Differentiation of Tuberculosis Strains in a Population with Mainly Beijing-family Strains

Nikolayevskyy, Vladyslav; Gopaul, Krishna K.; Balabanova, Yanina; Brown, Timothy J.; Fedorin, Ivan; Drobniewski, Francis

doi:10.3201/eid1209.041263

Cited by 35 publications

(29 citation statements)

References 37 publications

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“…In a study of TB cases in Singapore, Sun et al (25) reported a discriminatory power of 0.994 for 68 cases. Studies of TB cases performed in Khoozestan province in Iran, Taiwan, and Samara in Russia reported a discriminatory power of 0.991 for 61 cases, 0.972 for 502 cases, and 0.625 for 129 cases, respectively (22, 24, 26). As the study in Singapore was based on a small number of isolates, its discriminatory power was slightly lower than in the present study.…”

Section: Discussionmentioning

confidence: 99%

Molecular Diversity of Mycobacterium tuberculosis Strains in Northwestern Iran

Pourostadi

Rashedi

Poor

et al. 2016

Jundishapur J Microbiol

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Background: Years after the development of antituberculosis (TB) drugs, many people continue to suffer from this disease. To control the spread of TB, strains of the Mycobacterium tuberculosis complex need to be determined, and sources of infection must be identified. Such steps should help to prevent transmission of the infection. Objectives: The aim of this study was to perform molecular genotyping of isolates of the M. tuberculosis complex obtained from patients in northwestern Iran. Methods: One hundred ninety-four culture-positive M. tuberculosis isolates obtained from patients in northwestern Iran were analyzed using the mycobacterial interspersed repetitive unit-exact tandem repeats (MIRU-ETR) method. Results: The MIRU-ETR method distinguished 162 different patterns in the 194 isolates, comprising 23 clusters and 139 unique patterns. Its discriminatory power according to the Hunter-Gaston discriminatory index (HGDI) was 0.9978. The largest cluster contained six isolates. Conclusions: This research indicated that various strains of M. tuberculosis were responsible for TB and that the majority of cases were due to reactivation.

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Section: Discussionmentioning

confidence: 99%

Molecular Diversity of Mycobacterium tuberculosis Strains in Northwestern Iran

Pourostadi

Rashedi

Poor

et al. 2016

Jundishapur J Microbiol

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“…Typing with the standard markers in the reference laboratories was performed using capillary electrophoresis on a 3130-XL DNA analyzer (ABI) and the commercially available kit (n ϭ 2), or in-house protocols adapted from reference 2, combined with capillary electrophoresis on a Beckman Coulter CEQ8000 DNA analyzer (n ϭ 1) on the SV1210 system (Hitachi) (n ϭ 1), or electrophoresis on agarose gels (n ϭ 2). For the analysis of the hypervariable loci, the same electrophoresis platforms were used by the respective laboratories, using either previously published primers and protocols (14,15,30) (n ϭ 3) or protocols and primers used or newly designed by Genoscreen (n ϭ 3) ( Table 2). To homogenize the counting of repeat units especially for loci containing partial repeats (e.g., locus 0580, alias MIRU 04/ETR-D, or locus 3232, alias QUB-3232), a standard allele calling system (2) was used for the 24 standard markers, while the system used for the hypervariable loci was based on analysis of H37Rv genome sequence and conventions described in Table 2.…”

Section: Methodsmentioning

confidence: 99%

“…However, several studies suggested that 24-locus MIRU-VNTR typing can lack resolution power for discriminating closely related clones of the M. tuberculosis Beijing lineage (5,(10)(11)(12)(13)(14)(15)(16)(17)(18). This lineage constitutes the bulk of the East Asian lineage of M. tuberculosis (19).…”

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confidence: 99%

“…Beijing strains have been associated with large outbreaks and rapid spread of MDR TB in different geographic regions (reference 20 and references therein). So-called hypervariable MIRU-VNTR loci (2), because of their higher variability than that of the 24 standardized loci, have been tested and used to increase discriminatory power on Beijing strains (5,(10)(11)(12)(13)(14)(15)(16)(17)(18)21). Nonetheless, intra-and interlaboratory analyses suggested lack of reproducibility and robustness of results based on at least some of these hypervariable loci, questioning their informative value and justifying their exclusion from the standard 24-locus set for firstline typing (2).…”

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confidence: 99%

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Proposal of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat Loci for Subtyping of Mycobacterium tuberculosis Beijing Isolates

Allix‐Béguec¹,

Wahl²,

Hanekom

et al. 2014

J Clin Microbiol

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q Mycobacterium tuberculosis Beijing strains represent targets of special importance for molecular surveillance of tuberculosis (TB), especially because they are associated with spread of multidrug resistance in some world regions. Standard 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing lacks resolution power for accurately discriminating closely related clones that often compose Beijing strain populations. Therefore, we evaluated a set of 7 additional, hypervariable MIRU-VNTR loci for better resolution and tracing of such strains, using a collection of 535 Beijing isolates from six world regions where these strains are known to be prevalent. The typeability and interlaboratory reproducibility of these hypervariable loci were lower than those of the 24 standard loci. Three loci (2163a, 3155, and 3336) were excluded because of their redundant variability and/or more frequent noninterpretable results compared to the 4 other markers. The use of the remaining 4-locus set (1982, 3232, 3820, and 4120) increased the number of types by 52% (from 223 to 340) and reduced the clustering rate from 58.3 to 36.6%, when combined with the use of the standard 24-locus set. Known major clonal complexes/ 24-locus-based clusters were all subdivided, although the degree of subdivision varied depending on the complex. Only five single-locus variations were detected among the hypervariable loci of an additional panel of 92 isolates, representing 15 years of clonal spread of a single Beijing strain in a geographically restricted setting. On this calibrated basis, we propose this 4-locus set as a consensus for subtyping Beijing clonal complexes and clusters, after standard typing.

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“…It is considered the international standard for molecular typing (3,4), sometimes supplemented by spoligotyping (5). Despite its remarkable advantages in terms of technical simplicity, reproducibility, and portability compared with IS6110 restriction fragment length polymorphism (RFLP) analysis (6), several studies have highlighted the relative lack of resolution power of MIRU-VNTR analysis (7), particularly for highly clonal strain groups, such as the Beijing lineage (8,9).…”

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Implementation of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat Loci in Mycobacterium tuberculosis Molecular Epidemiology

et al. 2016

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bThis study shows that the addition of a consensus 4-locus set of hypervariable mycobacterial interspersed repetitive-unitvariable-number tandem repeat (MIRU-VNTR) loci to the spoligotyping-24-locus MIRU-VNTR typing strategy is a wellstandardized approach that can contribute to an improvement of the true cluster definition while retaining high typeability in non-Beijing strains.T he worldwide implementation of 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) analysis has deeply contributed to the development of molecular epidemiology in the tuberculosis (TB) field (1, 2). It is considered the international standard for molecular typing (3, 4), sometimes supplemented by spoligotyping (5). Despite its remarkable advantages in terms of technical simplicity, reproducibility, and portability compared with IS6110 restriction fragment length polymorphism (RFLP) analysis (6), several studies have highlighted the relative lack of resolution power of MIRU-VNTR analysis (7), particularly for highly clonal strain groups, such as the Beijing lineage (8, 9).The introduction of whole-genome sequencing (WGS) for Mycobacterium tuberculosis strain typing, due to its ability to discriminate closely related strains, appears to be the optimal solution for achieving the highest possible resolution (10, 11). However, the wider use of WGS for routine epidemiology is still hampered by cost, especially in resource-limited settings, and by the lack of standardization and established quality assurance programs (1) (12).A possible transitional strategy might involve the inclusion of additional MIRU-VNTR markers to the standard set. In this regard, four novel MIRU-VNTR loci, i.e., 1982, 3232, 3820, and 4120, have recently been suggested for the subtyping of clustered samples belonging to the highly homogeneous Beijing lineage (8). Nevertheless, scarce information is available on the possible contribution of these markers to the improvement of discrimination among non-Beijing M. tuberculosis lineages.Our study aimed at assessing the epidemiological value and technical feasibility of the inclusion of this 4-locus set of hypervariable loci for subtyping non-Beijing M. tuberculosis strains identified as clusters by the standard spoligotyping-24-locus MIRU-VNTR typing strategy.A total of 220 M. tuberculosis samples collected in Albania during the 2010 National TB Drug Resistance Survey (DRS), were genotyped by 43-spacer spoligotyping, as previously described (13), and by 24-locus MIRU-VNTR analysis using the GenoScreen MIRU typing kit (GenoScreen, Lille, France) (2).To infer lineages and clusters, a combined spoligotyping-VNTR analysis was carried out using the MIRU-VNTRplus Web application (http://www.miru-vntrplus.org) (14), requiring 100% identity (both in spoligotype and MIRU profile) for grouping samples.The recently developed consensus 4-locus set of hypervariable MIRU-VNTR markers, based on the 1982 (alias QUB-18), 3232 (alias QUB-3232), 3820, and 4120 loci, was used for further analysis on all ...

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Differentiation of Tuberculosis Strains in a Population with Mainly Beijing-family Strains

Abstract: A new panel of 25 VNTR-MIRU loci differentiates Beijing-family TB strains better than a panel of 15.

Cited by 35 publications

References 37 publications

Molecular Diversity of Mycobacterium tuberculosis Strains in Northwestern Iran

Molecular Diversity of Mycobacterium tuberculosis Strains in Northwestern Iran

Proposal of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat Loci for Subtyping of Mycobacterium tuberculosis Beijing Isolates

Implementation of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat Loci in Mycobacterium tuberculosis Molecular Epidemiology

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