Although BDQ has been proven to be highly effective in the treatment of MDR-TB [16], inadequate or incomplete use may lead to the emergence of resistant strains [17]. Unfortunately, few studies have explored the resistance status of MDR-TB against BDQ in Chongqing. Therefore, we performed drug susceptibility test and conducted sequence analyses of BDQ resistance genes for 205 MDR isolates. The resistance rate of MDR-TB to BDQ was 4.4%, lower than that of commonly used first- and second-line drugs, indicating that BDQ has strong activity against MDR isolates in Chongqing. Though the resistance rate lower than that reported in Shanxi (5.56%) [15] and in national survey in China (7.16%) [18], higher than reported in a retrospective cohort study in China (2.2%) [19] and national drug resistance surveillance in 2015 (1%) [20]. These inconsistent results may be attributed to the difference in the epidemic strains, medication background and the breakpoints used across studies. Given the cross resistance between BDQ and clofazimine, prior exposure to clofazimine could reduce the susceptibility to BDQ [21]. And the period from the start of treatment can also affect the BDQ MIC [22]. To our knowledge, all isolates were without documented prior use of BDQ, and 4.4% MDR-TB strains resistant to BDQ suggesting that though BDQ showed excellent activity against MDR-TB, the emergence of BDQ resistant isolates may lead to the rapid loss of this valuable new drug. Therefore, it is necessary to dynamically monitor the BDQ resistance to optimize BDQ administration regimen, further to avoid the occurrence of acquired resistance, and maximize the effectiveness of new drugs, even in patients who have not been exposed to BDQ.
The resistance rate of BDQ in isolates resistant to any first and second line drug (8.9%) was higher than that in isolates resistant to first line drugs (1.2%) and second line drugs 7.7%), indicating that with the increase of drug resistance types and the complexity of resistant background, the BDQ resistance rate also increased. In addition, we found that the BDQ resistance rate in retreated patients (66.7%) was higher than that of new patients (33.3%), whether this attributed to the past medical history needs to be further studied. Of the 9 BDQ resistant isolates, the proportion of OFX resistant isolates(8/9)was significantly higher than that of OFX sensitive isolate (1/9), and the resistance rate of BDQ in OFX resistant isolates (9.3%) was higher than that in SM resistant isolates (4.7%), EMB resistant isolates (6.5%), KM resistant isolates (3.3%), suggesting isolates resistant to OFX were more likely to develop BDQ resistance, which was a risk factor of BDQ resistance.
Since the development and approval of BDQ for clinical use, the number of BDQ resistant isolates associated with inadequate or incomplete treatment is steadily growing [22].To investigate the potential mechanisms and genetic background of BDQ resistant isolates, we performed whole-genome sequencing. Though the fact that mutations in the atpE, pepQ, and Rv1979c gene confer bedaquiline resistance [3, 7, 8], no mutations were observed in this study. The 66.7% (6/9) BDQ resistant isolates had variants in the Rv0678 gene, which was the main mechanism of primary BDQ resistance in Chongqing, and all belonged to low level resistance (0.5μg/ml~1μg/ml). The mutation loci in Rv0678 gene were scattered and the mutation types were complicated. Of the 6 isolates carrying Rv0678 mutations included two non-synonymous Single Nucleotide Polymorphisms SNPs and deletions, the most frequently variations were A152G (50%), which has reported to be associated with BDQ resistance in MDR isolates [23]. Besides, the A274 insertion identified in the present study was found in clinical BDQ-resistant isolates [6]. However, there were three BDQ resistance isolates (33.3%, 3/9) without mutations, suggesting additional mechanisms must be involved in the resistance, such as other potential target and non-target resistance mechanisms, such as changes in cell wall permeability caused by transcriptional and protein levels and drug efflux pump structure. Two BDQ susceptible isolates with mutations in Rv0678 gene were in the critical concentration of BDQ resistance and a gradient below the critical concentration, which may be attributed to operational factors, such as result interpretation, bacteria activity, drug concentration or other inaccurate factors. Two pepQ mutant strains and 11 Rv1979 mutant strains were all sensitive to BDQ, which were not related to drug resistance. Moreover, the other two (Rv0678 T56C and GA492 insertion) were novel mutation types, which were not reported previously. Further analysis in expression levels of MmpS5 and MmpL5 efflux pump will contribute to illustrate the role of these novel mutations in BDQ resistance.
The Beijing genotype was the predominant isolates in Chongqing with 47.8% modern Beijing genotype and 35.1% ancient Beijing genotype. However, the proportion of ancient Beijing strains (88.9%, 8/9) was significantly higher than that of modern Beijing strains (11.1%, 1/9) in BDQ resistant isolates, and 75% (6/8) BDQ resistant isolates with Rv0678 mutation were ancient Beijing type, indicating ancient Beijing genotype was more prone to BDQ resistance and Rv0678 mutation.
In this study, WGS for BDQ drug resistance was consistent with phenotypic drug susceptibility test. However, the relatively dispersed mutation loci of BDQ resistance associated genes may result in the presence of "false-susceptible" detected by PCR-sequencing of hot spots of current resistance-associated genes. Therefore, WGS can quickly and accurately determine the mutation loci, and has preferable specificity (99%) in predicting BDQ resistance. But for the non-target resistance mechanism, the phenotypic drug sensitive test was superior to WGS. So, the phenotypic drug sensitive test together with WGS was helpful to early diagnosis and individualized treatment of drug-resistant tuberculosis, which has excellent application value in the rapid detection of BDQ resistance.