TABLE 2.

Co-occurrence of regulator resistance mutations and regulon LoF mutations^a

Mutation in regulator				Mutation in regulated gene				Isolate information with co-occurring mutations
Type of mutation	Variant name	Codon position	No. of isolates	Type of mutation	Variant name	Codon position	No. of isolates	No. of isolates with both mutations	Isolate sublineage(s) (no. of isolates)
Indel	mmpR 192-198delG	64	20	Indel	mmpL5 2028insA	676	1	1	2.2.1.1.1 (1)
Indel	mmpR 192-198insG	64	86	Indel	mmpL5 606delC	202	83	82	4.11 (82)
Indel	mmpR 207insA	69	1	Indel	mmpL5 1160insCGATG	387	1	1	2.2.1 (1)
SNP	eis C-14T		181	Indel	eis 627insC	209	1	1	2.2.1.1.1.i3 (1)
SNP	eis C-14T		181	Indel	eis 486insCT	162	2	2	4.1.i1.1.1.1 (2)
SNP	eis C-14T		181	Indel	eis 473insT	158	1	1	2.2.1.1.1.i3 (1)
SNP	eis C-14T		181	Indel	eis 448delA	150	7	7	2.2.1.1.1.i3 (7)
SNP	eis C-14T		181	Indel	eis 400insG	134	1	1	2.2.1.1.1 (1)
SNP	eis C-14T		181	Indel	eis 279delCGGCGATGCGT	93	1	1	2.2.1.1.1.i3 (1)
SNP	eis C-14T		181	SNP	eis G39A	W13*	1	1	2.2.1.1.1 (1)
SNP	eis C-14T		181	SNP	eis G38A	W13*	1	1	2.2.1.1.1 (1)
SNP	eis C-14T		181	Indel	eis 16insC	6	1	1	2.2.1.1.1 (1)
SNP	eis C-14T		181	Indel	eis 15insC	5	1	1	2.2.1.1.1 (1)
SNP	eis C-14T		181	SNP	eis G3A	V1V	6	6	1.1.1.1.1 (1), 2.2.1.1.1.i3 (5)
SNP	ahpC G-88A		3350	Indel	ahpC 323delC	108	1	1	3.1.1 (1)
SNP	whiB7 T-147C		1	INDEL	whiB7 192delC	64	573	1	1.2.1.1.1 (1)
Indel	whiB7 −214delG		9	INDEL	whiB7 192delC	64	573	1	1.2.1.1.1 (1)
Indel	whiB7 −316insC		2	INDEL	whiB7 192delC	64	573	1	1.2.1.1.1 (1)

^aA list of antibiotic resistance mutations in regulator regions (mmpR, oxyR-ahpC, eis-Rv2417c, and whiB7-uvrD2) that co-occur with LoF mutations in corresponding regulated regions (mmpL5, mmpS5, mmpR, ahpC, eis, and whiB7) within our sample of 31,440 clinical isolates is shown. More details can be found in Table S3 in the supplemental material.