Use of DNA microarray chips for the rapid detection of Mycobacterium tuberculosis resistance to rifampicin and isoniazid

Abstract

The objective of the present study was to evaluate the potential development of DNA microarray chips to detect rifampicin (RFP) and isoniazid (INH) resistance in Mycobacterium tuberculosis (MTB), using samples from clinical tuberculosis (TB) patients in Soochow City, China. The sputum samples of 42 patients with TB in the Affiliated Hospital of Infectious Diseases of Soochow University (Soochow, China) were collected. The conventional Lowenstein-Jensen culture medium (Gold Standard) was used to assess drug sensitivity using the absolute concentration method. GeeDom MTB drug detection kits were also used to create a DNA microarray chip and examine the RFP-resistance associated gene mutation points rpoB-RRDR 511, 513, 516, 526, 531 and 533, and the INH-resistance associated gene mutation points katG315 and inhA-15 of the sputum samples. Compared with the results from the absolute concentration method, the susceptibility and specificity of RFP sensitivity detected by the DNA microarray chip were 92.8 and 93.8%, respectively. The susceptibility and specificity of INH sensitivity detected were 66.7 and 81%, respectively. The rpoB-RRDR 526, 531 mutations were the primary causes of MTB RFP resistance and the katG315 mutation was the primary cause of INH resistance. The detection of rpoB and katG gene mutation points by a DNA microarray chip may be used as a rapid, accurate and bulk clinical detection method for RFP and INH resistance in MTB. This is very valuable for the control of TB epidemics.

GeneChip analysis of resistant Mycobacterium tuberculosis with previously treated tuberculosis in Changchun

“…The overall sensitivity, specificity, agreement rate, PPV, NPV, and kappa values were 83.1, 98.7, 93.9, 96.6, 92.9% and 0.85 for detecting M. tuberculosis RFP resistance, respectively; 79.9, 99.6, 93.1, 98.8, 91.1% and 0.84 for detecting M. tuberculosis INH resistance, respectively; and 74.1, 99.8, 93.6, 99.2, 92.4% and 0.81 for detecting MDR-TB, respectively. These results were consistent with those reported by Guo, Y. et al, Pang, Y. et al, Tang, P et al, and Zhu, L. et al [ 10 , 19 – 21 ]. However, compared with the MeltPro TB assay method in detection of TB drug resistance [ 22 , 23 ].…”

“…Table 4 shows that INH mutations primarily occur at katG 315 and in the inhA promoter at − 15. For katG 315, AGC to ACC was the main mutation of this residue in our study, with 100% of cases showing the katG Ser315Thr AGC to ACC mutation, and we found no Ser315Asn AGC to AAC mutations, which was consistent with previous reports [ 21 , 33 ]. However, in our study, inhA − 15 locus mutations accounted for 46.4% of all INH resistance mutations, which was inconsistent with previous reports [ 34 – 36 ].…”

Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization

“…The data analysis is robust and can be automated, making the methodology simpler compared to next-generation sequencing approaches. Other groups have utilized microarray-based approaches, but are limited in their coverage of clinically relevant SNPs and use fewer probes per SNP [39, 40]. A large number of probes are not always necessary for each SNP, as this depends on the dynamic range in each case.…”

Evolution of tuberculosis diagnostics: From molecular strategies to nanodiagnostics

“…DNA microarray helps in the accurate and rapid identification of 17 mycobacterial species simultaneously by designing an oligonucleotide sequence complementary to the 16sRNA (most common). Recently few more oligonucleotide probes have been designed that target the 13 most common mutation sites from the rpoB gene, katG gene as well as mutations in the promoter region of the inhA gene [ 93 ]. This array can identify the exact nucleic acid substitution unlike conventional assays.…”