Abstract
Infection of Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) challenges effective pulmonary infectious disease control. Current phenotypic and molecular assays could not comprehensively and accurately diagnose MTB, NTM, and drug resistance. Next-generation sequencing allows an “all-in-one” approach providing results on expected drug susceptibility testing (DST) and the genotype of NTM strains. In this study, targeted capture sequencing was used to analyze the genetic backgrounds of 4 MTB strains and 32 NTM pathogenic strains in 30 clinical samples, including 14 sputum specimens and 16 bronchoalveolar lavage fluid samples. Through comparing with other TB diagnostic tests, we proved that targeted capture sequencing could be used as a highly sensitive (91.3%) and accurate (83.3%) method to diagnose TB, as well as MGIT 960. Also, we identified 7 NTM strains in 11 patients; among them, seven patients were MTB/NTM co-affected, which indicated that it was a meaningful tool for the diagnosis and treatment of NTM infection diseases in clinic. However, based on a drug-resistant mutation library (1,325 drug resistance loci), only 9 drug resistance strains and 22 drug resistance loci were discovered, having considerable discordance with the drug-resistant results of MGIT 960. Our finding indicated that targeted capture sequencing approach was applicable for the comprehensive and accurate diagnosis of MTB and NTM. However, from data presented here, the DST results identified by next-generation sequencing (NGS) showed a relatively low consistency with MGIT 960, especially in sputum samples. Further work should be done to explore the reasons for low drug-resistance detection rate of NGS.
Highlights
Tuberculosis, a largely infectious disease caused by Mycobacterium tuberculosis (MTB) infection, remains a major global health threat with an estimated 10.4 million new cases and 1.8 million deaths in 2015 alone (World Health Organization, 2016)
Among the 30 patients, targeted capture sequencing results showed 25 (83.3%) patients were positive for MTB and nontuberculous mycobacteria (NTM)
15 (50%) cases were diagnosed to be affected by NTM
Summary
Tuberculosis, a largely infectious disease caused by Mycobacterium tuberculosis (MTB) infection, remains a major global health threat with an estimated 10.4 million new cases and 1.8 million deaths in 2015 alone (World Health Organization, 2016). It is proved that various types of NTM can affect humans and may cause either symptomatic or asymptomatic infection (Baghaei et al, 2012). Resistance has been reported to all drugs that are used to treat tuberculosis and NTM diseases, especially those that are multidrug resistant (MDR) and extensively drug resistant (XDR) (Xu et al, 2014; Dheda et al, 2017). According to WHO’s report, the treatment success rates was 52% for MDR-TB and 28% for XDR-TB (World Health Organization, 2016)
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