Abstract:

Objective To analyze the drug resistance spectrum of the clinical multidrug-resistant Mycobacterium tuberculosis (MDR-MTB) isolates in Shenzhen using whole-genome sequencing data, to provide scientific basis for the treatment and prevention of MDR-TB patients. Methods A total of 420 MDR-MTB strains were successfully recovered from all strains stored in the tuberculosis laboratory of Shenzhen Center for Chronic Disease Control from 2013 to 2017. Whole-genome sequencing were conducted for the genomic DNA extracted from these strains. The sequencing data were analyzed using an in-house pipeline. Drug-resistance to isoniazid, rifampicin, streptomycin, ethambutol, fluoroquinolones, pyrazinamide, ethionamide, p-aminosalicylic acid, kanamycin, amikacin, capreomycin, linezolid, bedaquiline, and clofazimine were determined based on MTB drug resistance gene database and drug resistance determining and harmless mutations database. Simultaneously, a string diagram of bacterial resistance and a heat map were used to visualize drug resistance spectrum of all strains and pre-XDR-MTB/XDR-MTB strains, respectively. Results Among the 420 clinical MDR-MTB strains, 23 (5.48%) were XDR-MTB strains and 97 (23.10%) were pre-XDR-MTB strains; except for isoniazid and rifampicin resistance, the frequency of streptomycin resistance was the highest with 67.86% (285/420), followed by ethambutol (66.19%, 278/420), fluoroquinolones (28.57%, 120/420), pyrazinamide (28.33%, 119/420), ethionamide (13.33%, 56/420), p-aminosalicylic acid (7.38%, 31/420), kanamycin (6.67%, 28/420), amikacin (5.48%, 23/420), capreomycin (5.48%, 23/420), and linezolid (0.24%, 1/420). No strain was resistant to bedaquiline or clofazimine. A total of 212 drug-resistance mutation types were revealed using the whole genome sequencing data, and the most common mutations were katG-315-S/T (81.43%, 342/420), rpoB-450-S/L (58.57%, 246/420), rpsL-43-K/R (65.96%, 188/285), and embB-306-M/V (32.37%, 90/278). Conclusion It was found that, among clinical MDR-MTB isolates in Shenzhen, the proportion of pre-XDR-MTB and the resistance rates to the first-line anti-tuberculosis drugs and fluoroquinolones were high, indicating that the use of these drugs in the clinic should be combined with the results of drug sensitivity tests; while the drug resistance rates to the second-line anti-tuberculosis drugs such as ethionamide, clofazimine, and aminosalicylic acid were low, suggesting that these drugs can be used in the treatment plan for MDR-TB patients.

Key words: Tuberculosis,multidrug-resistant, Genome-wide association study, High-throughput nucleotide sequencing, Genome,bacterial, Shenzhen