Evaluation of methods for molecular typing and identification of members of the genus Brevibacterium and other related species

The genus Brevibacterium includes pleomorphic Gram-positive bacteria with a high mol% G+C content. Species in the genus are difficult to identify by classical methods. The discriminatory power of DNA-based methods is assessed. Strains representing the four well established Brevibacterium species, and other related bacteria, were compared by amplified ribosomal DNA restriction analysis (ARDRA), repetitive-sequence-based PCR (rep-PCR) and ribotyping. Fingerprinting by rep-PCR and ribotyping provided complex genomic profiles with the highest discriminatory potential for molecular typing at the strain level, whereas ARDRA showed differentiation from the genus to the species levels. A high degree of heterogeneity within the genus Brevibacterium is apparent, thus indicating that the taxonomy of the genus should be further studied.     

Polyphasic approach of bacterial classification — An overview of recent advances

Classification of microorganisms on the basis of traditional microbiological methods (morphological, physiological and biochemical) creates a blurred image about their taxonomic status and thus needs further clarification. It should be based on a more pragmatic approach of deploying a number of methods for the complete characterization of microbes. Hence, the methods now employed for bacterial systematics include, the complete 16S rRNA gene sequencing and its comparative analysis by phylogenetic trees, DNA-DNA hybridization studies with related organisms, analyses of molecular markers and signature pattern(s), biochemical assays, physiological and morphological tests. Collectively these genotypic, chemotaxonomic and phenotypic methods for determining taxonomic position of microbes constitute what is known as the ‘polyphasic approach’ for bacterial systematics. This approach is currently the most popular choice for classifying bacteria and several microbes, which were previously placed under invalid taxa have now been resolved into new genera and species. This has been possible owing to rapid development in molecular biological techniques, automation of DNA sequencing coupled with advances in bioinformatic tools and access to sequence databases. Several DNA-based typing methods are known; these provide information for delineating bacteria into different genera and species and have the potential to resolve differences among the strains of a species. Therefore, newly isolated strains must be classified on the basis of the polyphasic approach. Also previously classified organisms, as and when required, can be reclassified on this ground in order to obtain information about their accurate position in the microbial world. Thus, current techniques enable microbiologists to decipher the natural phylogenetic relationships between microbes.     

Sample processing for DNA chip array-based analysis of enterohemorrhagic <Emphasis Type="Italic">Escherichia coli</Emphasis> (EHEC)

Background  

Exploitation of DNA-based analyses of microbial pathogens, and especially simultaneous typing of several virulence-related genes in bacteria is becoming an important objective of public health these days.     

大肠埃希氏菌的分型方法及其研究进展

大肠埃希氏菌是一种条件性致病菌,致病性的大肠埃希氏菌具有高度的传染性,会严重危害健康。快速准确地测定大肠埃希氏菌的污染来源对有效缩小疫情影响范围极有帮助,从而避免对人类健康和经济贸易造成重大损失。建立简便高效的分型方法是微生物溯源的关键,常见的大肠埃希氏菌分型方法可分为表型分型和分子分型,这些分型方法各有优劣,具有不同的适用范围。本文详细介绍了大肠埃希氏菌的分型方法,并对国内外大肠埃希氏菌分型的研究进展进行综述,为致病菌溯源方法的选择提供参考依据,对防御并控制致病菌引起的流行病传播具有重要的意义。     

Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay

Background  

The classification of Brucella into species and biovars relies on phenotypic characteristics and sometimes raises difficulties in the interpretation of the results due to an absence of standardization of the typing reagents. In addition, the resolution of this biotyping is moderate and requires the manipulation of the living agent. More efficient DNA-based methods are needed, and this work explores the suitability of multiple locus variable number tandem repeats analysis (MLVA) for both typing and species identification.     

植物病原细菌检测和细菌病害诊断方法

植物病害诊断是通过病菌鉴定和致病性测定等步骤实现的。在过去的10年里用于细菌鉴定的基因组技术的快速发展极大地简化和促进了病菌的检测和鉴定,但是DNA分子检测方法不能完全取代传统的培养检验和表型检验方法。文中介绍了未显示病害症状的植物或植物产品中已知细菌的免疫检测和基因组DNA检测方法,以及细菌病害诊断鉴定的新方法。     

CRISPR在食源性致病菌进化分析、检测分型及毒力耐药调控中的应用进展

规律成簇间隔的短回文重复序列 (Clustered regularly interspaced short palindromic repeats,CRISPR) 与其相关蛋白基因系统可通过限制基因的水平转移而有效防御噬菌体等外源基因元件的入侵,不同细菌之间的CRISPR结构有所差异。基于CRISPR系统的差异性,文中对近几年CRISPR在食源性致病菌进化分析、检测与分型、毒力与耐药中的应用研究进行概述,并对基于CRISPR序列特点开发的细菌检测分型方法以及CRISPR与食源性致病菌的毒力、耐药性之间的相关性进行重点总结分析。此外,文中探讨了CRISPR在进化分析、检测与分型、毒力与耐药应用中的不足,提出将CRISPR分型方法标准化、完善与扩充致病菌CRISPR数据库、进一步探究噬菌体与细菌之间的共进化关系等建议,为进一步探索CRISPR功能提供参考。     

Identification of active bacterial communities in a model drinking water biofilm system using 16S rRNA-based clone libraries

Recent phylogenetic studies have used DNA as the target molecule for the development of environmental 16S rRNA gene clone libraries. As DNA may persist in the environment, DNA-based libraries cannot be used to identify metabolically active bacteria in water systems. In this study, an annular reactor was used to generate model drinking water biofilms grown on polycarbonate slides. High-quality RNA was extracted from 2-month-old biofilms and used to generate 16S rRNA-based clones. Sequencing analyses of 16S rRNA-based clones suggested that the active bacterial fraction consisted of a few dominant bacterial groups related to Nevskia ramosa and to uncultured bacteria. Several of these bacterial groups were closely related to clones characterized in a DNA-based clone library also generated in this study. Altogether, these results suggest that some of the predominant drinking water bacteria identified using DNA-based techniques are indeed active.     

耐甲氧西林金黄色葡萄球菌分子分型研究进展

近年来,耐甲氧西林金黄色葡萄球菌在全世界各地感染率和分离率不断提高,已成为目前院内感染的重要病原菌之一。运用有效、可靠、廉价的分子分型方法对分析耐甲氧西林金黄色葡萄球菌的流行病学特征及来源,对制定控制院感及流行的措施非常重要的。本研究概述了各种分子分型方法的原理及比较,如SCCmec分型、脉冲场凝胶电泳分型、多位点序列分型、葡萄球菌A蛋白分型和毒力因子分型等。脉冲场凝胶电泳仍然是暴发流行中MRSA分子分型的金标准,而其他分型方法更适合用于检测菌株的变异和建立国际监测。     

Multilocus sequence typing--what is resolved?

Nucleotide sequence-based methods for bacterial typing (multilocus sequence typing; MLST) allow rapid and global comparisons between results from different laboratories. Combining this advantage with the reduced cost of high throughput sequencing, increasing automation and the amenability of sequence data for evolutionary analysis, it seems inevitable that sequence-based typing will eventually predominate over gel-based methods such as pulsed-field gel electrophoresis (PFGE) for most bacterial species. The increasing availability of multiple genome sequences for single pathogenic species, and the recent development of many new MLST schemes, means that a re-examination of the utility of multilocus sequencing, and in particular the choice of gene loci, is now appropriate.     

A two-step strategy for molecular typing of multidrug-resistant Mycobacterium tuberculosis clinical isolates from Poland

Tuberculosis (TB) continues to be one of the most challenging public health problems in the world. An important contributor to the global burden of the disease is the emergence and spread of drug-resistant and particularly multidrug-resistant Mycobacterium tuberculosis strains (MDR), defined as being resistant to at least isoniazid and rifampicin. In recent years, the introduction of different DNA-based molecular typing methods has substantially improved the knowledge of the epidemiology of TB. The purpose of this study was to employ a combination of two PCR-based genotyping methods, namely spoligotyping and IS6110-Mtb1/Mtb2 PCR to investigate the clonal relatedness of MDR M. tuberculosis clinical isolates recovered from pulmonary TB patients from Poland. Among the 50 isolates examined, 28 (56%) were clustered by spoligotyping, whereas IS6110-Mtb1/Mtb2 PCR resulted in 16 (32%) clustered isolates. The isolates that clustered in both typing methods were assumed to be clonally related. A two-step strategy consisting of spoligotyping as a first-line test, performed on the entire pool of isolates, and IS6110-Mtb1/Mtb2 PCR typing as a confirmatory subtyping method, performed only within spoligotype-defined clusters, is an efficient approach for determining clonal relatedness among M. tuberculosis clinical isolates.     

Identification of industrial strains of lactic acid bacteria by methods of molecular genetic typing

Various methods currently used in microbiology for determining taxonomic state of bacteria are discussed. The main focus is aimed at identifying and gene typing of lactic acid bacteria, used as starter cultures for industrial process of production of sour milk products, meat products, and probiotics.     

Identification of industrial strains of lactic acid bacteria by methods of molecular genetic typing

Various methods currently used in microbiology for determining taxonomic state of bacteria are discussed. The main focus is aimed at identifying and gene typing of lactic acid bacteria, used as starter cultures for industrial process of production of sour milk products, meat products, and probiotics.     

Ethidium monoazide for DNA-based differentiation of viable and dead bacteria by 5'-nuclease PCR

PCR techniques have significantly improved the detection and identification of bacterial pathogens. Even so, the lack of differentiation between DNA from viable and dead cells is one of the major challenges for diagnostic DNA-based methods. Certain nucleic acid-binding dyes can selectively enter dead bacteria and subsequently be covalently linked to DNA. Ethidium monoazide (EMA) is a DNA intercalating dye that enters bacteria with damaged membranes. This dye can be covalently linked to DNA by photoactivation. Our goal was to utilize the irreversible binding of photoactivated EMA to DNA to inhibit the PCR of DNA from dead bacteria. Quantitative 5'-nuclease PCR assays were used to measure the effect of EMA. The conclusion from the experiments was that EMA covalently bound to DNA inhibited the 5'-nuclease PCR. The maximum inhibition of PCR on pure DNA cross-linked with EMA gave a signal reduction of approximately -4.5 log units relative to untreated DNA. The viable/dead differentiation with the EMA method was evaluated through comparison with BacLight staining (microscopic examination) and plate counts. The EMA and BacLight methods gave corresponding results for all bacteria and conditions tested. Furthermore, we obtained a high correlation between plate counts and the EMA results for bacteria killed with ethanol, benzalkonium chloride (disinfectant), or exposure to 70 degrees C. However, for bacteria exposed to 100 degrees C, the number of viable cells recovered by plating was lower than the detection limit with the EMA method. In conclusion, the EMA method is promising for DNA-based differentiation between viable and dead bacteria.     

Bacterial strain typing in the genomic era

Bacterial strain typing, or identifying bacteria at the strain level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Strain typing also has applications in studying bacterial population dynamics. Over the last two decades, molecular methods have progressively replaced phenotypic assays to type bacterial strains. In this article, we review the current bacterial genotyping methods and classify them into three main categories: (1) DNA banding pattern-based methods, which classify bacteria according to the size of fragments generated by amplification and/or enzymatic digestion of genomic DNA, (2) DNA sequencing-based methods, which study the polymorphism of DNA sequences, and (3) DNA hybridization-based methods using nucleotidic probes. We described and compared the applications of genotyping methods to the study of bacterial strain diversity. We also discussed the selection of appropriate genotyping methods and the challenges of bacterial strain typing, described the current trends of genotyping methods, and investigated the progresses allowed by the availability of genomic sequences.     

Methods for MHC genotyping in non-model vertebrates

Genes of the major histocompatibility complex (MHC) are considered a paradigm of adaptive evolution at the molecular level and as such are frequently investigated by evolutionary biologists and ecologists. Accurate genotyping is essential for understanding of the role that MHC variation plays in natural populations, but may be extremely challenging. Here, I discuss the DNA-based methods currently used for genotyping MHC in non-model vertebrates, as well as techniques likely to find widespread use in the future. I also highlight the aspects of MHC structure that are relevant for genotyping, and detail the challenges posed by the complex genomic organization and high sequence variation of MHC loci. Special emphasis is placed on designing appropriate PCR primers, accounting for artefacts and the problem of genotyping alleles from multiple, co-amplifying loci, a strategy which is frequently necessary due to the structure of the MHC. The suitability of typing techniques is compared in various research situations, strategies for efficient genotyping are discussed and areas of likely progress in future are identified. This review addresses the well established typing methods such as the Single Strand Conformation Polymorphism (SSCP), Denaturing Gradient Gel Electrophoresis (DGGE), Reference Strand Conformational Analysis (RSCA) and cloning of PCR products. In addition, it includes the intriguing possibility of direct amplicon sequencing followed by the computational inference of alleles and also next generation sequencing (NGS) technologies; the latter technique may, in the future, find widespread use in typing complex multilocus MHC systems.     

Molecular diagnostics in infectious diseases and public health microbiology: cottage industry to postgenomics

Molecular methods have been used increasingly over the past ten years to improve the sensitivity and speed of diagnosis in infectious diseases. Although their routine use is still limited to the detection of pathogens that are difficult to culture in vitro,'real-time' methods, commercial kits, quantification and automation will increase potential applications. Molecular methods are now widely used for epidemiological fingerprinting of isolates of public health importance. Sequence-based identification and strain typing, together with the development of tools that can probe for thousands of markers, will allow detailed strain fingerprinting to assist in disease management and control.     

Bacteria of the Burkholderia cepacia complex: specific features of diagnostics,genome organization and metabolism

Modern data, related with the identification and typing of the complex B. cepacia bacteria, are analyzed in the article by using the poly-phase taxonomic approach. An optimal scheme for identifying and typing the complex B. cepacia bacteria, involving the microbiological and molecular-biological methods of laboratory diagnostics, is presented. The key and assumed factors of pathogenicity of the discussed bacteria are described. The possible phylogenetic relations of the complex B. cepacia bacteria with phytopathgens as well as with pathogenic bacteria of species Burkholderia, Pseudomonas, Escherichia, B. mallei, B. pdeudomallei, P. seruginosa and E. coli are described. A possible role of genome alterations and mutations in the genome of the complex B. cepacia bacteria (with the latter genome having unusual properties, i.e. a big size, and a considerable quantity of insertion sequences) in creating the conditions for the "pulsing" evolution "jerks", i.e. for a rapid change-over from saprophytism in the soil to a pathogenic causative agent of a viral-and-bacteriological infection. Such mechanism can be regarded as a rapid and radical adaptation of a microorganism under the conditions of changing ecological niches.     

Use of molecular typing methods to trace the dissemination of Listeria monocytogenes in a shrimp processing plant.

Molecular typing of bacteria has been widely used in epidemiological studies but not as extensively for tracing the transmission of pathogenic bacteria in food plants. This study was conducted to examine the potential use of two molecular typing methods, random amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE), to trace Listeria monocytogenes contamination in a shrimp processing plant. Ribotyping and phase typing were also performed on a select number of strains. One hundred fifteen strains of L. monocytogenes collected in different areas of a shrimp processing plant were first serotyped and then subtyped by molecular typing. RAPD and PFGE showed great promise for typing L. monocytogenes isolates since distinguishable and reproducible DNA polymorphisms were obtained. When the composite profile from both (RAPD and PFGE) methods was generated, there was an increase in the discriminatory power to discern differences between strains of L. monocytogenes. The results indicated that environmental strains all fell into composite profile groupings unique to the environment, while strains from both water and utensils shared another composite profile group. L. monocytogenes fresh shrimp isolates belonging to one profile group were found in different areas of the processing line. This same profile group was also present in food handlers from the processing and packaging areas of the plant.