Abstract:

Objective To design and evaluate the value of next generation of microsequencing gene microarray on detecting the drug resistance of Mycobacterium tuberculosis (MTB).Methods The standard laboratory strains of the MTB H37Rv and 109 clinical isolates selected from the Beijing tuberculosis data and clinical sample data base were tested the phenotypic drug susceptibility using the absolute concentration method, and the drug resistance-related gene mutation of MTB (including inhA, katG, rpsL, gyrA, rrs, eis, rpoB and embB) using the gene sequencing method. The fluorescent labeled probes were set as the fundamental testing principle to design and prepare the microsequencing gene microarray, and then the 109 MTB clinical isolates were detected to analyze the detection performance of the microsequencing gene microarray.Results Based on the results of phenotypic drug susceptibility test and gene sequencing test, the mutation sites and forms of drug resistance-related genes (inhA, katG, rpsL, gyrA, rrs, eis, rpoB and embB) in 109 clinical isolates were identified. The microsequencing gene microarray contained 220 probes of the mutations that had been reported in the above genes, and 67 predominant probes were identified. The microsequencing drug-resistance gene microarray containing 67 probes was used to detect the mutations in 109 clinical isolates. The results showed that, except for the two probes in embB gene, the remaining 65 probes had more than 95% coincidence rate in the base mutation pattern detection, compared with the sequencing results, even 42 probes of them reached a coincidence rate of 100.00%. Taking sequencing results as the reference, the sensitivity of gene microarray detection method for embB gene, gyrA gene, inhA gene, katG gene, rpoB gene, rpsL gene, eis gene and rrs gene were 64.21% (61/95), 80.00% (8/10), 95.83% (23/24), 98.55% (68/69), 92.63% (88/95), 93.85% (61/65), 75.00% (3/4) and 94.44% (17/18), respectively. The specificity of the above genes were 92.86% (13/14), 100.00% (99/99), 97.65% (83/85), 87.50% (35/40), 85.71% (12/14), 63.64% (28/44), 100.00% (105/105) and 98.90% (90/91), respectively. After statistical analysis (Kappa test), the Kappa values of the above genes were 0.29, 0.88, 0.92, 0.88, 0.68, 0.60, 0.85 and 0.93, respectively.Conclusion The microsequencing gene microarray for drug-resistance detection with a set of 67 probes had been designed and developed. After preliminary verification, it showed a good performance on the detection of MTB drug-resistant gene mutation. However, for the embB gene, the detection probes needs to be further optimized, to better fulfill the clinical requirement.

Key words: Mycobacterium tuberculosis, Tuberculosis, multidrug-resistant, Microbial sensitivity tests, Genes, Mutation, Microchip analytical procedures, Technology assessment, biomedical