Table 1.
Concordance between single WGS and routine laboratory methods for mycobacterial speciation
| n | ||
|---|---|---|
| Routine methods and WGS identification failed | 9 | |
| Routine methods failed | 2* | |
| Identified by routine methods | 345 (100%) | |
| Concordant | 322 (93%) | |
| M tuberculosis complex | 157 (46%) | |
| M avium complex | 71 (21%) | |
| M abscessus complex | 39 (11%) | |
| M gordonae | 18 (5%) | |
| M xenopi | 11 (3%) | |
| M tuberculosis complex (BCG) | 8 (2%) | |
| M kansasii | 6 (2%) | |
| M malmoense | 3 (1%) | |
| M fortuitum | 2 (1%) | |
| M szulgai | 2 (1%) | |
| M tuberculosis complex (M africanum) | 2 (1%) | |
| M celatum | 1 (<1%) | |
| M lentiflavum | 1 (<1%) | |
| M tuberculosis complex and M avium complex | 1 (<1%) | |
| Part concordant | 10 (3%) | |
| WGS gained one species | 5 (1%)† | |
| WGS missed one species | 3 (1%)‡ | |
| WGS identified related species | 1 (<1%)§ | |
| WGS identified subspecies | 1 (<1%)¶ | |
| Discordant | 3 (1%)‖ | |
| WGS failed | 10 (3%) | |
Data in parentheses are % of specimens identified by routine methods. M=Mycobacterium. WGS=whole-genome sequencing.
WGS identified M avium complex (good quality WGS; 32 [97%] of 33 genes identified) and M kumamotonense (poor quality WGS; 58 [58%] of 100 genes identified).
One routine M tuberculosis complex (MTBC): WGS identified MTBC plus M avium complex (retesting not possible); three routine M avium complexes: WGS identified MTBC plus M avium complexes (two retesting supported routine; one supported WGS); one routine M abscessus complex: WGS identified M abscessus plus M avium complex (retesting supported routine); appendix.
One routine MTBC plus M avium complex: WGS identified MTBC (retesting supported WGS); two routine MTBC plus M avium complex: WGS M avium complex (one poor quality WGS; two [6%] of 33 genes identified; one unable to retest); appendix.
One undescribed mycobacterial species similar to M avium: WGS identified M avium complex (appendix).
One routine M fortuitum: WGS identified M fortuitum-acetamidolyticum (poor quality WGS; 33 [33%] of 100 genes identified); appendix.
One routine M kansasii: WGS identified M avium complex (routine testing subsequently confirmed M avium complex); one routine M avium complex: WGS M scrofulaceum (poor quality WGS; one [1%] of 72 genes identified); one routine MTBC: WGS identified M abscessus complex (good quality WGS; 38 [95%] of 40 genes identified; unable to retest specimen); appendix.