Supporting data for “Clinical Application of Target Amplicon Sequencing for Rapid Diagnosis of Drug Resistant Mycobacterium tuberculosis in Respiratory Specimens”

A total of 337 direct respiratory samples were collected during August 2020 to March 2021. All samples were tested with IS6110 real-time PCR and 76 samples tested with Ct values ranging 4.93 to 28.44 were selected for target amplicon sequencing, which covers 18 gene targets conferring anti-TB drug resistance. Target amplicon sequencing was performed using Illumina MiSeq on sample DNA purified and concentrated with our in-house validated protocol. Among the 76 selected samples, 69 of which were successfully sequenced and passed our defined acceptance criteria of 500X sequencing depth. Drug-resistance associated mutation(s) were detected in 17 samples with mutation frequency >95% and 1 sample with low mutation frequency at 37.04%, while no mutation was detected for the remaining 53 samples. Among the 17 samples detected with drug-resistance associated mutation(s) at frequency >95%, 10 of which were mono-drug resistant TB while the other 6 were multi-drug resistant TB. There were also 3 multi-drug resistant TB samples carrying mutations associated to fluoroquinolones (FQs) and considered as pre-XDR-TB. Concordant result was obtained in 16/17 (94.1%) when comparing the major variants at mutation frequency >95% with pDST results. One phenotypic pan-susceptible case was detected to harbour rpoB L533P mutation. The case with low variant frequency detected was phenotypic pan-susceptible. It could be well distinguished from the phenotypic resistant cases by variant frequency and hence the minor variants detected would not affect the overall result interpretation for target amplicon sequencing towards TB drug-resistance detection.