data are beneficial to establish clear clonal patterns among different serotype groups and to discern clonal groups among isolates within the same serotype. As highly variable VNTR loci could be serotype-specific, a common MLVA protocol that consists of only a small set of loci, for example four to eight loci, and that provides high resolving power to all S. flexneri serotypes may not be obtainable.
机译：背景弗氏志贺氏菌是志贺菌病的病原体之一，而志贺菌病是发展中国家儿童死亡率的主要原因。多基因座可变数目串联重复序列（VNTR）分析（MLVA）是一种重要的亚型方法，可解决密切相关的细菌分离株，以调查疾病暴发，并提供建立分离株之间系统发育模式的信息。本研究旨在开发一种用于弗氏链球菌的MLVA方法，并在242个弗氏链球菌菌株上测试鉴定出的VNTR基因座，以评估其在各种血清型中的变异性。还通过脉冲场凝胶电泳（PFGE）分析了分离物，以比较鉴别力并评估MLVA作为弗氏链球菌系统发育分析工具的有用性。结果通过探查志贺氏菌属基因组序列中的重复序列基因座，并在9种不同亚型的分离物中检测该基因座，鉴定出36个VNTR基因座。不同血清型组中的VNTR基因座变异性差异很大。基于四个可变性最强的VNTR基因座的MLVA分析的鉴别力比总的PFGE，一组相对较差的2a分离物和一组4a / Y分离物的PFGE更高，但不明显。密切相关。基于PFGE模式和MLVA配置文件的系统发育分组是相当一致的。分离株之间的遗传关系与血清型相关。使用PFGE模式和MLVA谱图构建的系统发育树显示了针对血清型3分离株的两个不同簇，针对每个血清型组1a / 1b / NT，2a / 2b / X / NT，4a / Y和6.在血清型Y和亚血清型4a，X血清型和亚血清型2b，亚血清型1a和1b，亚血清型3a和3b之间观察到了具有不同血清型但具有比相同血清型更近的遗传相关性的分离株。结论鉴定出的36个VNTR基因座在弗氏链球菌血清型组之间表现出不同程度的变异性。 VNTR基因座在血清型中可能高度可变，而在其他血清型中则恒定。基于四个高度可变的基因座的MLVA分析可以显示出与PFGE相当的分辨力。 MLVA还是弗氏链球菌系统发育分析的重要分子工具。所得数据有助于在不同血清型组之间建立清晰的克隆模式，并有助于辨别同一血清型内分离株之间的克隆组。由于高度可变的VNTR基因座可能是血清型特异性的，因此可能无法获得仅由一小部分基因座（例如4至8个基因座）组成的通用MLVA协议，该协议可以为所有弗氏链球菌血清型提供高解析力。

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