Comprehensive multicenter evaluation of a new line probe assay kit for identification of Mycobacterium species and detection of drug-resistant Mycobacterium tuberculosis

Abstract

We evaluated a new line probe assay (LiPA) kit to identify Mycobacterium species and to detect mutations related to drug resistance in Mycobacterium tuberculosis. A total of 554 clinical isolates of Mycobacterium tuberculosis (n = 316), Mycobacterium avium (n = 71), Mycobacterium intracellulare (n = 51), Mycobacterium kansasii (n = 54), and other Mycobacterium species (n = 62) were tested with the LiPA kit in six hospitals. The LiPA kit was also used to directly test 163 sputum specimens. The results of LiPA identification of Mycobacterium species in clinical isolates were almost identical to those of conventional methods. Compared with standard drug susceptibility testing results for the clinical isolates, LiPA showed a sensitivity and specificity of 98.9% and 97.3%, respectively, for detecting rifampin (RIF)-resistant clinical isolates; 90.6% and 100%, respectively, for isoniazid (INH) resistance; 89.7% and 96.0%, respectively, for pyrazinamide (PZA) resistance; and 93.0% and 100%, respectively, for levofloxacin (LVX) resistance. The LiPA kit could detect target species directly in sputum specimens, with a sensitivity of 85.6%. Its sensitivity and specificity for detecting RIF-, PZA-, and LVX-resistant isolates in the sputum specimens were both 100%, and those for detecting INH-resistant isolates were 75.0% and 92.9%, respectively. The kit was able to identify mycobacterial bacilli at the species level, as well as drug-resistant phenotypes, with a high sensitivity and specificity.

Fig 1

Distribution of LiPA results for 554 clinical isolates. ^a, number of clinical isolates. ^b, Mycobacterium species identified by conventional methods. ^c, M. kansasii subtype III. ^d, drug susceptibility testing and assays for pyrazinamidase activity were performed at each hospital (see the supplemental material). Of 316 M. tuberculosis isolates, 314 were subjected to RIF and INH susceptibility testing, 308 to PZA susceptibility testing, and 203 to LVX susceptibility testing. ^e, some isolates showed different results between DST and LiPA. DNA sequences of each target gene were determined for these discrepant isolates (see the footnote in Table S4 in the supplemental material).

Fig 2

Distribution of LiPA results obtained with NTM/MDR-TB strips for the detection of target species in 163 sputum samples. ^a, number of clinical samples. ^b, one of these isolates was Mycobacterium fortuitum. ^c, one of these isolates was Mycobacterium abscessus.

Fig 3

Distribution of LiPA results obtained with four strips for detection of a mutation(s) associated with drug resistance in 163 sputum samples. ^a, number of clinical samples. RIF, RIF susceptibility with NTM/MDR-TB strips; INH(1), INH susceptibility with INH strips; INH(2), INH susceptibility with NTM/MDR-TB strips; PZA, PZA susceptibility with PZA strips; FQ, LVX susceptibility with FQ strips.