Table 3.
A species identification algorithm by combining rpo B duplex PCR and hsp65 PCR-restriction fragment length polymorphism analysis
| |
rpo B DPCR-RFLP |
hsp 65 RFLP |
Final species identification |
||
|---|---|---|---|---|---|
| Pattern | MspI | HaeIII | BstEII | Hae III | |
|
A |
136 |
136 |
440 / 0 / 0 |
160 / 90 / 60 / 0 |
M. vaccae type 1 |
| |
|
|
440 / 0 / 0 |
160 / 85 / 55 / 0 |
M. flavescens type 3 |
| |
|
|
440 / 0 / 0 |
140 / 55 / 50 / 0 |
M. flavescens type 1 |
| |
|
|
440 / 0 / 0 |
130 / 115 / 70 / 60 |
M. aurum type 2 |
| |
|
|
320 / 130 / 0 |
200 / 70 / 60 / 55 |
M. immunogenum type 2 |
| |
|
|
320 / 130 / 0 |
200 / 60 / 55 / 50 |
M. chelonae type 1 |
| |
|
|
320 / 130 / 0 |
145 / 70 / 60 / 55 |
M. immunogenum type 1 |
| |
|
|
320 / 130 / 0 |
140 / 65 / 60 / 0 |
M. mucogenicum type 1 |
| |
|
|
320 / 115 / 0 |
185 / 145 / 0 / 0 |
M. fallax type 1 |
| |
|
|
320 / 115 / 0 |
170 / 140 / 0 / 0 |
M. neoaurum type 1 |
| |
|
|
320 / 115 / 0 |
145 / 65 / 60 / 0 |
M. mucogenicum type 2 |
| |
|
|
320 / 115 / 0 |
140 / 90 / 60 / 0 |
M. mucogenicum type 3 |
| |
|
|
235 / 210 / 0 |
200 / 70 / 60 / 50 |
M. abscessus type 2 |
| |
|
|
235 / 210 / 0 |
180 / 135 / 70 / 50 |
M. thermoresistibile type 1 |
| |
|
|
235 / 210 / 0 |
145 / 140 / 100 / 50 |
M. peregrinum type 1 |
| |
|
|
235 / 210 / 0 |
145 / 70 / 60 / 55 |
M. abscessus type 1 |
| |
|
|
235 / 210 / 0 |
140 / 125 / 100 / 50 |
M. peregrinum type 2 |
| |
|
|
235 / 210 / 0 |
140 / 125 / 60 / 50 |
M. senegalense type 3 |
| |
|
|
235 / 210 / 0 |
140 / 80 / 60 / 50 |
M. phlei type 1 |
| |
|
|
235 / 210 / 0 |
130 / 80 / 60 / 0 |
M. celatum type 1 |
| |
|
|
235 / 130 / 85 |
175 / 80 / 0 / 0 |
M. aurum type 1 |
| |
|
|
235 / 130 / 85 |
145 / 140 / 100 / 60 |
M. peregrinum type 3 |
| |
|
|
235 / 130 / 85 |
145 / 125 / 60 / 0 |
M. smegmatis type 1 |
| |
|
|
235 / 130 / 85 |
140 / 125 / 60 / 50 |
M. senegalense type 2 |
| |
|
|
235 / 120 / 85 |
180 / 140 / 50 / 0 |
M. senegalense type 4 |
| |
|
|
235 / 120 / 85 |
145 / 120 / 60 / 55 |
M. fortuitum type 1 |
| |
|
|
235 / 120 / 85 |
140 / 125 / 60 / 50 |
M. senegalense type 1 |
| |
|
|
235 / 120 / 85 |
140 / 120 / 60 / 55 |
M. fortuitum type 2 |
| |
|
|
235 / 120 / 85 |
135 / 90 / 85 / 0 |
M. fortuitum type 3 |
|
B |
136 |
108,28 |
320 / 115 / 0 |
140 / 90 / 60 / 0 |
M. chitae type 1 |
| |
|
|
235 / 210 / 0 |
145 / 130 / 0 / 0 |
M. avium subsp. avium type 3 |
| |
|
|
235 / 210 / 0 |
130 / 105 / 60 / 0 |
M. avium subsp. avium type 2 |
| |
|
|
235 / 210 / 0 |
130 / 105 / 0 / 0 |
M. avium subsp. avium type 1 |
| |
|
|
235 / 210 / 0 |
130 / 105 / 0 / 0 |
M. avium subsp. paratuberculosis type 1 |
|
C |
136 |
76,60 |
235 / 120 / 85 |
160 / 105 / 60 / 0 |
M. xenopi type 1 |
|
D |
75,61 or |
136 |
440 / 0 / 0 |
170 / 130 / 0 / 0 |
M. triviale type 1 |
| |
75,57,4 |
|
320 / 115 / 0 |
130 / 95 / 75 / 60 |
M. kansasii type 5 |
| |
|
|
235 / 210 / 0 |
190 / 105 / 80 / 0 |
M. ulcerans type 2 |
| |
|
|
(235 / 210 / 0 |
145 / 130 / 95 / 0 |
M. scrofulaceum type 1*) |
| |
|
|
235 / 210 / 0 |
145 / 105 / 80 / 45/20 |
M. marinum type 1 |
| |
|
|
235 / 210 / 0 |
145 / 105 / 80 / 0 |
M. ulcerans type 1 |
| |
|
|
235 / 210 / 0 |
130 / 105 / 80 / 0 |
M. kansasii type 1 |
| |
|
|
235 / 130 / 85 |
140 / 105 / 70 / 0 |
M. shimodei type 1 |
| |
|
|
235 / 120 / 85 |
130 / 115 / 75 / 60 |
M. kansasii type 4 |
| |
|
|
235 / 130 / 85 |
130 / 105 / 70 / 0 |
M. kansasii type 6 |
| |
|
|
235 / 130 / 85 |
130 / 105 / 0 / 0 |
M. kansasii type 2 |
| |
|
|
235 / 130 / 85 |
130 / 95 / 70 / 0 |
M. kansasii type 3 |
|
E |
75,61 or |
108,28 |
440 / 0 / 0 |
145 / 130 / 0 / 0 |
M. simiae type 5 |
| |
75,57,4 |
|
320 / 115 / 0 |
185 / 140 / 0 / 0 |
M. terrae type 2 |
| |
|
|
320 / 115 / 0 |
180 / 130 / 0 / 0 |
M. terrae type 1 |
| |
|
|
320 / 115 / 0 |
145 / 130 / 0 / 0 |
M. simiae type 4 |
| |
|
|
320 / 115 / 0 |
140 / 90 / 60 / 0 |
M. nonchromogenicum type 2 |
| |
|
|
320 / 115 / 0 |
140 / 60 / 50 / 0 |
M. terrae type 3 |
| |
|
|
320 / 115 / 0 |
125 / 105 / 0 / 0 |
M. genavense type 1 |
| |
|
|
235 / 210 / 0 |
185 / 130 / 0 / 0 |
M. simiae type 1 |
| |
|
|
235 / 210 / 0 |
185 / 130 / 0 / 0 |
M. genavense type 2 |
| |
|
|
235 / 210 / 0 |
155 / 140 / 0 / 0 |
M. simiae type 2 |
| |
|
|
235 / 210 / 0 |
145 / 130 / 0 / 0 |
M. simiae type 6 |
| |
|
|
235 / 210 / 0 |
140 / 115 / 70 / 0 |
M. terrae type 4 |
| |
|
|
235 / 130 / 85 |
145 / 130 / 0 / 0 |
M. simiae type 3 |
| |
|
|
235 / 130 / 85 |
130 / 105 / 70 / 0 |
M. gastri type 1 |
| |
|
|
235 / 120 / 85 |
145 / 60 / 55 / 0 |
M. nonchromogenicum type 1 |
|
F |
75,61 or |
76,60 |
440 / 0 / 0 |
130 / 105 / 70 / 0 |
M. szulgai type 1 |
| |
75,57,4 |
|
(320 / 115 / 0 |
130 / 115 / 60 / 0 |
M. gordonae type 4*) |
| |
|
|
240/210/0 |
130/110/0 |
M. interjectum |
| |
|
|
(235 / 210 / 0 |
145 / 130 / 0 / 0 |
M. intracellulare type 3*) |
| |
|
|
235 / 210 / 0 |
115 / 105 / 0 / 0 |
M. asiaticum type 1 |
| |
|
|
235 / 130 / 85 |
130 / 105 / 80 / 0 |
M. celatum type 2 |
| |
|
|
235 / 120 / 100 |
145 / 105 / 80 / 0 |
M. malmoense type 1 |
| |
|
|
235 / 210 / 0 |
145 / 105 / 80 / 0 |
M. malmoense type 2 |
| |
|
|
(235 / 120 / 100 |
130 / 115 / 0 / 0 |
M. gordonae type 3*) |
|
G |
75,61 or |
76,32,28 |
(440 / 0 / 0 |
145 / 130 / 0 / 0 |
M. simiae type 5*) |
| |
75,57,4 |
|
320 / 115 / 0 |
130 / 110 / 70 / 60 |
M. gordonae type 8 |
| |
|
|
320 / 115 / 0 |
130 / 115 / 60 / 0 |
M. gordonae type 4 |
| |
|
|
235 / 210 / 0 |
145 / 130 / 0 / 0 |
M. intermedium type 1 |
| |
|
|
235 / 210 / 0 |
145 / 130 / 0 / 0 |
M. intracellulare type 3 |
| |
|
|
235 / 210 / 0 |
140 / 105 / 80 / 0 |
M. intracellulare type 2 |
| |
|
|
235 / 210 / 0 |
130 / 115 / 0 / 0 |
M. gordonae type 5 |
| |
|
|
235 / 210 / 0 |
120 / 115 / 110 / 0 |
M. intracellulare type 4 |
| |
|
|
235 / 130 / 85 |
140 / 120 / 95 / 0 |
M. gordonae type 6 |
| |
|
|
235 / 120 / 100 |
160 / 115 / 60 / 0 |
M. gordonae type 9 |
| |
|
|
235 / 120 / 100 |
155 / 110 / 0 / 0 |
M. gordonae type 7 |
| |
|
|
235 / 120 / 100 |
145 / 130 / 60 / 0 |
M. intracellulare type 1 |
| |
|
|
235 / 120 / 100 |
130 / 115 / 0 / 0 |
M. gordonae type 3 |
| |
|
|
235 / 120 / 100 |
130 / 110 / 95 / 0 |
M. gordonae type 10 |
| |
|
|
235 / 120 / 85 |
160 / 115 / 60 / 0 |
M. gordonae type 1 |
| |
|
|
235 / 120 / 85 |
215 / 110 / 0 / 0 |
M. gordonae type 2 |
|
H |
75,61 or |
66,60,10 |
235 / 210 / 0 |
145 / 130 / 95 / 0 |
M. scrofulaceum type 1 |
| |
75,57,4 |
|
320 / 130 / 0 |
160 / 110 / 0 / 0 |
M. haemophilum type 1 |
|
T |
|
|
235 / 120 / 85 |
150 / 130 / 70 / 0 |
M. tuberculosis type 1 |
| (235 bp) | |||||
(*)species from Table 2 were included in this algorithm.