BioMed Research International / 2015 / Article / Tab 2 / Research Article
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