TABLE 1.
Results of testing by NG-Test CARBA 5, Xpert Carba-R, and mCIM/CIMTris compared with WGS as the reference method
| Bacterial species | Genotype by WGS a | No. of isolates | No. (%) concordant on NG-Test CARBA 5 | No. (%) concordant on Xpert Carba-R | No. (%) concordant by mCIM/ CIMTris b | |
|---|---|---|---|---|---|---|
| CP c status | Carbapenemase gene(s) | |||||
| Pseudomonas aeruginosa | Non-CP | None | 21 | 21 (100) | 21 (100) | 20 (95.2) |
| CP | blaNDM-1 | 71 | 70 (98.6) | 71 (100) | 71 (100) | |
| blaIMP-1 | 18 | 18 (100) | 18 (100) | 18 (100) | ||
| bla IMP-7 d | 6 | 6 (100) | 0 (0) | 6 (100) | ||
| bla IMP-13 d | 1 | 1 (100) | 0 (0) | 1 (100) | ||
| blaVIM-2 | 17 | 17 (100) | 17 (100) | 6 (35.3) | ||
| blaVIM-6 | 1 | 1 (100) | 1 (100) | 1 (100) | ||
| blaGES-5 | 2 | 0 (0) | 0 (0) | 1 (50) | ||
| blaNDM-1, blaOXA-48 | 1 | 0 (0) e | 0 (0) e | 1 (100) | ||
| On-panel (Xpert/ CARBA 5) “big five” CP types |
115 | 113 (98.3) | 107 (93.0) | 104 (90.4) | ||
| All CP types | 117 | 113 (96.6) | 107 (91.5) | 105 (89.7) | ||
| Total | 138 | 134 (97.1) | 128 (92.8) | 125 (90.6) | ||
| Acinetobacter baumannii complex | CP |
blaOXA-23 family,
f
blaOXA-51
family g |
88 | 0 (0) h | 0 (0) | 88 (100) |
|
blaOXA-23 family
f
, blaOXA-51
family g , blaOXA-72 |
1 | 0 (0) h | 0 (0) | 1 (100) | ||
| blaOXA-51 family g | 2 | 0 (0) h | 0 (0) | 1 (50) | ||
| blaNDM-1, blaOXA-51 family g , blaOXA-58 | 2 | 2 (100) | 2 (100) | 2 (100) | ||
| blaNDM-1, blaOXA-23 family f , blaOXA-51 family g | 1 | 1 (100) | 1 (100) | 1 (100) | ||
| blaNDM-1, blaOXA-51 family g | 1 | 1 (100) | 1 (100) | 1 (100) | ||
| blaNDM-1, blaOXA-58 | 1 | 1 (100) h | 1 (100) | 1 (100) | ||
| blaNDM-1, blaOXA-23 family f , blaOXA-58, blaOXA-51 family g | 1 | 1 (100) h | 1 (100) | 1 (100) | ||
| All CP types | 97 | 6 (6.2) | 6 (6.2) i | 96 (99.0) | ||
By multilocus sequence typing (MLST), the following STs were present: for CRPA, STs 111, 234, 235, 244, 253, 262, 307, 308, 313, 357, 377, 381, 399, 446, 606, 621, 823, 827, 1119, 1123, 1232, 1816, 2434, 3118; for CRAB, STs 1, 2, 25, 103, 149, 150, 164, 218, 782.
mCIM performed on CRPA isolates; CIMTris performed on CRAB isolates. All indeterminate results counted as positive.
CP, carbapenemase-producing.
The Xpert Carba-R package insert dated July 2020 (Table 19) states that IMP-7/13/14 genes were not detectable in a prior study of performance characteristics and were not predicted to be detected by in silico analysis.
Both NG-Test CARBA 5 and Xpert Carba-R detected NDM, but did not detect OXA-48.
AMRFinderPlus was unable to identify the exact OXA-23 family variant for four isolates, while all other isolates carried blaOXA-23.
OXA-51 family genes identified in our study cohort included blaOXA-51, blaOXA-64, blaOXA-65, blaOXA-66, blaOXA-69, blaOXA-70, blaOXA-91, blaOXA-104, and blaOXA-121. 85 isolates carried either blaOXA-66, blaOXA-69, or blaOXA-91. AMRFinderPlus was unable to identify the exact OXA-51 family variant for another four isolates.
CARBA five testing returned false-positive results for IMP on nearly all the test isolates (see Table 2 and Discussion), including two which were also true positive for NDM.
Xpert Carba-R detected 100% of on-panel targets (KPC/OXA-48/NDM/IMP/VIM).