Evaluation of the Epidemiologic Utility of Secondary Typing Methods for Differentiation of<i>Mycobacterium tuberculosis</i>Isolates

Kwara, Awewura; Schiro, Ronald; Cowan, Lauren S.; Hyslop, Newton E.; Wiser, Mark F.; Harrison, Stephanie R; Kissinger, Patricia; Diem, Lois; Crawford, Jack T.

doi:10.1128/jcm.41.6.2683-2685.2003

Cited by 72 publications

(65 citation statements)

References 12 publications

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“…Mycobacterial cultures were performed using liquid plus solid media at certified local laboratories. Isolates obtained at diagnosis and at the time of treatment failure or relapse underwent confirmatory drug-susceptibility testing (using solid media and the proportion method), DNA fingerprinting (20,21), and sequencing of the rpoB gene (22).…”

Section: Methodsmentioning

confidence: 99%

Acquired Rifamycin Resistance with Twice-Weekly Treatment of HIV-related Tuberculosis

Burman

Benator

Vernon

et al. 2006

Am J Respir Crit Care Med

133

114

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Rationale: Rifabutin was recommended in place of rifampin during treatment of HIV-related tuberculosis (TB) to facilitate concomitant potent antiretroviral therapy, but this approach has not been evaluated in a prospective study. Objective: To evaluate the activity of intermittent rifabutin-based therapy. Methods: Patients with culture-confirmed TB were treated under direct supervision with 2 mo of rifabutin, isoniazid, pyrazinamide, and ethambutol (given daily, thrice-weekly, or twice-weekly per the local tuberculosis control program), followed by 4 mo of twiceweekly rifabutin plus isoniazid. Measurements: Culture-positive treatment failure or relapse. Main Results: A total of 169 eligible patients were enrolled. Most had advanced HIV disease; the median CD4 cell count and HIV-RNA level were 90 cells/mm 3 (interquartile range, 35-175) and 5.3 log 10 copies/ml (interquartile range, 4.8-5.7), respectively. Nine (5.3%) patients had culture-positive treatment failure (n ϭ 3) or relapse (n ϭ 6). Eight of these nine (89%) cases had isolates with acquired rifamycin resistance. Treatment failure or relapse was associated with baseline CD4 lymphocyte count, being 12.3% (9/73; 95% confidence interval, 6.5-22.0%) among patients with CD4 Ͻ 100 cells/mm 3 versus 0% (0/65; 95% confidence interval, 0.0-4.5%) among those with higher CD4 lymphocyte counts (p Ͻ 0.01). One hundred thirty-seven (81%) patients received antiretroviral therapy during TB treatment. Adverse events were common, but only two patients (1%) permanently discontinued study drugs. Conclusions: Intermittent rifabutin-based therapy for HIV-related TB was well tolerated, but there was a high risk of treatment failure or relapse with acquired rifamycin resistance among patients with low CD4 lymphocyte counts.

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Section: Methodsmentioning

confidence: 99%

Acquired Rifamycin Resistance with Twice-Weekly Treatment of HIV-related Tuberculosis

Burman

Benator

Vernon

et al. 2006

Am J Respir Crit Care Med

133

114

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“…The major advantage of rapid typing of isolates is the capacity to immediately provide a strain designation, which in turn may facilitate prompt public health intervention. While the technical feasibility of these methods has been well demonstrated (12,26), their public health utility remains to be determined.To date, studies of small outbreaks have shown that results from spoligotyping and MIRU-VNTR typing are often identical among isolates clustered by IS6110-based RFLP (6,7,8,11,15,16,18,23). However, the capacity of these modalities to provide unique patterns among unrelated isolates (i.e., their specificities) in a population-based study has not yet been evaluated.…”

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confidence: 99%

“…To date, studies of small outbreaks have shown that results from spoligotyping and MIRU-VNTR typing are often identical among isolates clustered by IS6110-based RFLP (6,7,8,11,15,16,18,23). However, the capacity of these modalities to provide unique patterns among unrelated isolates (i.e., their specificities) in a population-based study has not yet been evaluated.…”

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confidence: 99%

Sensitivities and Specificities of Spoligotyping and Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing Methods for Studying Molecular Epidemiology of Tuberculosis

Scott¹,

Menzies

Tannenbaum³

et al. 2005

J Clin Microbiol

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The development of PCR-based genotyping modalities (spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat [MIRU-VNTR] typing) offers promise for real-time molecular epidemiological studies of tuberculosis (TB). However, the utility of these methods depends on their capacity to appropriately classify isolates. To determine the operating parameters of spoligotyping and MIRU-VNTR typing, we have compared results generated by these newer tests to the standard typing method, IS6110 restriction fragment length polymorphism, in analyses restricted to high-copy-number IS6110 isolates. Sensitivities of the newer tests were estimated as the percentages of isolates with identical IS6110 fingerprints that had identical spoligotypes and MIRU-VNTR types. The specificities of these tests were estimated as the percentages of isolates with unique IS6110 fingerprints that had unique spoligotypes and MIRU-VNTR types. The sensitivity of MIRU-VNTR typing was 52% (95% confidence interval [CI], 31 to 72%), and the sensitivity of spoligotyping was 83% (95% CI, 63 to 95%). The specificity of MIRU-VNTR typing was 56% (95% CI, 51 to 62%), and the specificity of spoligotyping was 40% (95% CI, 35 to 46%). The proportion of isolates estimated to be due to recent transmission was 4% by identical IS6110 patterns, 19% by near-identical IS6110 patterns, 33% by MIRU-VNTR typing, and 53% by spoligotyping. The low calculated specificities of spoligotyping and MIRU-VNTR typing led to misclassification of cases, inflated estimates of TB transmission, and low positive predictive values, suggesting that these techniques have unsuitable operating parameters for population-based molecular epidemiology studies.Tuberculosis (TB) molecular epidemiology exploits selected bacterial DNA targets to serve as markers for Mycobacterium tuberculosis strains. The most common method of DNA fingerprinting used is IS6110-based restriction fragment length polymorphism (RFLP). In a number of studies over the past decade, this modality has been validated for tracking TB transmission through two sets of observations. First, isolates from epidemiologically linked patients generally share identical or similar patterns (2, 3, 5). Second, matched RFLP patterns, when occurring among patients without known epidemiological links, are generally observed within groups with clear risk factors for TB transmission (1, 10, 13, 24).An important practical limitation of IS6110 RFLP is that results are usually obtained weeks to months after the initial diagnosis of TB. This limitation stems from the need to grow large numbers of bacteria to extract DNA of sufficient quantity and quality for RFLP analysis. Therefore, while useful for documenting transmission events, IS6110 RFLP often provides data once outbreaks are well established. In contrast, a number of PCR-based typing modalities have been recently developed, including spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis (MIRU-VNTR) typing, which offer...

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“…One comparison study has suggested that MIRU-VNTR typing may be more suitable for defining epidemiologically related isolates than are IS6110 typing and spoligotyping (16). Singapore is a Southeast Asian country with a heterogeneous population in which the majority is of Chinese origin and a substantial minority is of Indian origin.…”

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confidence: 99%

Use of Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing To Examine Genetic Diversity ofMycobacterium tuberculosisin Singapore

et al. 2004

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Strain typing using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) is a powerful tool for studying the epidemiology and genetic relationships of Mycobacterium tuberculosis isolates. For this study, isolates from 291 patients in Singapore were genotyped by this method. One hundred sixty-six distinct MIRU-VNTR patterns were detected. One hundred sixty-two strains were grouped into 1 of 35 different MIRU-VNTR clusters and 131 isolates were unique. In this sample collection, 9 of the 12 MIRU-VNTR loci were moderately or highly discriminative according to their allelic diversities. The HunterGaston discriminatory index was 0.975, indicating the high power of discrimination of MIRU-VNTR typing. By direct comparisons with previously typed MIRU-VNTR patterns and by genetic relationship analyses, we could identify and clearly define four epidemic groups of M. tuberculosis in our sample, corresponding to the W/Beijing, East-Africa-Indian, Haarlem, and Delhi genotype families. Furthermore, MIRU-VNTR typing was able to clearly distinguish ancestral and modern M. tuberculosis strains as defined by TbD1 genomic deletion analysis. These results indicate that MIRU-VNTR typing can be a useful first-line tool for studying the genetic diversity of M. tuberculosis isolates in a large urban setting such as Singapore.Tuberculosis remains a major infectious disease and causes high morbidity and mortality worldwide. Mycobacterium tuberculosis genotyping is a useful tool for the epidemiological surveillance and control of disease transmission. Although a large number of DNA-fingerprinting methods for typing M. tuberculosis isolates have been developed (15), only IS6110 restriction fragment length polymorphism (RFLP) typing (5) and spacer oligonucleotide typing (spoligotyping) (14) have gained wide acceptance.IS6110 typing is the most commonly used strain-typing method for M. tuberculosis. This method is based on variations among IS6110 insertion elements between strains. IS6110 typing has been shown to be reproducible and highly discriminatory (15). However, there are several drawbacks of IS6110 typing. Firstly, it has poor discriminatory power for M. tuberculosis strains with low copy numbers of IS6110 (7,15,17). Secondly, it requires relatively large quantities of purified DNA. Thirdly, it is time-consuming to perform and analyze. Finally, although a standardized methodology has been recommended (29), it is difficult to compare IS6110 RFLP results between laboratories. This hinders global studies of M. tuberculosis epidemiology and transmission. Spoligotyping is a PCRbased method which detects the presence or absence of 43 spacers in the direct repeat locus of the M. tuberculosis genome. This has advantages over IS6110 typing in that it is faster and easier to perform, it is reproducible, and it requires only small quantities of DNA. However, the major drawback of spoligotyping is that it has a lower discriminatory power than IS6110 typing. In particular, this method is not informative in are...

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Evaluation of the Epidemiologic Utility of Secondary Typing Methods for Differentiation ofMycobacterium tuberculosisIsolates

Cited by 72 publications

References 12 publications

Acquired Rifamycin Resistance with Twice-Weekly Treatment of HIV-related Tuberculosis

Acquired Rifamycin Resistance with Twice-Weekly Treatment of HIV-related Tuberculosis

Sensitivities and Specificities of Spoligotyping and Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing Methods for Studying Molecular Epidemiology of Tuberculosis

Use of Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing To Examine Genetic Diversity ofMycobacterium tuberculosisin Singapore

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