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

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

Patient	Specimen	Residual quantity	AFB smear	Xpert MTB/RIF results		Culture results^a	Drug resistance panel (10 loci)^b
Patient	Specimen	Residual quantity	AFB smear	MTB load	RIF	Culture results^a	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 & tlyA^c	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 amplified^d	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	inhA^P & tlyA^c	2
11	LN FNA	1.5 mL	Neg	Low	ND	No growth	eis^P, inhA^P, gyrA, katG, rpoB, rpsL, rrs & tlyA^c	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	eis^P, inhA^P, 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

AFB acid-fast bacilli, BA bronchial aspirate, Bx biopsy, eis^P eis promoter, FNA fine needle aspirate, Ind indeterminate, INH isoniazid, inhA^P: 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
^aFour first-line antibiotics were tested by local reference laboratory, including ethambutol, isoniazid, rifampicin and streptomycin
^bThe 10 loci were eis promoter, embB, gyrA, inhA promoter, katG, pncA, rpoB, rpsL, rrs and tlyA genes
^cNegative by first PCR, positive by second PCR
^deis promoter and rrs: negative by first PCR, positive by second PCR

ISSN: 1756-0500