TABLE 1.
Comparison of mycobacterial isolates identified by biochemical test panels, Accuprobes, and 16S rRNA gene sequencing to direct identification by hsp65 sequencing in primary liquid detection mediaa
| Identification by current algorithm | hsp65 identification from in-house database | Comment |
|---|---|---|
| M. abscessus (36) | M. abscessus (34) | Nine isolates identical to M. abscessus var. VM585 |
| M. mucogenicum (1) | Confirmed by NRCM as M. mucogenicum | |
| M. porcinum (1) | Confirmed by NRCM as M. porcinum | |
| M. asiaticum (2) | M. asiaticum (2) | |
| M. avium-M. intracellulareb complex (318) | M. avium (224) | |
| M. avium variant MS586 (5) | hsp65 sequence variant of M. avium | |
| M. avium complex group B8 (1) | Taxonomic group | |
| M. chimaera (1) | Confirmed by NRCM as M. chimaera | |
| M. intracellulare (79) | ||
| M. intracellulare X variant (7) | Putative variant of M. intracellulare | |
| Unable to amplify hsp65 gene (1) | Cause unknown | |
| M. branderic (4) | M. branderi (4) | |
| M. chelonae (7) | M. chelonae (5) | |
| M. abscessus (1) | Resembles M. abscessus by repeat biochemical testing | |
| Tsukamurella species (1) | Tsukamurella species on solid culture media | |
| M. chimaerac (1) | M. chimaera (1) | |
| M. fortuitum (9) | M. fortuitum (9) | |
| M. fortuitum complex (7) | M. fortuitum (5) | |
| M. peregrinum (1) | Confirmed by NRCM as M. peregrinum | |
| M. septicum (1) | Confirmed by 16S rRNA sequencing | |
| M. frederiksbergensec (1) | M. frederiksbergense (1) | |
| M. gastri (1) | M. gastri (1) | |
| M. goodiic (3) | M. goodii (3) | |
| M. gordonaeb (77) | M. gordonae sensu stricto (16) | |
| M. gordonae group I (16) | ||
| M. gordonae group II (27) | ||
| M. gordonae variant MS460 (18) | ||
| M. haemophilumc (1) | M. haemophilum (1) | |
| M. hassiacumc (1) | M. hassiacum (1) | |
| M. heckeshornensec (4) | M. heckeshornense (4) | |
| M. hiberniaec (1) | M. hiberniae (1) | |
| M. immunogenumc (2) | M. abscessus (2) | Full-fragment 16S rRNA sequencing; GenBank M. abscessus DSM 44196T (GenBank accession no. AJ536038), 99.8% match |
| M. interjectum (1) | M. interjectum (1) | |
| M. kansasii (4) | M. kansasii (3) | |
| M. gastri (1) | hsp65 GenBank match with M. kansasii type 3 (GenBank accession no. AY438087) | |
| M. lentiflavumc (1) | M. lentiflavum (1) | |
| M. malmoensec (2) | M. malmoense (2) | |
| M. marinum (4) | M. marinum (4) | |
| M. montefiorensec (1) | M. triplex “isolate 23” (1) | M. triplex “isolate 23” by full 16S rRNA gene sequencing |
| M. mucogenicumc (3) | M. mucogenicum (3) | |
| M. nebraskensec (2) | M. nebraskense (2) | |
| M. parascrofulaceumc (2) | M. parascrofulaceum (2) | |
| M. peregrinum (3) | M. peregrinum (3) | |
| M. scrofulaceum (3) | M. scrofulaceum (3) | |
| M. shimoideic (1) | M. shimoidei (1) | |
| M. simiae (7) | M. simiae (5) | |
| M. simiae VM938 (2) | hsp65 sequence variant of M. simiae | |
| Mycobacterium species, uniquec (5) | Mycobacterium species, unique (3) | |
| M. mucogenicum (1) | ||
| Mycobacterium species strain MCRO 6 (1) | ||
| M. szulgai (5) | M. szulgai (4) | |
| Mycobacterium species, unique (1) | Assumed to be M. szulgai variant | |
| M. terrae (9) | M. terrae (7) | |
| M. terrae variant VM372 (1) | ||
| M. terrae variant MS699 (1) | ||
| M. terrae complex (7) | M. terrae (3) | |
| Mycobacterium species strain MCRO 6 (3) | ||
| Mycobacterium species strain MCRO 6 variant (1) | ||
| M. triplex (1) | M. triplex (1) | |
| M. triviale (3) | M. terrae (2) | Confirmed by NRCM as M. terrae |
| M. terrae variant VM372 (1) | Confirmed by NRCM as M. terrae | |
| M. tuberculosisb (70) complex | M. tuberculosis complex (70) | |
| M. xenopi (5) | M. xenopi (5) | |
| Nocardia species (3) | Nocardia species (3) | Confirmed by biochemical testing |
| Tsukamurella species (16) | Tsukamurella species (16) | Confirmed by NRCM as Tsukamurella spp. |
| PLDM yielded mixed cultures (22) | Refer to Table 2 | |
| No organisms seen in PLDM smear (2) | No amplification of hsp65 (2) | |
| Acid-fast organism seen in PLDM smear, no growth on subculture (12) | No amplification of hsp65 (12) | |
| Acid-fast organism seen in PLDM smear, nonmycobacteria grown on culture (2) | Gordonia species (1) | Gordonia bronchialis by 16S rRNA gene sequencing of subculture |
| No amplification (1) |
a
Numbers in parentheses represent the numbers of isolates identified as a particular species.
b
Identity determined by group- or species-specific Accuprobe test.
c
Primary identification determined by 16S rRNA gene sequencing performed at NRCM.