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Table 1 Details of clinical specimens, routine test results and amplification of genomic regions associated with TB drug resistance

From: Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis

Patient Specimen Residual quantity AFB smear Xpert MTB/RIF results Culture resultsa Drug resistance panel (10 loci)b
MTB load RIF Amplified loci Total number
1 BA 1.8 mL Neg Low ND All susceptible All amplified 10
2 Lung Bx 4 pieces (~ 1 mm3) Neg Very low Ind All susceptible gyrA, rpoB, rpsL & tlyAc 4
3 Sputum ~ 0.1 mL Neg Very low ND All susceptible All amplified 10
4 BA 4.05 mL Neg Very low ND No growth All amplifiedd 10
5 Sputum 0.35 mL N/A Very low ND N/A gyrA 1
6 Sputum 0.2 mL N/A Very low ND N/A rpsL 1
7 Bone marrow ~ 0.1 mL N/A Very low ND N/A Nil 0
8 BA 3 mL Neg Low ND All susceptible All amplified 10
9 BA 4.25 mL Neg Low ND All susceptible All amplified 10
10 LN FNA 1.9 mL Neg Very low ND SM-resistant inhAP & tlyAc 2
11 LN FNA 1.5 mL Neg Low ND No growth eisP, inhAP, gyrA, katG, rpoB, rpsL, rrs & tlyAc 8
12 BA 3 mL Neg Low ND No growth All amplified 10
13 BA 4.5 mL Neg Low ND All susceptible All amplified 10
14 Sputum 3 mL Neg Low ND SM-resistant All amplified 10
15 LN FNA 1.6 mL Neg Low ND All susceptible All amplified 10
16 LN FNA 1.5 mL Neg Low ND No growth All amplified 10
17 BA 1 mL Neg Very low ND All susceptible embB 1
18 Sputum ~ 0.1 mL Neg N/A INH- & SM-resistant embB 1
19 Lung Bx 0.2 mL Pos Low ND INH-resistant All amplified 10
20 Cervical LN Bx 1 piece (~ 1 mm3) Neg N/A All susceptible Nil 0
21 BA 1.5 mL Neg Low ND All susceptible All amplified 10
22 Cervical LN Bx 0.1 mL Neg Very low ND All susceptible eisP, inhAP, embB, gyrA, katG, rpoB, rpsL, rrs & tlyA 9
23 BA 1.3 mL Neg N/A All susceptible embB 1
      Mean TAT: 69.5 days All amplified 12 cases
  1. AFB acid-fast bacilli, BA bronchial aspirate, Bx biopsy, eisP eis promoter, FNA fine needle aspirate, Ind indeterminate, INH isoniazid, inhAP: inhA promoter, LN lymph node, MTB M. tuberculosis, N/A not available, ND not detected, Neg negative, Pos positive, RIF rifampicin resistance, SM streptomycin, TAT turnaround time
  2. aFour first-line antibiotics were tested by local reference laboratory, including ethambutol, isoniazid, rifampicin and streptomycin
  3. bThe 10 loci were eis promoter, embB, gyrA, inhA promoter, katG, pncA, rpoB, rpsL, rrs and tlyA genes
  4. cNegative by first PCR, positive by second PCR
  5. deis promoter and rrs: negative by first PCR, positive by second PCR
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