Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies

Alonso-Rodriguez, Noelia; Martínez-Lirola, Miguel; Herránz, Marta; Sanchez-Benitez, Marisa; Barroso, Pilar; Bouza, Emilio; Viedma, Darío García de

doi:10.1186/1471-2180-8-34

Cited by 70 publications

(60 citation statements)

References 31 publications

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“…When we tolerated SLVs and compared the results from both techniques, identifying those isolates with more than 90% similarity in their RFLPs as clustered, the percentage of discrepancies fell from 14.6% to 8.6%. In addition, five of the remaining discrepancies involved a genotype belonging to the Haarlem lineage (identified with the code 28 in this study), which has been found to be markedly split by MIRU-VNTR analysis, suggesting that RFLP analysis is unable to offer enough discrimination to analyze with precision some of the isolates within this lineage (3,11,27,30,31,34). If we did not count cases involving these Haarlem strains, the number of discrepancies would fall to as low as 6.8%.…”

Section: Discussionmentioning

confidence: 99%

Prospective Universal Application of Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Genotyping To CharacterizeMycobacterium tuberculosisIsolates for Fast Identification of Clustered and Orphan Cases

et al. 2009

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When discrepant cases showing subtle genotypic differences were tolerated, the discrepancies fell from 14.6% to 8.6%. Epidemiological links were found for 83.8% of the cases clustered by both RFLP and MIRU-15 analyses, whereas for the cases clustered by RFLP or MIRU-VNTR analysis alone, links were identified for only 30.8% or 38.9% of the cases, respectively. The latter group of cases mainly comprised isolates that could also have been clustered, if subtle genotypic differences had been tolerated. MIRU-15 genotyping seems to be a good alternative to RFLP genotyping for real-time interventional schemes. The correlation between MIRU-15 and IS6110 RFLP findings was reasonable, although some uncertainties as to the assignation of clusters by MIRU-15 analysis were identified.Molecular tools have been widely used to characterize Mycobacterium tuberculosis isolates, with the aim of better understanding the epidemiology of tuberculosis (TB) (1,6,8,18,23). This has enabled us to document suspected outbreaks (4, 28, 34), identify risk factors associated with TB transmission (13,20,36), and evaluate the efficiency of control programs by observing the dynamics of clustered cases (9,12,17,22,24).Restriction fragment length polymorphism (RFLP) analysis based on the IS6110 sequence is the reference genotyping method for M. tuberculosis (35). However, its limitations (mainly response times) make its adaptation unsuitable for real-time intervention epidemiological schemes. New genotyping techniques based on PCR have recently been developed and are more suitable for these purposes.One of the most promising PCR-based methods is mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping (21,(30)(31)(32). A novel format based on 15 loci has improved upon the initial 12-loci version. Its discriminatory power has been found to be equivalent to that of the standard approach on the basis of reference method, and its response time could be competitive. However, very few long-term analyses apply this technique universally in parallel to the reference method to identify advantages and pitfalls (1,25,27,33).In order to compare both techniques, we selected the province of Almería, in southeast Spain, because of the complexity of its socioepidemiological population profile, which challenges us to develop new and more-efficient methods of surveying TB transmission. In Almería, around 60% of the cases

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Section: Discussionmentioning

confidence: 99%

Prospective Universal Application of Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Genotyping To CharacterizeMycobacterium tuberculosisIsolates for Fast Identification of Clustered and Orphan Cases

et al. 2009

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“…Many efforts have been made to establish a reference method for a high-resolution genotyping of Mycobacterium tuberculosis strains (2,3,26,35) that could be used for epidemiological and phylogenetic studies and, recently, a standardized MIRU-VNTR set of 15 or 24 loci optionally combined with spoligotyping has been proposed (2). Fewer attempts have been made to find an optimized genotyping method for M. bovis and M. caprae strains, and probably the M. bovis populations in the different countries are too diverse to achieve a consensus set of markers useful in any situation.…”

Section: Discussionmentioning

confidence: 99%

Molecular Typing ofMycobacterium bovisStrains Isolated in Italy from 2000 to 2006 and Evaluation of Variable-Number Tandem Repeats for Geographically Optimized Genotyping

et al. 2009

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Spoligotyping and exact tandem repeat (ETR) analysis ofAs a result, the official TB-free status was achieved starting from 1970 in some Italian areas such as the Autonomous Region of Trentino Alto Adige, Friuli Venezia Giulia Region (northeast Italy), and some provinces of northern and central Italy. In the rest of the national territory, TB still persists with different prevalence rates: 6.6% in Sicilia, 0.77% in Puglia, and 0.59% in Lazio and Campania. In northern Italy, where about the 70% of the cattle population is reared, TB is still present in the Piedmont (0.4%), Lombardy (0.15%), Veneto (0.1%), and Emilia-Romagna (0.08%) regions. In order to accelerate the achievement of a TB-free status, the authorities in these areas are implementing specific TB control measures, taking into account local situations and problems such as mean distance among herds, trade of animals from other territories, and common pasturing.In this respect, the origin of TB infection often remains undetermined despite its importance. Molecular typing of isolates has become a valuable tool in the study of M. bovis epidemiology, allowing investigators to better identify the sources of infection and achieve a wider knowledge of TB transmission routes. A genetic profile database collection of M. bovis isolates may help to confirm or reject hypotheses outlined by traditional epidemiological investigations.Genotyping of M. bovis probably lacks sufficiently informative methods. IS6110 restriction fragment length polymorphism (RFLP) typing has been considered a gold standard method for differentiation of M. tuberculosis strains for a long time; this has provided only limited discrimination among M. bovis populations where the majority of the isolates harbor only one or few IS copies (11). PCR-based spoligotyping (16) has been widely used to genotype M. bovis isolates (11); it is highly reproducible and rapid and represents the first universally recognized typing system for M. bovis populations. However, studies performed on M. bovis isolates in Northern Ireland (32,33), France (12), Australia, Canada, the Republic of Ireland, and Iran (7) showed a limited discrimination power of this method.Over the last 10 years several PCR-based genotyping methods have become available for rapid molecular epidemiology

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“…A 24-locus format is more informative phylogenetically, and it can be used to trace transmission paths of TB (210,369,370). The discriminatory power of the 24-locus MIRU-VNTR typing system provides a resolution com-parable to that of IS6110-RFLP profiling (252,363,370,371). Therefore, 24-locus MIRU-VNTR typing has been suggested to be the new "gold standard" for molecular typing of MTBC strains.…”

Section: Methods Based On Repetitive Sequencesmentioning

confidence: 99%

“…Therefore, 12-locus MIRU-VNTR analysis was suggested to be used in combination with other genotyping methods (e.g., spoligotyping) to approximate the discriminatory power of IS6110 profiling (361,363). At the same time, 12-locus MIRU-VNTR analysis can be more discriminatory than IS6110-RFLP analysis if M. tuberculosis isolates with low copy numbers of IS6110 are under study (291-293, 364, 365).…”

Section: Methods Based On Repetitive Sequencesmentioning

confidence: 99%

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

et al. 2016

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SUMMARYMolecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods forMycobacterium tuberculosisand nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.

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Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies

Cited by 70 publications

References 31 publications

Prospective Universal Application of Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Genotyping To CharacterizeMycobacterium tuberculosisIsolates for Fast Identification of Clustered and Orphan Cases

Prospective Universal Application of Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Genotyping To CharacterizeMycobacterium tuberculosisIsolates for Fast Identification of Clustered and Orphan Cases

Molecular Typing ofMycobacterium bovisStrains Isolated in Italy from 2000 to 2006 and Evaluation of Variable-Number Tandem Repeats for Geographically Optimized Genotyping

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

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