On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing

Grissa, Ibtissem; Bouchon, Patrick; Pourcel, Christine; Vergnaud, Gilles

doi:10.1016/j.biochi.2007.07.014

Cited by 129 publications

(91 citation statements)

References 53 publications

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“…Bioinformatic detection of putative VNTRs in the genome sequences of six A. baumannii strains was performed using web-based tools (6,9), and a standard laboratory protocol for MLVA was agreed upon by the two centers.…”

Section: Methodsmentioning

confidence: 99%

“…In a typical MLVA assay, a predefined set of VNTRs is analyzed, and a code corresponding to the number of repeats at each locus can be determined for individual strains. Therefore, MLVA is a cost-effective typing method which provides portable results (MLVA codes) that can easily be stored in a database and exchanged between laboratories (9,20,36). A previous study identified 13 putative VNTRs in A. baumannii ATCC 17978, but only 2 provided sufficient repeat polymorphism for fine typing of clinical isolates showing identical PFGE profiles (29).…”

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confidence: 99%

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Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme

et al. 2011

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Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and costeffective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR-and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/.The Gram-negative bacterium Acinetobacter baumannii has emerged worldwide as a major nosocomial pathogen and a serious threat to patients in intensive care units (ICUs) (18,27). Hallmarks of A. baumannii infection are resistance to a broad range of antimicrobial agents, the tendency for epidemic spread, and long-term persistence in the hospital setting (4,8,27).Most A. baumannii clinical strains from multiple hospital outbreaks throughout the world have been referred to a few epidemic lineages. Two of these, called international clonal lineages I and II, were first identified in northwestern Europe in the early 1980s and then worldwide (8, 17), while a third clone, called international clonal lineage III, was later detected in France, Netherlands, Italy, and Spain, probably persisting in European hospitals since the 1990s (17, 34).Several typing methods have been developed to trace A. baumannii epidemiology from the local to the global scale. Among them, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) (23) and multilocus sequence typing (MLST) (2, 7) are currently considered the methods of choice for epidemi...

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme

et al. 2011

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“…3. Initially, before an understanding of their physiological role, CRISPR-Cas systems were found to be a useful tool for typing bacterial diversity (23). In Mycobacterium tuberculosis (type III-A), for instance, CRISPR variability has been a gold standard for routine genotyping purposes and to study the epidemiology of M. tuberculosis (24)(25)(26)(27).…”

Section: Crispr-cas As a Typing Toolmentioning

confidence: 99%

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

Louwen

Staals

Endtz

et al. 2014

Microbiol Mol Biol Rev

208

178

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SUMMARY Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. The discovery that CRISPR spacers are often identical to sequence fragments of mobile genetic elements was a major breakthrough that eventually led to the elucidation of CRISPR-Cas as an adaptive immunity system. Key elements of this unique prokaryotic defense system are small CRISPR RNAs that guide nucleases to complementary target nucleic acids of invading viruses and plasmids, generally followed by the degradation of the invader. In addition, several recent studies have pointed at direct links of CRISPR-Cas to regulation of a range of stress-related phenomena. An interesting example concerns a pathogenic bacterium that possesses a CRISPR-associated ribonucleoprotein complex that may play a dual role in defense and/or virulence. In this review, we describe recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular.

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“…Databases for a variety of schemes and bacterial species have been made available by several institutions (Table 1). Some of these online databases offer users the possibility to create their own private or public database like MLVAbank [16], MLVAplus or MLVA-NET [17]. A particular application of an MLVA scheme is the MIRU-VNTRplus Internet application for Mycobacterium tuberculosis [18,19].…”

Section: Online Databases For Bacterial Typingmentioning

confidence: 99%

Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution

et al. 2013

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Advances in typing methodologies have been the driving force in the field of molecular epidemiology of pathogens. The development of molecular methodologies, and more recently of DNA sequencing methods to complement and improve phenotypic identification methods, was accompanied by the generation of large amounts of data and the need to develop ways of storing and analysing them. Simultaneously, advances in computing allowed the development of specialised algorithms for image analysis, data sharing and integration, and for mining the ever larger amounts of accumulated data. In this review, we will discuss how bioinformatics accompanied the changes in bacterial molecular epidemiology. We will discuss the benefits for public health of specialised online typing databases and algorithms allowing for real-time data analysis and visualisation. The impact of the new and disruptive next-generation sequencing methodologies will be evaluated, and we will look ahead into these novel challenges.

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On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing

Cited by 129 publications

References 53 publications

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution

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