Detecting mutation pattern of drug-resistant Mycobacterium tuberculosis isolates in Himachal Pradesh using GenoType(®) MTBDRplus assay

Detection of mutations in the rpoB gene of rifampicin-resistant Mycobacterium tuberculosis strains inhibiting wild type probe hybridization in the MTBDR plus assay by DNA sequencing directly from clinical specimens

Background

The potential of genetic testing for rapid and accurate diagnosis of drug-resistant Mycobacterium tuberculosis strains is vital for efficient treatment and reduction in dissemination. MTBDR plus assays rapidly detect mutations related to drug resistance and wild type sequences allied with susceptibility. Although these methods are promising, the examination of molecular level performance is essential for improved assay result interpretation and continued diagnostic development. Therefore this study aimed to determine novel mutations that were inhibiting wild type probe hybridization in the Line probe assay by DNA sequencing. Using data collected from Line Probe assay (GenoType MTBDRplus assay) the contribution of absent wild type probe hybridization to the detection of rifampicin resistance was assessed via comparison to a reference standard method i.e. DNA sequencing.

Results

Sequence analysis of the rpoB gene of 47 MTB resistant strains from clinical specimens showed that 37 had a single mutation, 9 had double mutations and one had triple mutations in the ropB gene.

Conclusions

The absence of wild type probe hybridization without mutation probe hybridization was mainly the result of the failure of mutation probe hybridization and the result of the novel or rare mutations. Additional probes are necessary to be included in the Line probe assay to improve the detection of rifampicin-resistant Mycobacterium tuberculosis strains.

Whole Genome Sequencing of Mycobacterium tuberculosis Clinical Isolates From India Reveals Genetic Heterogeneity and Region-Specific Variations That Might Affect Drug Susceptibility

Whole genome sequencing (WGS) of Mycobacterium tuberculosis has been constructive in understanding its evolution, genetic diversity and the mechanisms involved in drug resistance. A large number of sequencing efforts from across the globe have revealed genetic diversity among clinical isolates and the genetic determinants for their resistance to anti-tubercular drugs. Considering the high TB burden in India, the availability of WGS studies is limited. Here we present, WGS results of 200 clinical isolates of M. tuberculosis from North India which are categorized as sensitive to first-line drugs, mono-resistant, multi-drug resistant and pre-extensively drug resistant isolates. WGS revealed that 20% of the isolates were co-infected with M. tuberculosis and non-tuberculous mycobacteria species. We identified 12,802 novel genetic variations in M. tuberculosis isolates including 343 novel SNVs in 38 genes which are known to be associated with drug resistance and are not currently used in the diagnostic kits for detection of drug resistant TB. We also identified M. tuberculosis lineage 3 to be predominant in the northern region of India. Additionally, several novel SNVs, which may potentially confer drug resistance were found to be enriched in the drug resistant isolates sampled. This study highlights the significance of employing WGS in diagnosis and for monitoring further development of MDR-TB strains.

RDRioMycobacterium tuberculosis lineage in the Brazil/Paraguay/Argentina triple border

The high tuberculosis (TB) incidence rates, the closeness of the cities and the high migration flux on the Brazil/Paraguay/Argentina border deserves an in-depth study, using Mycobacterial Interspersed Repetitive Unit (MIRU) and Spoligotyping genetic markers to explore the impact of the Mycobacterium tuberculosis RD^Rio lineage on disease transmission and resistance to anti-TB drugs in this setting. Although without the totality of M. tuberculosis isolates causing TB in this studied setting, a number of 97 isolates obtained from sputa samples culture of patients with confirmed TB, from 2013 to 2015, were submitted to 24 loci MIRU, Spoligotyping, detection of RD^Rio lineage and detection of mutation related to isoniazid and rifampicin resistance by MTBDRplus/DNA STRIP. In this sample, it was observed high clonal variability of circulating M. tuberculosis isolates causing TB in Brazilian cities bordering Paraguay and Argentina. The percentage of RD^Rio lineage causing TB in this setting was 15.46%, and lower than the detected in different areas of Brazil. According to 24 loci MIRU, the major MIRU International Type (MIT) related with RD^Rio lineage were MIT 26, MIT 738, MIT 601 with four, two and one isolates, respectively. Eight isolates with RD^Rio marker were classified as orphans. The mainly Spoligofamily related with RD^Rio lineage was LAM1 and LAM9 and no relationship between RD^Rio lineage and resistance in M. tuberculosis isolates circulating in this setting could be established. This work is pioneer in studying the dynamics of RD^Rio lineage transmission on the Brazil/Paraguay/Argentina border and deserves further studies to analyze the real contribution of the RD^Rio lineage in outbreaks and the risk of significant development of MDR-TB in the setting studied.

Evaluation of genotype MTBDRplus line probe assay in detection of rifampicin and isoniazid resistance in comparison to solid culture drug susceptibility testing in a tertiary care centre of western Uttar Pradesh

BACKGROUND

Isoniazid (INH) and rifampicin (Rif) are the key first-line antituberculosis drugs, and resistance to these drugs i.e., multi-drug-resistant tuberculosis (MDR-TB), is likely to result in treatment failure and poor clinical outcomes. India has the highest burden of TB and MDR-TB in the world, disproportionately high even for India's population. The GenoType® MTBDRplus molecular method allows rapid detection of Rif and INH resistance.

AIM

The present study was done to compare the performance of line probe assay test (GenoType® MTBDRplus) with solid culture method for an early diagnosis of MDR-TB.

METHODS

Totally 1503 sputum samples of MDR-TB suspects were subjected to fluorescent microscopy. Decontamination was done by N-acetyl-L-cysteine and sodium hydroxide method. Fluorescent microscopy-positive samples were subjected to GenoType® MTBDRplus (HAIN Lifescience) assay. Sixty-two random samples were compared with phenotypic drug susceptibility testing (DST) (1% proportion method) using solid culture method by Lowenstein-Jensen media.

RESULTS

The sensitivity, specificity, positive predictive value and negative predictive value for detection of resistance to Rif were 94.74%, 95.35%, 90% and 97.62% and to INH were 92.00%, 91.89%, 88.46% and 94.44%, respectively, in comparison with the phenotypic DST.

CONCLUSION

GenoType® MTBDRplus has good sensitivity and specificity in detecting MDR-TB cases with a significantly lesser turnaround time as compared to conventional DST method and simultaneous detection of Rif and INH resistance. This technique saves several weeks of time required for culture and DST.