New Perspectives in the Molecular Epidemiology of Tuberculosis

Soolingen, Dick van; Kremer, Kristin; Vynycky, E.

doi:10.1159/000066887

Cited by 17 publications

(22 citation statements)

References 139 publications

(140 reference statements)

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“…The method most frequently used for molecular typing of M. tuberculosis strains is IS6110 RFLP, and its application has significantly increased our understanding of the epidemiology of tuberculosis (74,81). However, it takes several weeks before a strain is sufficiently grown for RFLP typing, and the method is labor-intensive and complicated.…”

Section: Discussionmentioning

confidence: 99%

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Discriminatory Power and Reproducibility of Novel DNA Typing Methods forMycobacterium tuberculosisComplex Strains

et al. 2005

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In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. (J. Clin. Microbiol. 37:2607-2618, 1999). This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.

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Section: Discussionmentioning

confidence: 99%

“…In the past decade, molecular typing methods have increasingly been applied to study the epidemiology and control of tuberculosis (74,81). When DNA typing is applied to local samples, it can be used to trace outbreaks of tuberculosis and transmission within institutions.…”

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confidence: 99%

Discriminatory Power and Reproducibility of Novel DNA Typing Methods forMycobacterium tuberculosisComplex Strains

et al. 2005

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“…At the individual clinical management level, the application of genotyping enables the detection (1) or exclusion (25) of laboratory errors and the follow-up of relapse cases to identify treatment failures, reactivations of latent disease, and exogenous reinfections (46). At the public health level, genotyping enables the detection of unsuspected outbreaks and the identification of transmission chains and secondary cases of infection (4,46).…”

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confidence: 99%

Evaluation and Strategy for Use of MIRU-VNTRplus, a Multifunctional Database for Online Analysis of Genotyping Data and Phylogenetic Identification ofMycobacterium tuberculosisComplex Isolates

et al. 2008

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Because of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing has become a major method for the epidemiological tracking of Mycobacterium tuberculosis complex (MTBC) clones. However, no public MIRU-VNTR database based on well-characterized reference strains has been available hitherto for easy strain identification. Therefore, a collection of 186 reference strains representing the primary MTBC lineages was used to build a database, which is freely accessible at http://www.MIRU-VNTRplus.org. The geographical origin and the drug susceptibility profile of each strain were stored together with comprehensive genetic lineage information, including the 24-locus MIRU-VNTR profile, the spoligotyping pattern, the singlenucleotide-and large-sequence-polymorphism profiles, and the IS6110 restriction fragment length polymorphism fingerprint. Thanks to flexible import functions, a single or multiple user strains can be analyzed, e.g., for lineage identification with or without the use of reference strains, by best-match or tree-based analyses with single or combined marker data sets. The results can easily be exported. In the present study, we evaluated the database consistency and various analysis parameters both by testing the reference collection against itself and by using an external population-based data set comprising 629 different strains. Under the optimal conditions found, lineage predictions based on typing by 24-locus MIRU-VNTR analysis optionally combined with spoligotyping were verified in >99% of the cases. On the basis of this evaluation, a user strategy was defined, which consisted of best-match analysis followed, if necessary, by tree-based analysis. The MIRU-VNTRplus database is a powerful tool for high-resolution clonal identification and has little equivalent in terms of functionalities among the bacterial genotyping databases available so far.Mycobacterium tuberculosis is among the most successful human pathogens worldwide and is responsible for extensive morbidity and mortality, with approximately 2 million deaths each year (51). The importance of tuberculosis (TB) as a major public health problem has been dramatically reinforced due to the human immunodeficiency virus coepidemic and the emergence of (multi)drug-resistant M. tuberculosis strains.Methods for genotyping of clinical M. tuberculosis complex (MTBC) strains have proven to be valuable tools for TB control. At the individual clinical management level, the application of genotyping enables the detection (1) or exclusion (25) of laboratory errors and the follow-up of relapse cases to identify treatment failures, reactivations of latent disease, and exogenous reinfections (46). At the public health level, genotyping enables the detection of unsuspected outbreaks and the identification of transmission chains and secondary cases of infection (4, 46).

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“…The majority of studies focused on particular strain types such as the Beijing genotype only, basically, because they are easy to recognize by applying genotyping techniques such as IS6110 DNA fingerprint and spoligotyping (34). Based on these markers, a variety of strains were not classifiable into phylogenetic lineages or clonal complexes since the genotyping information was not informative, e.g., due to homoplasy (4,6).…”

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confidence: 99%

Mycobacterium tuberculosis Beijing Lineage Favors the Spread of Multidrug-Resistant Tuberculosis in the Republic of Georgia

et al. 2010

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High rates and transmission of multidrug-resistant (MDR) tuberculosis (TB) have been associated with theMycobacterium tuberculosis complex (MTBC) Beijing lineage, pointing to the importance of pathogen genetic factors for the modulation of infection outcome and epidemiology. We present here an in-depth analysis of the population structure of MTBC strains from the Republic of Georgia, a high-incidence setting at the Black Sea Coast. Phylogenetic lineages were identified based on 24-locus MIRU-VNTR (for mycobacterial interspersed repetitive unit-variable number tandem repeat) and spoligotyping analysis. Clusters of strains with identical genotyping profiles were determined as an indicator for the rate of recent transmission. Among the 183 M. tuberculosis isolates investigated, the most prominent lineage found was Beijing (26%), followed by the LAM (18%), Ural (12%), and Haarlem (5%) strains. A closely related previously undefined phylogenetic group (62 strains) showed a genotyping pattern similar to laboratory strain H37RV and was denominated as "Georgia-H37RV-like." Although isoniazid resistance was found among strains of different lineages, MDR TB was nearly completely restricted to Beijing strains (P < 0.0001). Approximately 50% of the isolates were grouped in clusters, indicating a high rate of recent transmission. Our data indicate that, in addition to the confirmation of the importance of Beijing genotype strains for the TB epidemiology in former Soviet Union countries, a high-population diversity with strains of the LAM, Ural, Haarlem, and a previously undefined lineage represents nearly two-thirds of the strains found in Georgia. Higher rates among previously treated and MDR TB patients point to a higher potential of lineage Beijing to escape therapy and develop MDR TB.Drug-resistant Mycobacterium tuberculosis complex (MTBC) strains have emerged worldwide as a serious threat for tuberculosis (TB) control. Rates of multidrug-resistant (MDR) strains (i.e., resistance at least to isoniazid [INH] and rifampin [RIF]) have reached levels of up to 14% among patients never treated and up to 40% among previously treated patients in several MDR TB "hot spots" such as such as Karakalpakstan (Uzbekistan) and Kazakhstan in Eastern Europe (10, 37). Every year an estimated 489,000 cases of MDR TB arise globally (36). MDR TB is associated with much poorer treatment outcomes than for drug-susceptible TB, with a much higher risk of developing further resistances (2, 7). Prolonged periods of infectivity result in enhanced transmission of drug-resistant strains, further accelerating the rates of drug resistance (3). Even more worrisome is the emergence of a nearly untreatable form of TB, namely, extensively drug-resistant TB (XDR TB), which is defined as MDR plus additional resistance to any fluoroquinolone and at least one of three injectable drugs (i.e., amikacin, kanamycin, or capreomycin). A recent survey confirmed the worldwide presence of XDR strains, with rates of up 15% of MDR TB cases (30).Considering the difficulti...

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New Perspectives in the Molecular Epidemiology of Tuberculosis

Cited by 17 publications

References 139 publications

Discriminatory Power and Reproducibility of Novel DNA Typing Methods forMycobacterium tuberculosisComplex Strains

Discriminatory Power and Reproducibility of Novel DNA Typing Methods forMycobacterium tuberculosisComplex Strains

Evaluation and Strategy for Use of MIRU-VNTRplus, a Multifunctional Database for Online Analysis of Genotyping Data and Phylogenetic Identification ofMycobacterium tuberculosisComplex Isolates

Mycobacterium tuberculosis Beijing Lineage Favors the Spread of Multidrug-Resistant Tuberculosis in the Republic of Georgia

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