TABLE 2.

Antibiotic susceptibility profiles and genotypic characteristics of pretreatment and relapse isolates of M. intracellulare^a

Isolate by patient	Treatment status (mo)	MIC (μg/ml)b		Susceptibilityc		mmpT5 allele	MmpT5 sequenced	AtpE sequenced
		BDQ	CLF	AMK	CLR
1
1A	Pretreatment	0.004	≤0.06	R	R	3.1	WT	WT
1B	On BDQ (5)	0.008	0.12	R	R	3.2	Gly66→fs	WT
1F	Post-BDQ (3)	0.004	≤0.06	R	R	3.3	Arg25→Pro	Ala65→Pro
2
2A	Pretreatment	0.004	≤0.06	R	S	7.1	WT	WT
2C	On BDQ (9)	0.03	≤0.06	R	S	7.2	Val46→Gly	WT
2D	Post-BDQ (6)	0.03	0.12	R	S	7.2	Val46→Gly	WT
3
3B	Pretreatment	0.004	0.12	S	S	5.1	Glu177→Lys	WT
3F	On BDQ (10)	0.008	0.25	R	S	5.2	Ala23→Pro + Glu177→Lys	WT
3G	On BDQ (11)	0.008	0.5	R	S	5.2	Ala23→Pro + Glu177→Lys	WT
3H	On BDQ (15)	0.008	≤0.06	R	S	5.1	Glu177→Lys	WT
4
4A	Pretreatment	0.004	≤0.06	S	S	4.1	WT	WT
4C	On BDQ (4.5)	0.015	0.25	S	S	4.2	Pro104→fs	WT
5
5A	Pretreatment	0.004	≤0.06	R	R	1.1	WT	WT
5C	On BDQ (8)	0.004	≤0.06	R	R	1.2	Ala162→Pro	WT
5D	On BDQ (15)	0.008	≤0.06	R	R	1.2	Ala162→Pro	WT
5E	On BDQ (23)	2	ND	R	R	1.1	WT	Ala65→Pro
5F	On BDQ (28)	2	≤0.06	R	R	1.1	WT	Ala65→Pro
6
6A	Pretreatment	0.008	0.12	R	R	5.1	Glu177→Lys	WT
6B	On BDQ (7)	0.008	0.25	R	R	5.3	Ile19→Ser + Glu177→Lys	WT
6C	Post-BDQ (4.5)	0.008	0.25	R	R	5.4	Val35→Gly + Glu177→Lys	WT
6E	Post-BDQ (8.5)	0.03	0.5	R	R	5.1	Glu177→Lys	WT
7
7A	Pretreatment	0.004	≤0.06	S	S	7.1	WT	WT
7C	Post-BDQ (5)	0.015	0.5	S	S	7.3	Pro104→fs	WT
7D	Post-BDQ (5)	0.03	0.5	S	S	7.3	Pro104→fs	WT
7E	Post-BDQ (10)	0.03	0.5	S	S	7.3	Pro104→fs	WT

^aFor the complete list of pretreatment and relapse isolates, see Table S1.

^bCLF, clofazimine; ND, not determined.

^cAMK, amikacin; CLR, clarithromycin; R, resistant; S, susceptible.

^dWT, wild-type sequence; fs, frameshift mutation.