Characterization of Fluoroquinolone-Resistant and Multidrug-Resistant Mycobacterium tuberculosis Isolates Using Whole-Genome Sequencing in Tianjin, China

Figures & data

Table 1 Drug Resistance Phenotypic Pattern of 21 Fluoroquinolone-Resistant and Multidrug- Resistant Mycobacterium tuberculosis Strains

Strain Number	Collection Time Point	RFP	INH	Fluoroquinolone		STR	EMB	KAN	AMI	CAP	PTO	PAS	PZA
				OFX	MXF
5	Aug. 2017	R	R	R	R	R	R	S	S	S	S	S	R
11	Sept. 2017	R	R	R	R	R	S	S	S	S	S	S	S
15	Sept. 2017	R	R	R	S	R	S	S	S	S	S	S	R
18	Oct. 2017	R	R	R	R	R	S	S	S	S	S	S	R
20	Oct. 2017	R	R	R	R	R	R	R	R	S	S	S	R
25	Nov. 2017	R	R	R	R	R	R	S	S	S	S	S	R
39	Jan. 2018	R	R	R	S	R	R	S	S	S	S	S	R
40	Jan. 2018	R	R	R	R	R	R	S	S	S	S	S	R
56	Mar. 2018	R	R	R	R	R	S	S	S	S	S	S	R
62	May 2018	R	R	R	R	R	R	S	S	S	S	R	R
63	May 2018	R	R	R	S	R	R	S	S	S	S	S	R
85	Aug. 2018	R	R	R	R	R	R	S	S	S	S	S	R
86	Aug. 2018	R	R	R	S	R	R	R	R	R	S	S	R
93	Sept. 2018	R	R	R	R	R	R	S	S	S	S	S	R
95	Oct. 2018	R	R	R	R	R	S	S	S	S	S	S	S
97	Oct. 2018	R	R	R	R	R	R	S	S	S	S	S	R
99	Oct. 2018	R	R	R	S	R	R	S	S	S	S	S	S
110	Jan. 2019	R	R	R	S	R	S	S	S	S	R	S	R
122	Jun. 2019	R	R	R	S	R	S	S	S	S	S	S	R
130	Aug. 2019	R	R	R	R	R	R	S	S	S	S	S	R
139	Jan. 2020	R	R	R	R	R	R	S	S	S	S	S	R

Abbreviations: RFP, rifampicin; INH, isoniazid; OFX, ofloxacin; MXF, moxifloxacin; STR, streptomycin; EMB, ethambutol; KAN, kanamycin; AMI, amikacin; CAP, capreomycin; PTO, protionamide; PAS, para-aminosalicylic acid; PZA, pyrazinamide; R, resistant; S, susceptible.

Table 2 Lineages of 21 Fluoroquinolone-Resistant and Multidrug-Resistant Mycobacterium tuberculosis Strains

Strain Number	Lineage
5	2.2.1
11	2.2.1
15	2.2.1
18	2.2.1
20	2.2.1
25	2.2.1
39	2.2.1
40	2.2.1
56	2.2.2
62	2.2.1
63	2.2.1
85	2.2.1
86	2.2.1
93	2.2.1
95	4.4.2
99	2.2.1
97	2.2.1
110	2.2.1
122	2.2.1
130	2.2.1
139	2.2.1

Table 3 Gene Mutation Pattern of 21 Fluoroquinolone-Resistant and Multidrug-Resistant Mycobacterium tuberculosis Strains

Strain Number	Mutations in Genes Associated with Drug Resistance
	rpoB	katG	inhA	inhA Promoter	gyrA	gyrB	rpsL	rrs	pncA	panD	embB	embC-embA	aftA	ubiA	folC	ethA
5	S531L	S315T			D94G			A514C			M306V
11	H526D	S315T			D94G		K43R		H71Y
15	S531L	S315T			D94A		K43R		W68C
18	S531L			C-15T	D94G		K43R
20	S531L			C-15T	D94G		K43R		S104R	L132P		C-16G
25	S531L	S315T			A90V		K43R		K96R			C-12T
39	S531L	S315T			A90V	A597T	K43R		541, del-G		M306V
40	D516V		I21T	C-15T	D94G		K43R		L19P		M306V
56	S531L	S315T			D94G		K43R				V50A, Q497K
62	H526Y, D173G	S315T					K43R				M306I		I164V		I43T
63	S531L	S315T			A90V		K43R		G24D		M306V
85	L533P	S315T			D94G			A514C	S164P		M306V
86	S531L	S315T			A90V	S447F	K43T	A514C, A1401G	162, ins-G					F140V
93	L533P	S315T			D94G			A514C	S164P		M306V
95	S531L				D94G
97	S531L	S315T		T-8A	D94Y		K43R		G132A
99	S531L				D94A			A514C				C-12T
110	S531L			C-15T	D94G		K43R									T88P
122	L533P	S315T			A90V			A514C	476, ins-G
130	S531L, T480I	S315T			A90V		K43R		Y103H			C-16T
139	S531L	S315T			D94A		K43R				M306I		A33P

Abbreviations: ins, insertion; del, deletion.

Table 4 Performance of WGS Compared with DST

Drug*	WGS	DST		Sensitivity, % (95% CI)	Specificity, % (95% CI)	PPV, % (95% CI)	NPV, % (95% CI)
		R	S
Rifampicin	R	21	0	100 (100–100)	–	100 (100–100)	–
	S	0	0
Isoniazid	R	19	0	90.48 (77.61–103.34)	–	100 (100–100)	0 (0–0)
	S	2	0
Ofloxacin	R	20	0	95.24 (85.9–104.57)	–	100 (100–100)	–
	S	1	0
Moxifloxacin	R	13	7	92.86 (78.86–106.86)	0 (0–0)	65 (43.55–86.45)	–
	S	1	0
Streptomycin	R	20	0	95.24 (85.9–104.57)	–	100 (100–100)	–
	S	1	0
Ethambutol	R	12	0	85.71 (66.69–104.74)	–	100 (100–100)	77.78 (48.97–106.59)
	S	2	7
Pyrazinamide	R	12	1	66.67 (44.26–89.08)	66.67 (1.33–132)	92.31 (77.23–107.38)	25 (−7.08–57.08)
	S	6	2
Amikacin	R	1	0	50.00 (−48.00–148.00)	100 (100–100)	–	95.00 (85.2–104.8)
	S	1	19
Kanamycin	R	1	0	50.00 (−48.00–148.00)	100 (100–100)	–	95.00 (85.2–104.8)
	S	1	19
Capreomycin	R	1	0	–	100 (100–100)	–	100 (100–100)
	S	0	20
Protionamide	R	0	0	–	100 (100–100)	–	95.24 (85.9–104.57)
	S	1	20
Para-aminosalicylic	R	1	0	–	100 (100–100)	–	100 (100–100)
	S	0	20

Note: *The sensitivity, specificity, PPV, and NPV of protionamide resistance were not calculated because mutations associated with protionamide resistance were not detected via WGS.

Abbreviations: R, resistant; S, susceptible; WGS, whole-genome sequencing; DST, drug susceptibility testing; CI, confidence interval; PPV, positive predictive value; NPV, negative predictive value.