TABLE 1.
Comparison of mycobacterial identification by conventional methods and nucleic acid sequencing
| Organism(s) identified by phenotypic methods | No. of isolates | Result obtained when organisms were identified to species level or group or complex level by using <1% match score and MicroSeq 500 database
|
||
|---|---|---|---|---|
| % Concordant resultsa | Distance score range (%) | Sequencing-based identification (no. of isolates) | ||
| M. abscessusb | 1 | 100 | 0.0 | M. chelonae-M. abscessus (1) |
| M. avium-M. intracellulare complex | 6 | 66.7 | 0-0.97 | M. avium (1), M. malmoense (1), M. paratuberculosis (3), M. simiae-M. genavense (1) |
| M. avium-M. intracellulare- M. scrofulaceum complex | 11 | 54.5 | 0-0.79 | M. scrofulaceum (6), M. gilvum (1), M. intermedium (1), M. kansasii-M. gastri (1), M. novocastrense (2) |
| M. alvei | 1 | 100 | 0.2 | M. alvei (1) |
| M. asiaticum | 11 | 100 | 0-0.78 | M. asiaticum (11) |
| M. aurum | 7 | 85.7 | 0-0.2 | M. neoaurum (6), M. obuense (1) |
| M. celatum | 3 | 66.6 | 0.19 | M. celatum (2), M. simiae-M. genavense (1) |
| M. chelonae | 7 | 85.7 | 0-0.60 | M. chelonae-M. abscessus (6), M. porcinum (1) |
| M. chelonae-M. abscessus | 18 | 100 | 0-0.6 | M. chelonae-M. abscessus (18) |
| M. flavescens | 1 | 100 | 0.38 | M. novocastrense (1) |
| M. fortuitum-M. peregrinum | 8 | 100 | 0-0.2 | M. farcinogenes (3), M. septicum-M. peregrinum (3), M. porcinum (2) |
| M. fortuitum | 10 | 80.0 | 0-0.6 | M. fortuitum-M. fortuitum subsp., M. acetamidolyticum (6), M. peregrinum (2), M. mageritense (1), M. alvei (1) |
| M. gastri | 1 | 100 | 0 | M. kansasii-M. gastri (1) |
| M. gordonae | 5 | 100 | 0-0.78 | M. gordonae (5) |
| M. haemophilum | 8 | 100 | 0-0.58 | M. haemophilum (8) |
| M. hassiacum | 1 | 100 | 0 | M. hassicum (1) |
| M. interjectum | 7 | 57.1 | 0-0.80 | M. interjectum (4), M. simiae-M. genavense (3) |
| M. intermedium | 1 | 100 | 0.20 | M. intermedium (1) |
| M. kansasii | 6 | 100 | 0-0.39 | M. kansasii-M. gastri (6) |
| M. mageritense | 5 | 100 | 0-0.20 | M. mageritense (5) |
| M. malmoense | 5 | 80 | 0 | M. malmoense (4) M. novocastrense (1) |
| M. marinum | 7 | 100 | 0 | M. marinum (7) |
| M. mucogenicum | 18 | 100 | 0-0.97 | M. mucogenicum (18) |
| M. nonchromogenicum | 9 | 100 | 0.97 | M. nonchromogenicum (9) |
| M. obuense | 1 | 100 | 0 | M. obuense (1) |
| M. peregrinum | 2 | 100 | 0 | M. peregrinum-M. septicum (1), M. farcinogenes (1) |
| M. porcinum | 1 | 100 | 0 | M. porcinum (1) |
| M. scrofulaceum | 11 | 42.8 | 0.30-0.59 | M. scrofulaceum (4), M. pulveris (1), M. neoaurum (1), M. gilvum (1), M. novocastrense (4) |
| M. simiae | 15 | 100 | 0.0-0.80 | M. simiae-M. genavense (14) |
| M. shimodei | 2 | 100 | 0 | M. shimodei (2) |
| M. smegmatis | 10 | 100 | 0-0.20 | M. smegmatis (3), M. mageritense (1), M. goodii (6) |
| M. szulgai | 9 | 100 | 0-0.19 | M. szulgai (9) |
| M. tuberculosis | 8 | 100 | 0-0.58 | M. tuberculosis (8) |
| M. terrae | 8 | 100 | 0-0.97 | M. terrae (8) |
| M. thermoresistibile | 3 | 100 | 0 | M. thermoresistibile (3) |
| M. triplex | 6 | 100 | 0-0.20 | M. triplex (6) |
| M. wolinskyi | 1 | 100 | 0.20 | M. wolinskyi (1) |
| M. xenopi | 9 | 100 | 0.1-0.91 | M. xenopi (9) |
a
Sequencing identification concordant with identification to species level or complex or group level.
b
Known isolate confirmed by PRA.