Owen Robert J., Taylor Diane E., Wang Ge, van Doorn Leen-Jan
Helicobacter Reference Unit, Laboratory of Enteric Pathogens, Central Public Health Laboratory, 61 Colindale Avenue, London, NW9 5HT, United Kingdom
Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
MATCHING AIMS WITH METHODS: Genomic diversity within is now well established and a plethora of molecular typing techniques is available, many of which have been applied successfully to distinguish between isolates. However, no single molecular method has yet emerged as an internationally accepted basis for typing or subtyping purposes. Although consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems have been proposed (129), they are aimed mainly at phenotypic methods applicable in the characterization of isolates implicated in community or hospital outbreaks. For , the situation is perhaps unique as no reliable phenotyping methods are available for comparison, and outbreaks of infection, which usually provide an important basis for validating typing methods, are not a feature of the epidemiology of the species. The earliest typing methods used for , such as restriction digest analysis (including PFGE), ribotyping, and other forms of blot hybridization, have been now largely superceded by PCR-based methods such as RAPD, REP, and RFLP analysis. This trend was highlighted in a recent analysis of performance criteria for typing methods, in which the superiority of the PCR methods was demonstrated, including better typeability, higher discrimination power, and better general ease of use (17). While there are a number of important reasons to characterize individual strains of , the typing method employed is largely dictated by the specific aim of the investigation, and there is no single method that can satisfy all requirements. Some guidelines are provided in Table 1 for various typing methods and the purposes for which they might be most appropriate. They are grouped in three general categories, i.e., markers for potentially enhanced pathogenicity, precise identification of strain differences, and global population structure analysis. Some comments on the relative advantages and disadvantages of the different methods are provided.
The enormous expansion in detailed information about the fine genetic structure of , promoted by the availability of two complete genome sequences, continues to focus interest on strain-specific attributes, and hence a wider recognition of the importance of precise methods for strain identification. The present evidence is that strain genotypes appear to be relatively stable, at least under in vitro conditions. However, in view of the in vivo plasticity of the genome, it will be essential to monitor how typing markers are affected by genetic drift. Aspects that could merit development in the future include direct typing from clinical specimens without the need for culture, development of global standardized data sets of genomic fingerprints for different PCR-based methods, and development of sequence-based typing using standard sets of loci in housekeeping as well as pathogenicity marker genes.
使目标与方法相匹配： 内的基因组多样性现已得到充分证实，并且有大量分子分型技术可供使用，其中许多技术已成功应用于区分分离株。然而，尚未出现一种单一的分子方法成为国际公认的分型或亚型分型的基础。尽管已经提出了关于微生物流行病学分型系统的适当使用和评估的共识指南(129)，但它们主要针对适用于社区或医院暴发中涉及的分离株特征描述的表型方法。对于 而言，情况可能较为独特，因为没有可靠的表型方法可供比较，而且感染暴发通常为验证分型方法提供重要依据，但在该物种的流行病学中并非其特征。用于 的最早分型方法，如限制性酶切分析(包括脉冲场凝胶电泳)、核糖体分型和其他形式的印迹杂交，现在已在很大程度上被基于PCR的方法如随机扩增多态性DNA分析、重复序列PCR和限制性片段长度多态性分析所取代。最近对 分型方法性能标准的分析突出了这一趋势，其中证明了PCR方法的优越性，包括更好的分型能力、更高的鉴别力和更好的总体易用性(17)。虽然有许多重要原因需要对 的各个菌株进行特征描述，但所采用的分型方法在很大程度上取决于研究的具体目标，而且没有一种单一方法能够满足所有要求。表1针对各种分型方法及其可能最适用的目的提供了一些指南。它们分为三大类，即潜在致病性增强的标志物、菌株差异的精确鉴定以及全球群体结构分析。还对不同方法的相对优缺点进行了一些评论。
两个完整基因组序列的可得性推动了关于 精细遗传结构的详细信息的大幅扩展，这继续使人们关注菌株特异性属性，从而更广泛地认识到精确的菌株鉴定方法的重要性。目前的证据表明，菌株基因型似乎相对稳定，至少在体外条件下是如此。然而，鉴于 基因组在体内的可塑性，监测分型标志物如何受到遗传漂变的影响至关重要。未来可能值得发展的方面包括无需培养即可直接从临床标本进行分型、为不同的基于PCR的方法开发全球标准化的基因组指纹数据集，以及使用管家基因和致病性标志物基因的标准位点集进行基于序列的分型。
