Table 5.

Distribution of region of difference 1 (RD1) genes among M. kansasii strains and other mycobacterial outgroup species.

No.	Species/genotype	ID	Strain no.a	Locusb									GenBank no.
				Rv3879c	Rv3876	Rv3878	Rv3877	Rv3873	Rv3871	Rv3874	Rv3875	Rv3872
1	M. kansasii I	5MK	NLA001000521D*	–	+	–	+	+	+	+	+	+	MWKY01
2	M. kansasii I	6MK	ATCC25221D*	+	+	–	+	+	+	+	+	+	CP019885
3	M. kansasii I	1MK	NLA001000927D*	–	+	–	+	+	+	+	+	+	CP019883
4	M. kansasii I	4MK	NLA001000449D*	–	+	–	+	+	+	+	+	+	CP019884
5	M. kansasii I	10MK	6200D*	–	+	–	+	+	+	+	+	+	CP019886
6	M. kansasii I	9MK	7728D*	+	+	–	+	+	+	+	+	+	CP019888
7	M. kansasii I	11MK	7744D*	–	+	–	+	+	+	+	+	+	CP019887
8	M. kansasii I	5JD	1010001495E*	–	+	–	+	+	+	+	+	+	LWCL01
9	M. kansasii I	K4	K4D*	+	+	–	+	+	+	+	+	+	NKQW01
10	M. kansasii I	K14	K14D*	+	+	–	+	+	+	+	+	+	NKQY01
11	M. kansasii I	K19	K19N*	+	+	–	+	+	+	+	+	+	NKQX01
12	M. kansasii I	–	ATCC12478D	–	+	–	+	+	+	+	+	+	CP0006835
13	M. kansasii I	–	824NI	–	+	–	+	+	+	+	+	+	CP009483
14	M. kansasii I	–	BR3657D	–	+	–	+	+	+	+	+	+	PQOL01
15	M. kansasii I	–	BR6849D	–	+	–	+	+	+	+	+	+	PQOP01
16	M. kansasii I	–	SMC1E	–	+	–	+	+	+	+	+	+	JNDJ01
17	M. kansasii I	–	BR8837D	–	+	–	+	+	+	+	+	+	PQOV01
18	M. kansasii I	–	BR6498D	+	+	–	+	+	+	+	+	+	PQOM01
19	M. kansasii I	–	11_3813R	–	+	–	+	+	+	+	+	–	MVBM01
20	M. kansasii I	–	BR6884D	+	+	–	+	+	+	+	+	+	PQOO01
21	M. kansasii I	–	BR10742D	+	+	–	+	+	+	+	+	+	PQOR01
22	M. kansasii I	–	BR1580D	+	+	–	+	+	+	+	+	+	PQOS01
23	M. kansasii I	–	BR4404D	+	+	–	+	+	+	+	+	+	PQOT01
24	M. kansasii I	–	BR8839D	+	+	–	+	+	+	+	+	+	PQOW01
25	M. kansasii I	–	662NI	+	+	–	+	+	+	+	+	+	CP009481
26	M. kansasii I	–	BR7287D	+	+	–	+	+	+	+	+	+	PQON01
27	M. kansasii I	–	BR10953D	+	+	–	+	+	+	+	+	+	PQOQ01
28	M. kansasii I	–	BR8835D	+	+	–	+	+	+	+	+	+	PQOU01
29	M. kansasii I	–	11_3469R	+	+	–	+	+	+	+	+	+	MVBN01
30	M. kansasii I	–	MK40U	+	+	–	+	+	+	+	+	+	UPHI01
31	M. kansasii I	–	MK7U	+	+	–	+	+	+	+	+	+	UPHJ01
32	M. kansasii II	12MK	2193N*	–	–	–	+	+	+	+	+	+	MWQA01
33	M. kansasii II	3MK	NLA001001128N*	–	–	–	+	+	+	+	+	+	MWKX01
34	M. kansasii II	7MK	B11073207N*	–	–	–	+	+	+	+	+	+	MWKZ01
35	M. kansasii II	8MK	B11063838N*	+	–	–	+	+	+	+	+	+	MWKV01
36	M. kansasii II	3B/6JD	1010001469E*	–	–	–	+	+	+	+	+	+	LWCM01
37	M. kansasii II	H47	H47D*	–	–	–	+	+	+	+	+	+	NKRA01
38	M. kansasii II	H48	H48N*	–	–	–	+	+	+	+	+	+	NKQZ01
39	M. persicum	–	AFPC−000227D	–	–	–	+	+	+	+	+	+	MVIF01
40	M. persicum	–	MK15U	–	–	–	+	+	+	+	+	+	UPHK01
41	M. persicum	–	MK4U	–	–	–	+	+	+	+	+	+	UPHM01
42	M. persicum	–	MK42U	–	–	–	+	+	+	+	+	+	UPHL01
43	M. kansasii III	14_15	14_15N*	+	+	–	+	+	+	+	+	+	NKRB01
44	M. kansasii III	174_15	174_15D*	–	+	–	+	+	+	+	+	+	NKRD01
45	M. kansasii III	3JD	1010001468E*	+	+	–	+	+	+	+	+	+	LWCJ01
46	M. kansasii III	–	732U	+	+	–	+	+	+	+	+	+	JANZ01
47	M. pseudokansasii	–	MK142D	–	+	–	+	+	+	+	+	+	UPHU01
48	M. pseudokansasii	–	MK21U	–	+	–	+	+	+	+	+	+	UPHO01
49	M. pseudokansasii	–	MK35U	+	+	–	+	+	+	+	+	+	UPHN01
50	M. kansasii IV	2JD	1010001458E*	+	+	–	+	+	+	+	+	+	LWCI01
51	M. kansasii IV	241/15	241/15N*	–	+	–	+	+	+	+	+	+	NKRE01
52	M. kansasii V	1JD	1010001454E*	–	+	–	+	+	+	+	+	+	LWCH01
53	M. kansasii V	4JD	1010001493E*	–	+	–	+	+	+	+	+	+	LWCK01
54	M. kansasii V	49_11	49_11N*	–	+	–	+	+	+	+	+	+	NKRC01
55	M. innocens	–	MK13U	–	+	–	+	+	+	+	+	+	UPHQ01
56	M. kansasii VI	2MK	NLA001001166N*	–	–	–	+	+	+	+	+	+	MWKW01
57	M. attenuatum	–	MK41N	–	–	–	+	+	+	+	+	+	UPHT01
58	M. attenuatum	–	MK136U	–	–	–	+	+	+	+	+	+	UPHP01
59	M. attenuatum	–	MK191U	+	–	–	+	+	+	+	+	+	UPHS01
60	M. tuberculosis	–	Beijing–like	+	+	–	+	+	+	+	+	+	CP017597
61	M. africanum	–	GM041182	+	+	+	+	+	+	+	+	+	NC_015758
62	M. bovis	–	09_1191	+	+	–	+	+	+	+	+	+	JPFP01
63	M. caprae	–	Allgaeu	+	+	+	+	+	+	+	+	+	CP016401
64	M. microti	–	12	+	+	+	+	–	–	–	–	–	CP010333
65	M. conspicuum	–	DSM44136	ND									LQOR01.1
66	M. gastri	–	DSM43505	–	+	–	+	+	+	+	+	+	LQOX01
67	M. marinum	–	E11	–	+	–	+	+	+	+	+	–	HG917972
68	M. riyadhense	–	DSM45176	–	–	–	+	+	+	+	+	+	LQPQ01
69	M. szulgai	–	DSM44166	+	–	–	+	+	+	+	+	–	LQPW01

^aThe presence of a given gene was marked with a “+” and highlighted in gray; the superscript letters refer to isolation source:

^D–clinical strains implicated in NTM disease;

^N–clinical strains not implicated in NTM disease;

^R–clinical strain from the rhesus macaque (Macaca mulatta);

^U–clinical strains with unknown relation to NTM disease;

^E–environmental strains. Strains whose genomes were sequenced in this study are marked with an asterisk (*).