Collated data of mutation frequencies and associated genetic variants of bedaquiline, clofazimine and linezolid resistance in Mycobacterium tuberculosis.

A comprehensive literature search was conducted to obtain previously published resistance associated mutations for bedaquiline, clofazimine and linezolid for Mycobacterium tuberculosis. Where possible, mutation frequencies for these three drugs were also identified. This catalog of previously published mutations could serve as a reference for comparing mutations associated with either in vitro or clinical resistant mutants. The usage of these data was seen in our study relating to approaches for resistance mutant creation (in vitro approaches for generation of Mycobacterium tuberculosis mutants resistant to bedaquiline, clofazimine or linezolid and identification of associated genetic variants (Ismail et al., 2018 in press). Previously published mutations for clofazimine were described in the rv0678 and rv1979c genes, for bedaquiline in atpE, rv0678 and rv2535c (pepQ) genes and for linezolid in the rplC and rrl genes.

Specifications table

Value of the data

The data pertaining to genetic variants for bedaquiline, clofazimine and linezolid resistance are vital for understanding drug mechanisms of action.

A catalog such as this may prevent data replication and serve as a comparator or reference for other studies related to resistance-associated mutation.

The combined data of the resistance-associated variants could provide a starting point for the design of molecular susceptibility tests.

Data

The data in this article includes previously published mutations identified in both in vitro (Tables 1 and 3) as well as clinical isolates (Tables 2 and 4) associated with bedaquiline, clofazimine or linezolid resistance. Data were filtered according to the type of mutation identified and the gene in which the mutation occurred. Where available the in vitro approach used to generate the mutant, any information around the strain the mutants were derived from, the mutant MIC value as well as the article from which the data was derived from were included in the data. As bedaquiline- and clofazimine-resistant isolates tend to harbor rv0678 mutations, data for these mutants were presented together. The final data table (Table 5) describes previously published mutation frequencies. A diversity of mutations were identified in the rv0678 gene and were scattered along the gene. For the atpE gene, hotspots have been identified at positions 28 and 63. Mutations in the rplC and rrl target genes appear to be associated with either high or low-level linezolid resistance respectively. Four mutations in rv2535c were identified in in vivo bedaquiline and clofazimine resistant isolates. Rv1979c mutations were found in clinical pre-XDR and XDR isolates.

Table 1

Catalog of previously published mutations from bedaquiline- and clofazimine-resistant in vitro and in vivo isolates.

Mutation			Approach	Notes	MIC (µg/mL)		Refs.
rv0678	atpE	rv2535c			BDQ	CFZ
–	G187C	–	Serial Passage	Fully susceptible strain	>8	–	[1]
T461C	A83G			Isoniazid-resistant strain	>8
201_206del	A83C			Kanamycin-resistant strain	>8
–	G183T			Pyrazinamide-resistant strain	>8
	A83G
A63T	A83G			Rifampicin-resistant strain	>8
G74A	–			Fully susceptible strain	–	4
T131C				Isoniazid-resistant strain		>4
T407C				Kanamycin-resistant strain		4
C204A				Pyrazinamide-resistant strain		>4
T131C				Rifampicin-resistant strain		4
–	A83T	–	Spontaneous	Fully susceptible strain	>8	–
C403G				Pyrazinamide-resistant strain	4
–	A83G			Pyrazinamide-resistant strain	8
–	G187C			Pyrazinamide-resistant strain	>8
193delG	–			Fully susceptible strain	–	2
193delG				Fully susceptible strain		4
A65T				Fully susceptible strain		4
T407C				Pyrazinamide-resistant strain		1
C214T				Pyrazinamide-resistant strain		2
G137A				Pyrazinamide-resistant strain		4
A97G
–	–	CinArg271	in vivo	Mice treated with BDQ only	0.12	0.5-1	[2]
		+CinAla14		Mice treated with BDQ and CFZ	0.12
		+CinAla14			0.12
		L44P			0.12
A413G	WT	–	in vitro mutants	Mutants derived from H37Rv	0.25	–	[3], [5]
G281A	WT				0.5
A202G	WT			Mutants derived from MDR M. tuberculosis clinical strain	0.5
Ins G 192-193	I66M				4
IS6110 nt 272	WT				1
Ins A 38–39	WT				1
–	A95T	–	Mutagenesis	M. smegmatis	–	–	[4], [5]
–	C198G	–	Spontaneous	M. tuberculosis	–	–	[6]
	G187C				–	–
–	G183T	–	Spontaneous	2 isolates from MDR strain	0.24–0.48	–	[7]
	G187C			3 isolates from MDR strain	0.9–3.84
	A83T			1 isolate from MDR strain	0.48
	C198G			1 isolate from MDR strain	0.48
	A83G			1 isolate from WT strain	0.3
	G183T			3 isolates from WT strain	0.48–0.96
	G187C			4 isolates from WT strain	0.24–0.9
–	G187C	–	Spontaneous	–	4–8x MIC	–	[8]
	A95T				4–8x MIC
C189A	–	–	Spontaneous	–	0.5	1.25	[9]
C400T					0.5	1.25
G193 deletion	–	–	Spontaneous	23 isolates	–	All ≤1	[10]
G193 insertion				21 isolates
C466T				11 isolates
C364 insertion				5 isolates
A202G				5 isolates
T2C				2 isolates
G58T				1 isolate
C107T				1 isolate
G125A				1 isolate
T29 insertion				1 isolate
C98A				1 isolate
T128G				1 isolate
G137A				2 isolate
A152G				1 isolate
C158T				1 isolate
C176T				1 isolate
G188A				1 isolate
G194A				2 isolates
G197T				1 isolate
C226T				1 isolate
C251A				1 isolate
G266T				1 isolate
G269C				1 isolate
A292 deletion				1 isolate
G304A				1 isolate
C305T				2 isolates
T341C				1 isolate
T365C				1 isolate
CGCTGGGC371–378 deletion				1 isolate
CG444–445 deletion				1 isolate
G193 insertion				1 isolate
–				3 isolates
–		G265T		1 isolate
–	A63P	–	–	Mutants from H37Rv reference strain	4	–	[11]
	D28G			Mutants from M. tuberculosis clinical isolates	0.5
	E61D				0.5
	L59V				0.25
	I66M				1

Mutations described in rv0678, atpE and rv2535c genes. A dash (–) is used to indicate where no data is available. WT-wild type, no variants detected. BDQ-Bedaquiline. CFZ-Clofazimine.

Table 3

Catalog of previously published mutations from linezolid-resistant in vitro mutants.

Mutation		Approach	Note	MIC value (µg/ml)	Refs.
rrl	rplC
–	T460C	Serial passage	Isoniazid-resistant strain	>8	[1]
	T460C		Kanamycin-resistant strain	8
	T460C		Pyrazinamide-resistant strain	>8
	T460C		Rifampicin-resistant strain	8
–	T460C	Spontaneous	Fully susceptible strain	>8
G2270C	–		Pyrazinamide-resistant strain (13 mutants derived)	4
A2810C	–			4
–	T460C			8 to >8
G2061T	–	Spontaneous	4 isolates	32	[23], [24]
G2576T	–		1 isolate	16
none	–		5 isolates	4-8
C2848A	–	Serial passage	17 of 32 had rrl mutations, remainder had rplC	–	[25]
A2810T	–
G2270C	–
G2270T	–
G2746A	–
–	T460C
–	T460C	Spontaneous	3 in vitro mutants selected for sequencing	16	[26]
	T460C			32
G2270T	–			8
G2814T	–	Spontaneous	4 isolates	25–50	[27]
–	T460C		12 isolates	50
G2299T	–		7 isolates	65–156
A2689T	–		1 isolate	60
G2814T	–		4 isolates	94

Mutations described in rrl and rplC genes. A dash (–) is used to indicate where data was not available.

Table 2

Catalog of previously published mutations from bedaquiline- and clofazimine-resistant clinical isolates.

Mutation			Notes	MIC (µg/ml)		Refs.
rv0678	atpE	rv1979c		BDQ	CFZ
T124C	–	–	Clinical strains from BDQ trial	0.25		[3]
A97C				0.5	–
C107T				0.5
Del C 212				0.5
Ins IS6110 nt 272				0.5
Ins C 141–142				0.25
2T>C	WT	–	fMet1Ala-relapse isolate after	0.5	4	[12], [13], [14]
			BDQ compassionate use
T437C	WT	WT	XDR	0.78	1.2	[15]
G5T	WT	WT	Pre-XDR	0.73	4
C158T	WT	WT	Pre-XDR	0.39	2.09
T350G	WT	WT	XDR	1.54	4.16
WT	WT	A155C	Pre-XDR	0.08	1.2
Del gg 18–19	–	–	MDR isolates	0.5	–	[16]
Ins G140				0.25
M139T				0.25
198–199 Ins G	–	–	Mix: WT + rv0678 mutant	0.24;0.48;1	–	[17], [18]
274–275 Ins A				1
C148T, A187G			intergenic mutation, rv0678 mutant	0.48
G334C, (-13) Ins IS6110				0.48
C185T				0.48
C155T				0.48
C176T				0.48
224–225 Ins A				0.24
T(-44)C				0.24
A263G			Mix: WT + rv0678 mutant	0.12
T116C				0.12
T124C			Mix: WT + rv0678 mutant (silent mutation)	0.12
C45T				0.12
G256A				0.12
[Ins139g]	WT	–		0.12–0.25	–	[19]
L142R	WT		Baseline and post-treatment BDQ isolates from BDQ clinical trials	0.25
L142R	A63V			0.25–1
[Del198G] [Del212C] [G233C, G78A]	WT			0.12
[G66W] [Del198G] [Ins263A] [Del435T]	WT			0.12
[Del198G] [Ins466C]	WT			0.25
[Del435T]	WT			0.25
[E113K] [Del198G] [Del435T]	WT			0.25
[Del435T]	WT			0.25
G121E	WT			0.25
[L40S] [Del291C] [Ins386C]	WT			0.25
Del291C	WT			0.25
[S53P] [Del198G] [Del336C]	WT			0.25
M23L	WT			0.06
M23L Ins142C	WT			0.12
M23L [Ins142C] [Ins419G]	WT			0.12
M23L Ins419g	WT			0.12
[Del19G] [E49stop] [Del198G] [Ins468GA]	WT			0.12
-[V85A] [R135W]	WT			0.12
V85A	WT			0.12
Ins44A	WT			0.06
[Ins144C]	WT			0.12–0.25
Ins421G	WT			0.12–0.25
Del32G	WT			0.06; 0.25
[Y26stop] [L122P]	WT			0.12
L122P	WT			0.12
[Del214C] [Del198G]	WT			0.06
[F79S] [Ins137G]	WT			0.12
[Del19G] [Del198G]	WT			0.12
A98V	WT			0.12–0.25
WT	D28N			0.12
[Ins139G] + [Ins318CG]	WT			0.12
[Del274–283] [Ins139TG]	WT			0.12
[C46R] [Ins139TG] [L40S]	WT			0.12
Ser53Pro	WT	–	2 XDR isolates	0.5	2–4	[20]
Ser53Leu			1 XDR isolate	0.25	2
Tyr157Asp			1 XDR isolate	0.125	2
WT			1 XDR isolate	0.5	2
WT	WT	G1226A	3 XDR isolates: Culture negative at 6 months	0.25–1 (MGIT) 0.06–0.125 (BMD)	0.5 (MGIT)	[21]
136_137insG		G1226A	XDR: : Culture positive at 6 months	2 (MGIT) 0.25 (BMD)	0.5 (MGIT)
138_139insG		G1226A	XDR: Culture positive at 6 months	2 (MGIT) 0.5 (BMD)	2 (MGIT)
141_142insC		G1226A	2 XDR isolates: Culture positive at 6 months	4 (MGIT) 0.25–0.5 (BMD)	0.5–1 (MGIT)
T200G		G1226A	XDR: Culture positive at 6 months	4 (MGIT) 0.5 (BMD)	2 (MGIT)
345delG		G1226A	XDR: Culture positive at 6 months	4 (MGIT) 0.5 (BMD)	1 (MGIT)
-11C>A	WT	–	Fully susceptible clinical isolate	0.016	–	[22]
D5G	WT		Fully susceptible clinical isolate	0.016
M23V	WT		STR resistant clinical isolate	0.063
D47fs	WT		XDR clinical isolate	0.5
E55D	WT		Fully susceptible clinical isolate	0.063
G87R	WT		Fully susceptible clinical isolate	0.063
R96Q	WT		INH resistant	0.25
L117R	WT		Fully susceptible clinical isolate	0.016
WT	-53G>A		Fully susceptible clinical isolate	0.125
WT	-72T>C		RIF and INH resistant clinical isolate	8
WT	-138T>C		3 RIF and INH resistant clinical isolates	0.031
WT	183G>A		Fully susceptible clinical isolate	0.063
WT	I66V		Fully susceptible clinical isolate	0.125

Mutations described in rv0678, atpE and rv1979c genes. A dash (–) is used to indicate where no data was available. WT-wild type, no variants detected. MGIT- MGIT960 platform used to determine MIC. BMD- Broth Micro Dilution method used to determine MIC. BDQ-Bedaquiline. CFZ-Clofazimine.

Table 4

Catalog of previously published mutations from linezolid-resistant clinical isolates.

Mutation		Note	MIC value (µg/ml)	Refs.
rrl	rplC
WT	–	No mutations in rplD, rplV, whiB7, rrl, erm-37	8 (3 strains)	[23]
WT			4 (1 strain)
–	T460C	2 resistant, 3 acquired resistance during treatment	4–16	[24]
G2447T	–	acquired resistance during treatment	16
–	T460C	–	2	[28]
–	T460C		0.5
–	T460C		4
G2576T	–		4
G2576T	–		4
–	T460C	8 isolates	–	[19]
G2814T	–	1 isolate
C1921T	–	1 isolate
G2294A	–	1 isolate acquired resistance during treatment
G2576T	–	1 MDR-TB isolate	4	[13]
A2572C	–
–	T460C	2 XDR-TB isolates	4–16	[12]

Mutations described in rrl and rplC genes. A dash (–) is used to indicate where data was not available. WT- wild type, no variants detected.

Table 5

Mutation frequencies and selection concentrations for bedaquiline-, clofazimine- and linezolid-resistant spontaneous mutants from previously published studies.

Drug	Conc (µg/ml)	Strain	Mutation frequency	Refs.
Bedaquiline	0.12	Fully susceptible M. tuberculosis	5 × 10–7	[8]
	0.12	M. smegmatis	2 × 10–8
	0.24	Fully susceptible M. tuberculosis	5 × 10–8
	0.24	M. smegmatis	1 × 10–8
	0.03-0.05	Fully susceptible M. tuberculosis	1 × 10–8	[11]
		Clinical M. tuberculosis	5 × 10–8
		Clinical M. tuberculosis	1 × 10–8
		Clinical M. tuberculosis	1 × 10–8
	0.015-0.5	Clinical strain M. fortuitum	1.5 × 10–8
	0.25-8	Clinical strain M. abscessus	1.5 × 10–8
	1	Fully susceptible M. tuberculosis	6 × 10–9	[1]
		Pyrazinamide-resistant M. tuberculosis	4 × 10−7
Clofazimine	0.25	Fully susceptible M. tuberculosis	5 × 10−6	[10]
	1	Fully susceptible M. tuberculosis	5 × 10−5	[1]
		Pyrazinamide-resistant M. tuberculosis	7 × 10−7
Linezolid	–	Fully susceptible M. tuberculosis	2 × 10−8	[23]
	–	Fully susceptible M. tuberculosis	5 × 10−9
	2	Fully susceptible M. tuberculosis	1 × 10−8	[1]
		Pyrazinamide-resistant M. tuberculosis	1 × 10−7

A dash (–) is used to indicate where data was not available.

Experimental design, materials and methods

A catalog was compiled of mutations observed for in vitro, in vivo and clinical M. tuberculosis strains resistant to bedaquiline, clofazimine and linezolid as reported in studies that were identified through a comprehensive literature search. This was done by searching for combinations of each drug (or drug class) together with terms like “resistant”, “resistance”, “mutant”, “mutations” as well as “Mycobacterium tuberculosis”. Related and citing articles were also reviewed. The articles were then analyzed on the basis of the approach used and the mutations documented. Mutations were delineated as arising from either in vivo or clinical and in vitro.

Subject area	Biology
More specific subject area	Microbiology
Type of data	Tables
How data was acquired	Literature search for mutation frequencies and genetic variants related to bedaquiline, clofazimine and linezolid resistance
Data format	Filtered
Experimental factors	Published articles regarding bedaquiline, clofazimine and linezolid resistant isolates and associated mutations
Experimental features	Previously published mutations in rv0678, rv1979c, rv2535c, atpE, rplC and rrl genes and mutation frequencies associated with either bedaquiline-, clofazimine- or linezolid-resistant M. tuberculosis
Data source location	South Africa
Data accessibility	Data is included in this article and accessible in related referenced articles
Related research article	Ismail, N., Omar, S.V., Ismail, N.A., Peters, R.P.H. (2018). in vitro approaches for generation of Mycobacterium tuberculosis mutants resistant to bedaquiline, clofazimine or linezolid and identification of associated genetic variants, JMM (In press)