TABLE 2.
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 (% [avg range]) | Sequence-based identification (no. of isolates) | ||
| M. avium-M. intracellulare complex | 5 | 20 | 1.0-1.79 | M. avium-M. intracellulare-M. paratuberculosis (1), M. gastri-M. kansasii (1), M. simiae-M. genavense (3) |
| M. avium-M. intracellulare- M. scrofulaceum complex | 10 | 30 | 1.2-1.96 | M. scrofulaceum (2), M. simiae-M. genavense (3), M. intracellulare-M. szulgai-M. conspicuum (1), M. celatum (1), M. malmoense (2), M. moriokaense (1) |
| M. aurum | 8 | 50 | 1.2-2.59 | M. neoaurum-M. diernhoferi (4), M. mucogenicum-M. farcinogenes (1), M. tokaiense-M. porcinum (1), M. flavescens-M. austroafricanum (1), M. madagascariense (1) |
| M. celatum | 3 | 100 | 1.1-4.6 | M. celatum (3) |
| M. chelonae | 1 | 100 | 1.0 | M. chelonae-M. abscessus (1) |
| M. flavescens | 3 | 0 | 1.19-2.65 | M. moriokaense (2), M. tokaiense-M. murale (1) |
| M. fortuitum | 1 | 0 | 1.79 | M. simiae/M. genavense (1) |
| M. gordonae | 4 | 100 | 1.17-2.54 | M. gordonae (4) |
| M. interjectum | 2 | 0 | 1.0 | M. simiae-M. genavense (2) |
| M. kansasii | 3 | 100 | 1.56-3.50 | M. kansasii-M. gastri (3) |
| M. lentiflavum | 9 | 0 | 1.0-1.29 | M. simiae-M. genavense (9) |
| M. malmoense | 2 | 0 | 1.0-1.36 | M. terrae (1), M. simiae-M. genavense (1) |
| M. mucogenicum | 3 | 100 | 1.0-1.40 | M. mucogenicum (3) |
| M. nonchromogenicum | 12 | 75 | 1.16-2.91 | M. nonchromogenicum (9), M. hiberniae (2), M. neoaurum-M. diernhoferi (1) |
| M. scrofulaceum | 4 | 0 | 1.39-2.18 | M. pulveris (1), M. goodii (1), M. thermoresistibile (1), M. simiae- M. genavense (1) |
| M. smegmatis | 2 | 0 | 2.20-2.59 | M. madagascariense (1), M. chitae (1) |
| M. terrae | 10 | 40 | 1.16-2.37 | M. terrae (4), M. nonchromogenicum (5), M. tokaiense-M. murale (1) |
| M. triplex | 1 | 0 | 2.79 | M. simiae-M. genavense (1) |
| M. triviale | 1 | 100 | 2.40 | M. triviale (1) |
| M. xenopi | 1 | 0 | 4.06 | M. celatum (1) |
a
Sequence identification concordant with identification to species level or complex or group level.