TABLE 1.

The phenotypic/genotypic characteristics of M. tuberculosis isolates from the six patients who acquired cross-resistance to bedaquiline and clofazimine

Strain or patient IDa	Previous second-line treatment regimen/outcomeb	DST profile at start of BDQ-containing regimen	BDQ exposure (mo)	M. tuberculosis strain testing results										Treatment outcome
				pDST results for MIC (mg·liter−1) for:			Genome coverage (×)	WGSc
				BDQ in 7H11	BDQ in MGIT	CFZ in MGIT		Rv0678	pepQ	atpE	Rv1979c	NCBI accession no.	Lineage
Strain
H37Rv (NC_000962.3)				0.03	0.25	0.25	43.28	WT	WT	WT	WT
Patients
1	NO	Pre-XDR	0	0.125	0.5	0.5	71.67	WT	WT	WT	WT	SRR9028486	Delhi-CAS(3)	Failure
			4	0.5	Not tested	Not tested	40.57	779130_141-142_Ins-C	WT	WT	WT	SRR9028477
			6	0.5	Not tested	Not tested	58.11		WT	WT	WT	SRR9028476
			9	>0.5	4	4	68.20		WT	WT	WT	SRR9028485
2	Am(8), Lfx, Cs, Eto, Z, E, B6/failure	MDR	0	0.03	0.5	0.5	80.97	WT	WT	WT	2221732_P478G	SRR9028481	Delhi-CAS(3)	Cured
			2	0.06	Not tested	Not tested	127.50	WT	WT	WT		SRR9028488
			5	0.5	4	4	90.23	779130_141-142_Ins-C	WT	WT		SRR9028489
3	Am, Lfx, Eto, CS, Z, PAS, B6/failure	MDR	0	0.06	0.25	0.5	96.26	WT	WT	WT	WT	SRR9028483	Delhi-CAS(3.1.2)	Failure
			1	0.06	Not tested	Not tested	86.92	WT	WT	WT	WT	SRR9028490
			6	0.25	2	2	100.78	779048_V20G	WT	WT	WT	SRR9028494
4	Cm(12), Mfx, Cs, Eto, Cfz, Z, Amx-clv/failure	XDR	0	0.03	0.25	0.5	81.93	WT	WT	WT	WT	SRR9028487	Delhi-CAS(3)	Still on treatment
			2	0.03	Not tested	Not tested	111	WT	WT	WT	WT	SRR9028484
			7	0.25	2	4	102.74	779127_138-139_Ins-G	WT	WT	WT	SRR9028491
5	Cm(12), Mfx, Cs, Eto, Cfz, Z, PAS, Clr, Amx-clv, H, E, B6/failure	XDR	0	0.03	0.5	0.5	68.40	WT	WT	WT	WT	SRR9028482	Delhi-CAS(3)	Failure
			1	0.06	1	Not tested	125.22	WT	WT	WT	WT	SRR9028493
			3	0.125	2	Not tested	116.61	779127_138-139_Ins-G	WT	WT	WT	SRR9028480
			6	0.125	2	4	109.03		WT	WT	WT	SRR9028478
6	Cm(12), Mfx, Cs, Eto, Cfz, LNZ, PAS, Z, Amx-clv, B6/failure	XDR	0	0.03	0.5	1	99.35	WT	WT	WT	WT	SRR9028479	Euro-American -4.9	Failure
			1	0.5	4	4	83.34	779181_192-193_Ins-G	WT	WT	WT	SRR9028492

^aID, identifier.

^bAM, amikacin; Amx-clv, amoxicillin-clavulanic acid; Cfz, clofazamine; Cm, capreomycin; Cs, cyclocerine; E, ethambutol; Eto, ethionamide; Lfx, levofloxacin; LNZ, linozolid; Mfx, moxifloxacin; PAS, para-aminosalicylic acid; B6, vitamin B6; Z, pyrazinamide. Numbers in parentheses indicate the duration of the administration of the antibiotic in months.

^cWT, wild type.