Evaluation of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping as performed in laboratories in Canada, France, and the United States

Compilation of 10 Years of MIRU-VNTR Data: Canadian National Tuberculosis Laboratory's Experience

Tuberculosis is a significant cause of morbidity worldwide and is a priority at the provincial and federal levels in Canada. It is known that tuberculosis transmission networks are complex and span many years as well as different jurisdictions and countries. MIRU-VNTR is a universal tuberculosis genotyping method that utilizes a 24-loci pattern and it has shown promise in identifying inter and intrajurisdictional clusters within Canada. MIRU-VNTR data collected over 10 years from the National Reference Centre for Mycobacteriology (NRCM) were analyzed in this study. Some clusters were unique to a single province/territory, while others spanned multiple provinces and/or territories in Canada. The use of a universal laboratory test can enhance contact tracing, provide geographical information on circulating genotypes, and hence, aid in tuberculosis investigation by public health. The housing of all data on one platform, technical ease of the method, easy exchange of data between jurisdictions, and strong collaboration with laboratories and surveillance units at the provincial and federal levels have the potential to identify possible outbreaks in real time.

Extensive Homoplasy but No Evidence of Convergent Evolution of Repeat Numbers at MIRU Loci in Modern Mycobacterium tuberculosis Lineages

More human deaths have been attributable to Mycobacterium tuberculosis than any other pathogen, and the epidemic is sustained by ongoing transmission. Various typing schemes have been developed to identify strain-specific differences and track transmission dynamics in affected communities, with recent introduction of whole genome sequencing providing the most accurate assessment. Mycobacterial interspersed repetitive unit (MIRU) typing is a family of variable number tandem repeat schemes that have been widely used to study the molecular epidemiology of M. tuberculosis. MIRU typing was used in most well-resourced settings to perform routine molecular epidemiology. Instances of MIRU homoplasy have been observed in comparison with sequence-based phylogenies, limiting its discriminatory value. A fundamental question is whether the observed homoplasy arises purely through stochastic processes, or whether there is evidence of natural selection. We compared repeat numbers at 24 MIRU loci with a whole genome sequence-based phylogeny of 245 isolates representing three modern M. tuberculosis lineages. This analysis demonstrated extensive homoplasy of repeat numbers, but did not detect any evidence of natural selection of repeat numbers, at least since the ancestral branching of the three modern lineages of M. tuberculosis. In addition, we observed good sensitivity but poor specificity and positive predictive values of MIRU-24 to detect clusters of recent transmission, as defined by whole-genome single nucleotide polymorphism analysis. These findings provide mechanistic insight, and support a transition away from VNTR-based typing toward sequence-based typing schemes for both research and public health purposes.

The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex

Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.

Drug-resistant tuberculosis can be predicted by Mycobacterial interspersed repetitive unit locus

It is unknown whether MIRU-VNTR (Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeat) is associated with drug resistance of Mycobacterium tuberculosis. The purpose of this study was to explore the ability of 24 MIRU loci to predict the drug resistance of Isoniazid (INH), Rifampicin (RFP), Streptomycin (SM), Ethambutol (EMB) and Pyrazinamide (PZA). We collected the drug resistance and MIRU loci information of 109 strains of M. tuberculosis from an open database. The results of multivariate logistic regression showed that the VNTR polymorphism of MTUB04 was related to INH resistance [odds ratio (OR) = 2.82, P = 0.00], RFP resistance (OR = 1.91, P = 0.02), SM resistance (OR = 1.98, P = 0.01) and EMB resistance (OR = 1.95, P = 0.03). MIRU40 was associated with INH resistance (OR = 2.22, P = 0.00). MTUB21 was connected with INH resistance (OR = 1.63, P = 0.02) and SM resistance (OR = 1.69, P = 0.01). MIRU26 was correlated with SM resistance (OR = 1.52, P = 0.04). MIRU39 was associated with EMB resistance (OR = 4.07, P = 0.02). The prediction power of MIRU loci were 0.84, 0.70, 0.85, and 0.74 respectively for INH (predicted by MTUB04, MIRU20, and MTUB21), RFP (predicted by MTUB04), SM (predicted by MTUB21 and MIRU26) and EMB (MTUB04 and MIRU39) through ROC analysis. Our results showed that MIRU loci were related to anti-tuberculosis drug and could predict the drug resistance of tuberculosis.

Predictive Power of ETRE Polymorphism and Katg463 Mutation to INH-Resistance of M.tuberculosis

BACKGROUND

The MIRU-VNTR polymorphism and katG463 mutation are used to genotype the mycobacterium tuberculosis, but the correlation between them and INH-resistance were unknown. This study was aimed to explore whether ETRE polymorphism and katG463 mutation could predict the INH-resistance, and the relationship between ETRE polymorphism and katG463 mutation.

METHODS

The ETRE, katG463 mutation and drug resistance information of 109 M. tuberculosis strains were collected from online public database. We constructed the predictive diagnostic tool of ETRE polymorphism and katG463 mutation. Chi-square test was used to analyze the relationship between ETRE polymorphism, katG463 mutation and INH-resistance. ROC curve analysis and Z-test were used to evaluate the predictive ability of ETRE and katG463. The relationship between ETRE polymorphism and katG463 mutation was analyzed with Spearman correlation analysis.

RESULTS

The mutation rate of katG463 was 27.50%, and the h value of ETRE polymorphism was 0.67. KatG463 mutation was associated with INH resistance (OR=3.72). The INH drug resistance rate in VNTR≧5 group was 3.43 times higher than that in VNTR≦3 group (χ(2) =24.77, P<0.01), and there was no significant difference of INH resistance between the VNTR=4 group and VNTR≦3 group. The areas under the ROC curve of two loci prediction diagnostic tools were 0.64 and 0.70 respectively. The katG463 mutation was significantly related to the ETRE polymorphism (r=0.79, P<0.01).

CONCLUSION

Both katG463 mutation and the ETRE polymorphism can predict the INH-resistance of tuberculosis. The katG463 mutation was associated with ETRE VNTR polymorphism.

A four-year nationwide molecular epidemiological study in Estonia: risk factors for tuberculosis transmission

SETTING

Estonia has a high proportion of multidrug-resistant tuberculosis (MDR-TB). It is important to link molecular and epidemiological data to understand TB transmission patterns.

OBJECTIVE

To use 24-locus variable numbers of tandem repeat (VNTR) typing and national TB registry data in Estonia from 2009 to 2012 to identify the distribution of drug resistance patterns, Mycobacterium tuberculosis isolate clustering as an index for recent transmission, socio-demographic and clinical characteristics associated with recent transmission, and the distribution of transmission between index and secondary cases.

DESIGN

A retrospective nationwide cross-sectional study.

RESULTS

Of 912 cases with isolate and patient information, 39.1% of isolates were from the Beijing lineage. Cluster analysis identified 87 clusters encompassing 69.1% of isolates. The largest cluster comprised 178 isolates from the Beijing lineage, of which 92.1% were MDR- or extensively drug-resistant TB (XDR-TB). Factors associated with recent transmission were polyresistant TB, MDR- and XDR-TB, human immunodeficiency virus positivity, Russian ethnicity, non-permanent living situation, alcohol abuse and detention. XDR-TB cases had the highest risk of recent transmission. The majority of transmission cases involved individuals aged 30-39 years.

CONCLUSION

Recent TB transmission in Estonia is high and is particularly associated with MDR- and XDR-TB and the Beijing lineage.

Transmission of multidrug-resistant tuberculosis in the USA: a cross-sectional study

BACKGROUND

Multidrug-resistant (MDR) tuberculosis is a potential threat to tuberculosis elimination, but the extent of MDR tuberculosis disease in the USA that is attributable to transmission within the country is unknown. We assessed transmission of MDR tuberculosis and potential contributing factors in the USA.

METHODS

In a cross-sectional study, clinical, demographic, epidemiological, and Mycobacterium tuberculosis genotype data were obtained during routine surveillance of all verified cases of MDR tuberculosis reported from eight states in the USA (California from Jan 1, 2007, to Dec 31, 2009; Texas from Jan 1, 2007, to March 31, 2009; and the states of Colorado, Maryland, Massachusetts, New York, Tennessee, and Washington from Jan 1, 2007 to Dec 31, 2008). In-depth interviews and health-record abstraction were done for all who consented to ascertain potential interpersonal connections.

FINDINGS

168 cases of MDR tuberculosis were reported in the eight states during our study period. 92 individuals (55%) consented to in-depth interview. 20 (22%) of these individuals developed MDR tuberculosis as a result of transmission in the USA; a source case was identified for eight of them (9%). 20 individuals (22%) had imported active tuberculosis (ie, culture-confirmed disease within 3 months of entry into the USA). 38 (41%) were deemed to have reactivation of disease, of whom 14 (15%) had a known previous episode of tuberculosis outside the USA. Five individuals (5%) had documented treatment of a previous episode in the USA, and so were deemed to have relapsed. For nine cases (10%), insufficient evidence was available to definitively classify reason for presentation.

INTERPRETATION

About a fifth of cases of MDR tuberculosis in the USA can be linked to transmission within the country. Many individuals acquire MDR tuberculosis before entry into the USA. MDR tuberculosis needs to be diagnosed rapidly to reduce potential infectious periods, and clinicians should consider latent tuberculosis infection treatment-tailored to the results of drug susceptibility testing of the putative source case-for exposed individuals.

FUNDING

Centers for Disease Control and Prevention.