Sequence analysis of rpoB mutations in rifampin-resistant clinical Mycobacterium tuberculosis isolates from Turkey

Tuberculosis drug resistance isolates from pulmonary tuberculosis patients, Kassala State, Sudan

BACKGROUND

This study was conducted in Kassala Teaching Hospital, Kassala State, Sudan (January 2006-June 2008) to determine the rate of mycobacterium drug resistance to anti-tuberculous treatment and to explore the genotype of Mycobacterium tuberculosis resistant isolates using rpoB gene.

METHODS

53 isolates of mycobacterium isolated from pulmonary tuberculosis (PTB) patients from Kassala State were subjected to drug susceptibility testing (DST) to anti-tuberculous drugs; 10 M.tuberculosis complex (MTBC) resistant isolates were subjected to polymerase chain reaction (PCR), and commercially the amplified DNA was sequenced.

RESULTS

DST detected resistance in 23/53 (43.39%) isolates, among which rifampicin had a high number of resistant isolates (13/23), followed by streptomycin (11/23), and multi-drug resistance was detected in 5 isolates. DNA sequence analysis of 10 MTBC-resistant isolates detected variations within and outside the rifampicin resistant determining region (RRDR). Variation within RRDR was detected at positions 512 (AGC/ATC, Ser/Ile), and 528 (CGC/CTC, Arg/Leu). Outside the RRDR region variations were detected at positions 498 (GTG/GGG, Val/gly), 488 (ACA/ACC, Thr/Thr), which is a silent mutation. Insertions were observed at positions 484, 496 (GTG/GTGA, CGG/CAGG, respectively). Deletion was observed at position 487 (ATC/_TC).

DISCUSSION AND CONCLUSION

This study revealed that high resistance to rifampicin was associated with various point mutations in and out of the RRDR of the rpoB gene. Molecular methods are needed for early detection of TB disease and drug resistance.

Evaluation of the GenoType MTBDR assay for detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis complex isolates

Detection of drug resistance plays a critical role in tuberculosis treatment. The aim of this study was to evaluate the performance of GenoType Mycobacteria Drug Resistance (MTBDR) assay (Hain Lifescience, Germany) and to compare it with radiometric BACTEC 460 TB system (Becton Dickinson, USA) for the detection of rifampicin (RIF) and isoniazid (INH) resistance in 84 Mycobacterium tuberculosis complex (MTBC) isolates. RIF resistance was identified in 6 of 7 (85.7%) isolates and INH resistance was identified in 8 of 14 (57.1%) isolates by the GenoType MTBDR assay. Compared with BACTEC system, the sensitivity, specificity, positive predictive value and negative predictive values were 85.7%, 98.7%, 85.7% and 98.7% for RIF resistance; and 57.1%, 100%, 100% and 92.1% for INH resistance, respectively. GenoType MTBDR assay is reliable when tested specimen is resistant to the tested drugs. Although test was more successful in the detection of RIF resistance, it exhibited low sensitivity for the detection of INH resistance.

Restriction endonuclease analysis as a solution for determining rifampin resistance mutations by automated DNA sequencing in heteroresistant Mycobacterium tuberculosis strains

Rifampin resistance in Mycobacterium tuberculosis is mainly due to a small number of mutations in the rpoB gene coding for the beta subunit of RNA polymerase. Heteroresistance, which is defined as a mixture of wildtype and resistant subpopulations in the same culture, can influence the sensitivity of molecular tests for determining drug resistance by leading to false negative or indeterminable results. In our laboratory, we identified one heteroresistant strain during sequencing of the rpoB gene mutations, which are responsible for Rifampin resistance in M. tuberculosis. The sequence analysis of this isolate demonstrated the mixture of different strains, and the exact nature of the mutation could not be determined. In order to solve this problem, the possible mutation site was digested with Tsp509I restriction endonuclease, which made us separate the different strains. Sequencing of the separated mutated product revealed the mutation responsible for Rifampin resistance. From this result, we propose that, when the suggested mutation site creates and/or deletes a restriction endonuclease recognition site in heteroresistant populations, restriction endonuclease analysis can be used to ease the determination of resistance mutations by sequencing.