Evaluation of the Ribosomal Protein S1 Gene (rpsA) as a Novel Biomarker for Mycobacterium Species Identification

Table 2

Sequence pair distances of 47 type strains of mycobacteria and 1 out-group strain determined byusing the multiple alignment algorithm in the MegAlign package (version 7.1.0; DNASTAR, Madison, WI).

Percent identity
	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48
1	—	100.0	98.7	98.1	96.0	95.3	95.4	96.4	96.2	94.5	94.5	95.1	94.5	94.5	92.0	93.9	94.1	94.3	94.5	94.5	92.8	95.6	93.7	94.7	93.2	92.4	88.8	89.2	91.1	91.1	91.1	91.1	91.1	91.3	91.5	93.9	94.1	91.3	93.0	92.8	92.6	92.6	92.4	93.4	93.4	92.4	92.8	89.2	1	M.  thermoresistibile
2	0.0	—	98.7	98.1	96.0	95.3	95.4	96.4	96.2	94.5	94.5	95.1	94.5	94.5	92.0	93.9	94.1	94.3	94.5	94.5	92.8	95.6	93.7	94.7	93.2	92.4	88.8	89.2	91.1	91.1	91.1	91.1	91.1	91.3	91.5	93.9	94.1	91.3	93.0	92.8	92.6	92.6	92.4	93.4	93.4	92.4	92.8	89.2	2	M.  senegalense
3	1.3	1.3	—	98.3	96.6	95.8	95.8	96.8	96.8	94.7	94.7	95.6	95.4	95.4	92.0	94.1	95.4	94.9	95.1	95.1	93.0	96.2	94.7	95.6	94.5	93.0	89.4	89.8	91.1	91.1	91.1	91.1	91.1	91.3	92.0	94.5	94.7	92.0	93.4	93.5	93.2	93.2	92.8	93.7	93.7	93.0	92.8	89.4	3	M.  porcinum
4	1.9	1.9	1.7	—	96.2	95.8	95.8	96.2	96.2	94.1	94.1	95.4	94.5	94.5	92.0	94.3	94.5	94.3	94.5	94.5	93.9	96.2	94.9	94.9	93.7	93.7	90.1	90.5	90.9	90.9	90.9	90.9	90.9	91.1	92.0	94.7	94.9	91.3	93.2	93.2	93.0	93.4	92.8	93.5	93.7	92.8	93.0	89.2	4	M.  fortuitum
5	4.1	4.1	3.5	3.9	—	94.3	95.4	96.4	96.0	93.9	93.9	93.4	94.3	94.3	91.5	94.3	94.3	94.5	94.7	94.7	91.5	94.3	94.1	94.9	92.8	91.1	89.8	90.3	90.1	90.1	90.1	90.1	90.1	90.3	91.1	93.5	93.7	91.3	93.4	93.0	93.5	93.5	93.0	93.7	93.4	93.0	92.0	89.6	5	M.  phlei
6	4.9	4.9	4.3	4.3	5.9	—	95.1	95.3	94.1	93.7	93.7	94.7	94.1	94.1	91.3	93.7	93.5	93.4	93.5	93.5	93.2	93.7	93.7	93.7	93.0	92.4	88.6	89.0	90.7	90.7	90.7	90.7	90.7	90.9	91.5	94.3	94.1	90.7	93.2	92.0	91.8	92.2	91.5	93.0	93.2	91.8	91.5	88.0	6	M.  gadium
7	4.7	4.7	4.3	4.3	4.7	5.1	—	96.6	96.0	95.4	95.4	94.7	94.7	94.7	93.0	95.1	95.3	95.6	95.8	95.8	93.2	94.1	94.9	94.7	92.4	92.0	90.1	90.5	92.4	92.4	92.4	92.4	92.4	92.6	92.8	94.9	94.7	93.0	94.1	94.9	93.7	93.7	93.5	93.9	94.3	92.6	93.4	90.3	7	M.  flavescens
8	3.7	3.7	3.3	3.9	3.7	4.9	3.5	—	96.6	96.6	96.6	95.3	96.2	96.2	92.0	96.2	96.2	96.4	96.2	96.2	93.5	94.7	94.5	94.5	93.9	91.5	90.5	90.9	91.1	91.1	91.1	91.1	91.1	91.3	92.2	93.7	93.5	92.0	94.3	93.5	93.2	93.2	93.0	93.4	93.5	92.4	92.2	90.9	8	M.  smegmatis
9	3.9	3.9	3.3	3.9	4.1	6.1	4.1	3.5	—	96.6	96.6	95.1	96.8	96.8	92.4	95.8	95.6	96.2	96.4	96.4	93.0	95.6	94.9	94.7	92.4	92.0	91.5	91.8	90.9	90.9	90.9	90.9	90.9	91.1	92.2	94.3	94.5	92.4	93.9	92.8	93.4	93.4	93.2	93.9	93.5	92.8	92.8	89.2	9	M.  vaccae
10	5.7	5.7	5.5	6.1	6.3	6.5	4.7	3.5	3.5	—	100.0	94.9	96.2	96.2	93.0	94.9	95.8	96.4	96.6	96.6	93.0	94.3	92.8	93.0	92.4	91.7	89.8	90.1	89.9	89.9	89.9	89.9	89.9	90.1	91.5	92.6	92.4	91.3	93.2	92.0	91.1	91.1	91.3	91.8	91.5	90.3	91.7	89.0	10	M.  parafortuitum
11	5.7	5.7	5.5	6.1	6.3	6.5	4.7	3.5	3.5	0.0	—	94.9	96.2	96.2	93.0	94.9	95.8	96.4	96.6	96.6	93.0	94.3	92.8	93.0	92.4	91.7	89.8	90.1	89.9	89.9	89.9	89.9	89.9	90.1	91.5	92.6	92.4	91.3	93.2	92.0	91.1	91.1	91.3	91.8	91.5	90.3	91.7	89.0	11	M.  triviale
12	5.1	5.1	4.5	4.7	7.0	5.5	5.5	4.9	5.1	5.3	5.3	—	96.4	96.4	91.8	94.5	95.3	95.1	95.3	95.3	94.1	95.1	92.8	92.2	92.6	93.0	90.3	90.7	89.9	89.9	89.9	89.9	89.9	90.1	91.3	93.2	92.8	89.9	92.0	92.0	91.7	91.7	91.1	91.8	92.4	90.9	89.9	88.2	12	M.  neoaurum
13	5.7	5.7	4.7	5.7	5.9	6.1	5.5	3.9	3.3	3.9	3.9	3.7	—	100.0	92.6	95.3	95.8	95.6	95.8	95.8	94.1	94.9	94.1	93.7	92.8	92.2	91.3	91.7	89.4	89.4	89.4	89.4	89.4	89.6	90.7	92.0	91.8	91.1	93.0	91.8	91.5	91.5	91.3	91.7	91.8	91.3	90.5	89.8	13	M.  diernhoferi
14	5.7	5.7	4.7	5.7	5.9	6.1	5.5	3.9	3.3	3.9	3.9	3.7	0.0	—	92.6	95.3	95.8	95.6	95.8	95.8	94.1	94.9	94.1	93.7	92.8	92.2	91.3	91.7	89.4	89.4	89.4	89.4	89.4	89.6	90.7	92.0	91.8	91.1	93.0	91.8	91.5	91.5	91.3	91.7	91.8	91.3	90.5	89.8	14	M.  duvalii
15	8.4	8.4	8.4	8.4	9.1	9.3	7.4	8.5	8.0	7.4	7.4	8.6	7.8	7.8	—	93.0	93.9	93.0	93.2	93.2	91.7	91.8	91.1	91.1	89.4	91.1	89.8	90.1	89.2	89.2	89.2	89.2	89.2	89.4	88.8	90.1	90.5	91.5	90.5	90.5	89.6	89.8	89.8	89.2	90.1	89.6	89.0	87.7	15	M.  aurum
16	6.3	6.3	6.1	5.9	5.9	6.5	5.1	3.9	4.3	5.3	5.3	5.7	4.9	4.9	7.4	—	96.6	96.0	95.8	95.8	93.9	94.7	94.7	93.5	92.8	92.4	91.8	92.4	90.5	90.5	90.5	90.5	90.5	90.7	91.7	93.2	93.0	91.1	92.6	92.4	92.6	93.0	91.3	92.4	93.5	91.5	90.9	88.4	16	M.  chubuense
17	6.1	6.1	4.7	5.7	5.9	6.8	4.9	3.9	4.5	4.3	4.3	4.9	4.3	4.3	6.3	3.5	—	97.2	97.0	97.0	94.1	95.6	94.5	94.1	93.5	93.4	91.3	91.7	90.3	90.3	90.3	90.3	90.3	90.5	91.3	93.0	93.2	92.0	92.8	93.2	92.6	93.0	91.7	92.8	92.8	91.5	91.1	90.1	17	M.  gilvum
18	5.9	5.9	5.3	5.9	5.7	7.0	4.5	3.7	3.9	3.7	3.7	5.1	4.5	4.5	7.4	4.1	2.9	—	99.8	99.8	94.1	94.9	92.8	93.4	92.6	93.0	90.7	91.1	90.1	90.1	90.1	90.1	90.1	90.3	91.3	92.8	92.6	91.3	92.4	92.8	92.0	92.0	91.3	92.0	92.4	91.3	92.0	89.2	18	M.  vanbaalenii
19	5.7	5.7	5.1	5.7	5.5	6.8	4.3	3.9	3.7	3.5	3.5	4.9	4.3	4.3	7.2	4.3	3.1	0.2	—	100.0	93.9	95.1	93.0	93.5	92.8	93.2	90.9	91.3	90.3	90.3	90.3	90.3	90.3	90.5	91.5	93.0	92.8	91.5	92.6	93.0	92.2	92.2	91.5	92.2	92.6	91.5	92.2	89.0	19	M.  terrae
20	5.7	5.7	5.1	5.7	5.5	6.8	4.3	3.9	3.7	3.5	3.5	4.9	4.3	4.3	7.2	4.3	3.1	0.2	0.0	—	93.9	95.1	93.0	93.5	92.8	93.2	90.9	91.3	90.3	90.3	90.3	90.3	90.3	90.5	91.5	93.0	92.8	91.5	92.6	93.0	92.2	92.2	91.5	92.2	92.6	91.5	92.2	89.0	20	M.  austroafricanum
21	7.6	7.6	7.4	6.3	9.1	7.2	7.2	6.7	7.4	7.4	7.4	6.1	6.1	6.1	8.9	6.3	6.1	6.1	6.3	6.3	—	93.7	91.8	91.7	91.1	92.6	88.8	89.2	89.4	89.4	89.4	89.4	89.4	89.6	90.3	91.5	91.7	90.1	90.9	90.9	89.9	90.1	89.6	90.7	91.3	90.9	89.9	89.6	21	M.  rhodesiae
22	4.5	4.5	3.9	3.9	5.9	6.6	6.1	5.5	4.5	5.9	5.9	5.1	5.3	5.3	8.7	5.5	4.5	5.3	5.1	5.1	6.5	—	93.7	94.5	93.4	94.1	90.3	90.7	90.3	90.3	90.3	90.3	90.3	90.5	90.5	93.7	93.9	90.3	92.6	92.8	92.2	92.2	91.8	92.6	93.0	91.7	90.9	89.2	22	M.  obuense
23	6.5	6.5	5.5	5.3	6.1	6.5	5.3	5.7	5.3	7.6	7.6	7.6	6.1	6.1	9.5	5.5	5.7	7.6	7.4	7.4	8.6	6.5	—	95.8	93.9	93.0	91.7	92.0	90.9	90.9	90.9	90.9	90.9	91.1	92.2	93.7	93.9	91.7	93.2	92.6	93.4	93.7	92.2	93.7	93.9	92.4	91.7	89.0	23	M.  aichiense
24	5.5	5.5	4.5	5.3	5.3	6.5	5.5	5.7	5.5	7.4	7.4	8.2	6.5	6.5	9.5	6.7	6.1	7.0	6.7	6.7	8.9	5.7	4.3	—	93.7	93.4	91.3	91.8	91.5	91.5	91.5	91.5	91.5	91.7	91.5	93.7	94.1	92.2	93.0	93.5	92.8	93.0	93.0	93.4	94.1	93.2	92.4	89.2	24	M.  sphagni
25	7.2	7.2	5.7	6.5	7.6	7.4	8.0	6.3	8.0	8.0	8.0	7.8	7.6	7.6	11.5	7.6	6.7	7.8	7.6	7.6	9.5	7.0	6.3	6.5	—	92.0	88.8	89.4	89.6	89.6	89.6	89.6	89.6	89.8	90.5	94.5	94.5	90.7	93.0	92.8	91.8	92.2	92.0	92.4	93.4	92.2	91.5	88.2	25	M.  tokaiense
26	8.0	8.0	7.4	6.5	9.5	8.0	8.4	9.1	8.4	8.9	8.9	7.4	8.2	8.2	9.5	8.0	7.0	7.4	7.2	7.2	7.8	6.1	7.4	7.0	8.4	—	91.5	91.8	89.6	89.6	89.6	89.6	89.6	89.8	89.8	92.2	92.6	89.4	90.5	91.1	90.7	91.1	89.8	92.0	91.7	90.7	90.3	87.1	26	M.  chelonae
27	12.1	12.1	11.5	10.6	11.0	12.4	10.6	10.1	9.1	11.0	11.0	10.4	9.3	9.3	11.0	8.6	9.3	9.9	9.7	9.7	12.1	10.4	8.9	9.3	12.1	9.1	—	98.7	86.7	86.7	86.7	86.7	86.7	86.9	88.4	88.4	88.8	88.4	88.6	89.4	89.6	89.6	88.4	90.1	89.8	88.2	87.1	87.1	27	M.  abscessus
28	11.7	11.7	11.0	10.1	10.4	11.9	10.1	9.7	8.6	10.6	10.6	9.9	8.9	8.9	10.6	8.0	8.9	9.5	9.3	9.3	11.7	9.9	8.4	8.6	11.5	8.7	1.3	—	87.5	87.5	87.5	87.5	87.5	87.7	88.8	88.8	89.2	88.8	89.0	89.8	89.9	89.9	89.0	90.5	90.1	88.6	87.5	87.7	28	M.  abscessus
29	9.5	9.5	9.5	9.7	10.6	10.0	8.0	9.5	9.7	10.8	10.8	10.8	11.5	11.5	11.7	10.1	10.4	10.6	10.4	10.4	11.5	10.4	9.7	9.1	11.3	11.3	14.6	13.7	—	100.0	100.0	100.0	100.0	99.8	90.9	91.7	92.0	90.9	91.7	92.2	92.0	91.8	92.0	92.8	93.4	92.2	91.8	88.0	29	M.  tuberculosis
30	9.5	9.5	9.5	9.7	10.6	10.0	8.0	9.5	9.7	10.8	10.8	10.8	11.5	11.5	11.7	10.1	10.4	10.6	10.4	10.4	11.5	10.4	9.7	9.1	11.3	11.3	14.6	13.7	0.0	—	100.0	100.0	100.0	99.8	90.9	91.7	92.0	90.9	91.7	92.2	92.0	91.8	92.0	92.8	93.4	92.2	91.8	88.0	30	M.  tuberculosis
31	9.5	9.5	9.5	9.7	10.6	10.0	8.0	9.5	9.7	10.8	10.8	10.8	11.5	11.5	11.7	10.1	10.4	10.6	10.4	10.4	11.5	10.4	9.7	9.1	11.3	11.3	14.6	13.7	0.0	0.0	—	100.0	100.0	99.8	90.9	91.7	92.0	90.9	91.7	92.2	92.0	91.8	92.0	92.8	93.4	92.2	91.8	88.0	31	M.  bovis
32	9.5	9.5	9.5	9.7	10.6	10.0	8.0	9.5	9.7	10.8	10.8	10.8	11.5	11.5	11.7	10.1	10.4	10.6	10.4	10.4	11.5	10.4	9.7	9.1	11.3	11.3	14.6	13.7	0.0	0.0	0.0	—	100.0	99.8	90.9	91.7	92.0	90.9	91.7	92.2	92.0	91.8	92.0	92.8	93.4	92.2	91.8	88.0	32	M.  africanum
33	9.5	9.5	9.5	9.7	10.6	10.0	8.0	9.5	9.7	10.8	10.8	10.8	11.5	11.5	11.7	10.1	10.4	10.6	10.4	10.4	11.5	10.4	9.7	9.1	11.3	11.3	14.6	13.7	0.0	0.0	0.0	0.0	—	99.8	90.9	91.7	92.0	90.9	91.7	92.2	92.0	91.8	92.0	92.8	93.4	92.2	91.8	88.0	33	M.  bovis
34	9.3	9.3	9.3	9.5	10.4	9.7	7.8	9.3	9.5	10.6	10.6	10.6	11.2	11.2	11.5	9.9	10.2	10.4	10.2	10.2	11.2	10.2	9.5	8.9	11.1	11.0	14.4	13.5	0.2	0.2	0.2	0.2	0.2	—	91.1	91.8	92.2	90.7	91.8	92.4	91.8	91.7	91.8	92.6	93.2	92.0	91.7	88.0	34	M.  canettii
35	9.1	9.1	8.4	8.4	9.5	9.1	7.6	8.2	8.2	9.1	9.1	9.3	9.9	9.9	12.2	8.9	9.3	9.3	9.1	9.1	10.4	10.2	8.2	9.1	10.2	11.0	12.6	12.1	9.8	9.8	9.8	9.8	9.8	9.5	—	92.2	92.4	90.7	91.7	92.0	91.1	91.1	90.5	91.8	93.0	91.5	90.9	87.7	35	M.  xenopi
36	6.3	6.3	5.7	5.5	6.7	5.9	5.3	6.5	5.9	7.8	7.8	7.2	8.4	8.4	10.6	7.2	7.4	7.6	7.4	7.4	9.1	6.5	6.5	6.5	5.7	8.2	12.6	12.1	8.9	8.9	8.9	8.9	8.9	8.7	8.2	—	99.4	93.0	95.6	94.7	93.9	94.3	94.1	95.1	95.8	94.7	93.7	88.6	36	M.  avium
37	6.1	6.1	5.5	5.3	6.5	6.1	5.5	6.7	5.7	8.0	8.0	7.6	8.6	8.6	10.1	7.4	7.2	7.8	7.6	7.6	8.9	6.3	6.3	6.1	5.7	7.8	12.1	11.7	8.4	8.4	8.4	8.4	8.4	8.2	8.0	0.6	—	93.5	95.4	95.1	94.5	94.9	94.5	95.4	96.0	95.3	93.9	88.8	37	M.  avium
38	9.3	9.3	8.4	9.3	9.3	9.9	7.4	8.4	8.0	9.3	9.3	10.8	9.5	9.5	9.1	9.5	8.4	9.3	9.1	9.1	10.6	10.4	8.9	8.2	9.9	11.5	12.6	12.1	9.7	9.7	9.7	9.7	9.7	10.0	9.9	7.4	6.7	—	94.3	93.7	93.5	93.4	92.4	93.9	93.0	93.7	93.0	89.0	38	M.  malmoense
39	7.4	7.4	7.0	7.2	7.0	7.2	6.1	5.9	6.3	7.2	7.2	8.4	7.4	7.4	10.2	7.8	7.6	8.0	7.8	7.8	9.7	7.8	7.2	7.4	7.4	10.2	12.3	11.9	8.9	8.9	8.9	8.9	8.9	8.7	8.9	4.5	4.7	5.9	—	94.5	94.1	94.1	93.4	95.1	94.7	94.3	94.3	90.7	39	M.  intracellulare
40	7.6	7.6	6.7	7.2	7.4	8.4	5.3	6.7	7.6	8.4	8.4	8.4	8.6	8.6	10.1	8.0	7.2	7.6	7.4	7.4	9.7	7.6	7.8	6.7	7.6	9.5	11.5	11.0	8.2	8.2	8.2	8.2	8.2	8.0	8.4	5.5	5.1	6.5	5.7	—	94.3	94.3	94.9	95.1	95.4	93.9	93.4	89.6	40	M.  scrofulaceum
41	7.8	7.8	7.2	7.4	6.8	8.6	6.5	7.2	7.0	9.5	9.5	8.9	9.1	9.1	11.2	7.8	7.8	8.4	8.2	8.2	10.8	8.2	7.0	7.6	8.7	9.9	11.2	10.8	8.4	8.4	8.4	8.4	8.4	8.7	9.5	6.3	5.7	6.8	6.1	5.9	—	99.6	94.5	96.0	95.6	95.6	93.7	89.6	41	M.  marinum
42	7.8	7.8	7.2	7.0	6.8	8.2	6.5	7.2	7.0	9.5	9.5	8.9	9.1	9.1	11.0	7.4	7.4	8.4	8.2	8.2	10.6	8.2	6.5	7.4	8.2	9.5	11.2	10.8	8.7	8.7	8.7	8.7	8.7	8.9	9.5	5.9	5.3	7.0	6.1	5.9	0.4	—	94.3	96.0	95.6	95.4	93.9	89.4	42	M.  ulcerans
43	8.0	8.0	7.6	7.6	7.4	9.1	6.7	7.4	7.2	9.3	9.3	9.5	9.3	9.3	11.0	9.3	8.9	9.3	9.1	9.1	11.2	8.6	8.2	7.4	8.4	11.0	12.6	11.9	8.4	8.4	8.4	8.4	8.4	8.7	10.1	6.1	5.7	8.0	7.0	5.3	5.7	5.9	—	94.3	95.3	95.1	93.4	89.0	43	M.  gordonae
44	7.0	7.0	6.5	6.7	6.5	7.4	6.3	7.0	6.3	8.6	8.6	8.6	8.9	8.9	11.7	8.0	7.6	8.4	8.2	8.2	9.9	7.8	6.5	7.0	8.0	8.4	10.6	10.1	7.6	7.6	7.6	7.6	7.6	7.8	8.6	5.1	4.7	6.3	5.1	5.1	4.1	4.1	5.9	—	95.6	95.4	94.5	90.1	44	M.  szulgai
45	7.0	7.0	6.5	6.5	7.0	7.2	5.9	6.7	6.7	9.1	9.1	8.0	8.6	8.6	10.6	6.7	7.6	8.0	7.8	7.8	9.3	7.4	6.3	6.1	7.0	8.9	11.0	10.6	7.0	7.0	7.0	7.0	7.0	7.2	7.4	4.3	4.1	7.4	5.5	4.7	4.5	4.5	4.9	4.5	—	96.4	94.7	88.8	45	M.  asiaticum
46	8.0	8.0	7.4	7.6	7.4	8.6	7.8	8.0	7.6	10.4	10.4	9.7	9.3	9.3	11.2	9.1	9.1	9.3	9.1	9.1	9.7	8.9	8.0	7.2	8.2	9.9	12.8	12.3	8.2	8.2	8.2	8.2	8.2	8.5	9.1	5.5	4.9	6.5	5.9	6.3	4.5	4.7	5.1	4.7	3.7	—	95.8	88.8	46	M.  kansasii
47	7.6	7.6	7.6	7.4	8.4	9.1	7.0	8.2	7.6	8.9	8.9	10.8	10.1	10.1	11.9	9.7	9.5	8.4	8.2	8.2	10.8	9.7	8.9	8.0	9.1	10.4	14.2	13.7	8.7	8.7	8.7	8.7	8.7	8.9	9.7	6.5	6.3	7.4	5.9	7.0	6.6	6.3	7.0	5.7	5.5	4.3	—	87.9	47	M.  gastri
48	11.7	11.7	11.5	11.7	11.2	13.0	10.4	9.7	11.7	11.9	11.9	12.8	11.0	11.0	13.5	12.6	10.6	11.7	11.9	11.9	11.2	11.7	11.9	11.7	12.8	14.2	14.2	13.5	13.0	13.0	13.0	13.0	13.0	13.0	13.5	12.4	12.1	11.9	9.9	11.2	11.2	11.5	11.9	10.6	12.1	12.1	13.2	—	48	Rhodococcus equi
	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48