Evaluation of the EasyScreen™ ESBL/CPO Detection Kit for the Detection of ß-Lactam Resistance Genes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Media Tested
2.2. EasyScreen™ Sample Processing Kit
2.3. EasyScreen™ ESBL/CPO Detection Kit
2.4. Discrepant Results Analysis
2.5. Bacterial Isolates
2.6. Statistical Analysis
3. Results
3.1. Experimental Setup and Evaluation of Culture Media
3.2. Evaluation of the EasyScreenTM ESBL/CPO Detection Kit on Well Characterized Enterobacterales
3.3. Evaluation of the EasyScreenTM ESBL/CPO Detection Kit on Characterized Pseudomonas spp. Isolates
3.4. Evaluation of the EasyScreenTM ESBL/CPO Detection Kit on Characterized A. baumannii Isolates
3.5. Overall Assay Performance for Carbapenemase Detection Extrapolated to the French Epidemiology of CP-GNB
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Detection Channel | Mix A | Mix B | Mix C | Mix D | Mix E | Mix F |
---|---|---|---|---|---|---|
# 1 | TEM | GES | OXA-48 | MCR-1 | VIM | CMY |
# 2 | EC a | EC a | EC a | EC a | EC a | EC a |
# 3 | CTX-M | KPC | OXA-23-like | DHA | IMI | IMP |
# 4 | Not used | NDM | SHV | OXA-51-like | SME | Not used |
Species | Resistance Mechanism | EasyScreenTM ESBL/CPO Detection Kit Results | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
KPC | OXA-48 | NDM | VIM | IMP | SME | IMI | GES | CTX-M | TEM | SHV | DHA | CMY | OXA-23 | OXA-51 | Mcr-1 | ||
Non-targeted β-lactamase producers (17)a | |||||||||||||||||
E. coli (2) a, P. mirabilis (2), E. cloacae (3) H. alvei (2), S. marcescens (1) | ↗↗↗ b Case (7) a, pACC-1 (3) | - c | - | - | - | - | - | - | - | - | 1/1 | - | - c | - | - | - | - |
E. cloacae (3), P. mirabilis (1), C. freundii (2) | GIM-1, LMB-1, TMB-1, OXA-372, OXA-58 | - | - | - | - | - | - | - | - | - | 1/1 | - | - | 0/2 | - | - | - |
Targeted AmpC producers | |||||||||||||||||
E. coli (3), K. pneumoniae (2), M. morganii (1) | DHA (5), CMY-136 | - | - | - | - | - | - | - | - | - | 1/1 | 3/3 | 5/5 | 1/1 | - | - | - |
Targeted ESBLproducers | |||||||||||||||||
E. coli (32), K. pneumoniae (13), C. freundii (2), C. koseri (1), M. morganii (1), E. cloacae (4), P. mirabilis (1) | CTX-M-1(5), -2(3), -3(2), -8(2), -9(1), -10(1), -13(1), -14(3), -15(16), -17(1), -18(1), -19(1), -24(1), -27(2), -32(2), -37(1), -55(2), -57(1), -65(1), -71(2), -82(1), -93(1), 101(1), 182(1) | - | - | - | - | - | - | 52/54 | 29/29 | 11/13 | 1/1 | 1/3 | - | - | - | ||
K. pneumoniae | GES-1, | - | - | - | - | - | - | 1/1 | - | - | 1/1 | - | - | - | - | - | |
K. pneumoniae, E. cloacae, S. marcescens | OXA-163 (2), OXA-405 | - | 3/3 | - | - | - | - | - | - | - | 2/2 | 2/2 | - | - | - | - | - |
K. pneumoniae (6), C. freundii | SHV-2a (2), -11, -12, -36, -38, -99 | - | - | - | - | - | - | - | - | 1/1 | 3/3 | 7/7 | - | 1/1 | - | - | - |
E. coli (1), E. cloacae (1), K. aerogenes (2), C. freundii (2), K. pneumoniae (1), P. mirabilis | TEM-3 (4), -24(2), -52 (2) | - | - | - | - | - | - | - | - | - | 8/8 | 1/1 | - | 0/2 | - | - | - |
Targeted carbapenemase producers | |||||||||||||||||
P. mirabilis | OXA-23 | - | - | - | - | - | - | - | - | - | - | - | 1/1 | - | - | ||
S. marcescens (3) | Sme-1, Sme-2, Sme-4 | - | - | - | - | 3/3 | - | - | - | - | - | - | - | - | - | ||
E. cloacae complex (6) | IMI-1, IMI-2 (2), IMI-3, IMI-17, NMCA | - | - | - | - | - | 6/6 | - | - | - | - | - | - | - | - | ||
K. pneumoniae (1), E. cloacae (2),) | GES-5 (2), GES-6 | - | - | - | - | - | - | 3/3 | 1/1 | - | 2/2 | - | - | - | - | ||
E. coli (11), K. pneumoniae (4), E. cloacae (2), C. freundii, S. marcescens | KPC-2 (7), KPC-3 (4), KPC-5, KPC-6, KPC-7, KPC-14, KPC-28, KPC-31, KPC-33, KPC-39 | 19/19 | - | - | - | - | - | - | 4/4 | 9/9 | 4/4 | 0/1 | - | - | - | ||
E. coli (9), K. pneumoniae (1), S. enterica | NDM-1 (5), NDM-4, NDM-6, NDM-6, NDM-9, NDM-19 (2) | - | - | 11/11 | - | - | - | - | 8/8 | 9/9 | 1/1 | 2/2 | 4/4 | - | - | ||
E. coli (2), K. pneumoniae (3), E. cloacae, C. freundii (2) | VIM-1 (4), VIM-2 (2), VIM-4, VIM-19 | - | - | - | 8/8 | - | - | - | - | 1/1 | 3/3 | 4/4 | - | 1/3 | - | - | |
E. coli (3), K. pneumoniae (3), E. cloacae, S. marcescens | IMP-1 (2), IMP-8 (4), IMP-10, IMP-IMP-14 | - | - | - | - | 8/8 | - | - | - | - | 6/6 | 6/6 | - | - | - | - | |
E. coli (12), K. pneumoniae (11), E. cloacae, C. koseri, C. freundii (2), Shewanella sp. | OXA-48 (8), OXA-162, OXA-181 (2), OXA-204 (5), OXA-232 (2), OXA-244 (4), OXA-370, OXA-484, OXA-517, OXA-519, OXA-535, OXA-793 | 28/28 | 16/16 | 15/15 | 14/14 | 8/8 | |||||||||||
Targeted multiple carbapenemase producers | |||||||||||||||||
E. coli (3), K. pneumoniae (4), E. cloacae, C. freundii (2) | OXA-48-like + NDM-Like (6); OXA-48-like + VIM-like (3); OXA-48-like + KPC-28 | 1/1 | 10/10 | 6/6 | 3/3 | 8/8 | 7/7 | 5/5 | 0/2 | 1/1 | |||||||
K. pneumoniae | OXA-48-like + NDM-5 + VIM-1 | 1/1 | 1/1 | 1/1 | 1/1 | ||||||||||||
K. pneumoniae (2) | NDM + KPC (2) | 2/2 | 2/2 | 1/1 | 2/2 | 1/2 | |||||||||||
E. coli | NDM-1 + VIM-2 | 1/1 | 1/1 | 1/1 | |||||||||||||
K. pneumoniae | KPC-2 +VIM-1 | 1/1 | 1/1 | 1/1 | 1/1 | ||||||||||||
Plasmid-encoded colistin resistance | |||||||||||||||||
E. coli (6), K. pneumoniae, Salmonella (4) | mgrB mutation (6), mcr-3.2, mcr-4, mcr-5(2), mcr-2. | 1/1 | 3/3 | 1/1 | - | ||||||||||||
E. coli (6), K. pneumoniae (3), Salmonella sp. | Mcr-1 | - | 2/2 | 1/1 | - | - | - | - | - | 5/5 | 6/6 | 3/3 | - | - | - | - | 10/10 |
Total | 23/23 | 44/44 d | 22/22 | 14/14 | 8/8 | 3/3 | 6/6 | 4/4 e | 98/100 f | 107/107 g | 65/68 h | 8/8 | 16/27 i | 1/1 | 0/0 | 10/10 | |
Sensitivity | 100% (85.2% to 100%) | 100% (91.4% to 100%) | 100% (84.6% to 100%) | 100% (76.8% to 100%) | 100% (63.1% to 100%) | 100% (29.2% to 100%) | 100% (54.1% to 100%) | 100% (29.2% to 100%) | 98.0% (92.9% to 99.8%) | 7.5% (3.3% to 14.2% | 10.3% (4.24% to 20.1%) | 100% (63.1% to 100%) | 59.3% (38.8% to 77.6%) | 100% (2.5% to 100%) | 100% (69.2% to 100%) | ||
Specificity | 100% (98.1% to 100% | 98.3% (95.2% to 99.6% | 100% (98.1% to 100% | 100% (98.2% to 100% | 100% (98.3% to 100% | 100% (98.3% to 100% | 100% (98.3% to 100% | 99.5% (97.5% to 100% | 100% (96.9% to 100% | 100% (96.7% to 100% | 100% (97.6% to 100% | 100% (98.3% to 100% | 100% (98.1% to 100% | 100% (98.3% to 100% | 100% (98.3% to 100% | 100% (98.3% to 100% |
Species | β-Lactamase Content | EasyScreenTM ESBL/CPO Detection Kit Results | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
KPC | OXA-48 | NDM | VIM | IMP | SME | IMI | GES | CTX-M | TEM | SHV | DHA | CMY | OXA-23 | OXA-51 | Mcr-1 | ||
Non-targeted β-lactamase producers (22) a | |||||||||||||||||
P. aeruginosa (2) a | Mex A/B-OprM, Mex C/D-OprJ | - c | - | - | - | - | - | - | - | - | - | - | - c | - | - | ||
P. aeruginosa (4) | ↗↗↗ b Case + OprD deficient | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
P. aeruginosa (9) | BEL-1, VEB-1, PER-1, OXA-10, OXA-13, OXA-14, OXA-18/20, OXA-32, CARB-2 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
P. aeruginosa (7) | GIM-1, AIM-1, SPM-1, DIM-1 (2), PME-1, OXA-198 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Targeted ESBLproducers | |||||||||||||||||
P. aeruginosa | GES-9, | - | - | - | - | - | - | 1/1 | - | - | - | - | - | - | - | - | |
P. aeruginosa | CTX-M-2 | + | - | - | - | - | - | - | - | 1/1 | - | - | - | - | - | - | - |
P. aeruginosa (2) | SHV-2a, SHV-5 | + | - | - | - | - | - | - | - | - | - | 2/2 | - | - | - | - | - |
P. aeruginosa | TEM-4 | + | - | - | - | - | - | - | - | - | 1/1 | - | - | - | - | - | - |
Targeted carbapenemase producers | |||||||||||||||||
P. aeruginosa (3) | GES-2, GES-5, GES-14 | - | - | - | - | - | - | 3/3 | - | - | - | - | - | - | - | ||
P. aeruginosa (4) | KPC-2 (4) | 4/4 | - | - | - | - | - | - | - | - | - | - | - | - | - | ||
P. aeruginosa (2) | NDM-1 (2) | - | - | 2/2 | - | - | - | - | - | - | - | - | - | - | |||
P. aeruginosa (7), P. putida 2), P. stutzeri, P. fluorescens | VIM-1 (2), VIM-2 (7), VIM-4 (1), VIM-5 (1) | - | - | - | 11/11 | - | - | - | - | - | 2/2 | - | - | - | - | - | |
P. aeruginosa (12), P. putida (2), P. stutzeri | IMP-1 (3), IMP-2(2), IMP-7, IMP-15, IMP-19, IMP-26, IMP-31, IMP-39, IMP-46, IMP-56, IMP-63, IMP-71 | - | - | - | - | 15/15 | - | - | - | - | 2/2 | - | - | - | - | ||
P. aeruginosa (3), | IMP-13 (2), IMP-29 | - | - | - | - | 0/3 | - | - | - | - | - | - | - | - | - | - | |
Total | 4/4 | - | 2/2 | 11/11 | 15/18 d | 4/4 e | 1/1 | 5/5 g | 2/2 f | - | - | - | - | - | |||
Sensitivity | 100% (39.8% to 100%) | 100% (15.8% to 100%) | 100% (71.5% to 100%) | 83.3% (58.6% to 96.4%) | 100% (29.2% to 100%) | 100% (2.5% to 100%) | 100% (2.5% to 100%) | 100% (15.8% to 100%) | |||||||||
Specificity | 100% (94.1% to 100%) | 100% (94.5% to 100%) | 100% (94.3% to 100%) | 100% (93.4% to 100%) | 100% (92.4% to 100%) | 100% (94.5% to 100%) | 100% (94.5% to 100%) | 98.4% (91.3% to 99.9%) | 100% (94.4% to 100%) | 93.8% (84.8% to 98.3%) | 100% (94.3% to 100%) | 100% (94.5% to 100%) | 100% (94.5% to 100%) | 100% (94.5% to 100%) | 100% (94.5% to 100%) | 100% (94.5% to 100%) |
Species | β-Lactamase Content | EasyScreenTM ESBL/CPO Detection Kit Results | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
KPC | OXA-48 | NDM | VIM | IMP | SME | IMI | GES | CTX-M | TEM | SHV | DHA | CMY | OXA-23 | OXA-51 | Mcr-1 | ||
Non-targeted β-lactamase producers (15) a | |||||||||||||||||
A. baumannii (8) a | WT (2), OXA-21, PER-1, VEB-1 (2), SCO-1, RTG-4, | - b | - | - | - | - | - | - | - | - | 2/2 | - | - c | - | - | 2/8 | - |
A. baumannii (7) | SIM-1, OXA-143, OXA-253, OXA-24/40, OXA-72, OXA-58, OXA-97 | - | - | - | - | - | - | - | - | - | 1/1 | - | - | - | - | 4/7 | - |
Targeted ESBLproducers (5) | |||||||||||||||||
A. baumannii | GES-12, | - | - | - | - | - | - | - | 1/1 | - | - | - | - | - | 1/1 | - | |
A. baumannii (2) | CTX-M-2, CTX-M-15 | - | - | - | - | - | - | - | - | 2/2 | 2/2 | - | - | - | - | 2/2 | - |
A. baumannii | SHV-5 | - | - | - | - | - | - | - | - | - | 1/1 | 1/1 | - | - | - | 1/1 | - |
A. baumannii | TEM-1 | - | - | - | - | - | - | - | - | - | 1/1 | - | - | - | - | 1/1 | - |
Targeted carbapenemase producers (36) | |||||||||||||||||
A. baumannii (6) | GES-11 (3), GES-14 (3) | - | - | - | - | - | - | 7/7 | - | 1/1 | - | - | 1/1 | 7/7 | - | ||
A. baumannii (8) | ISAba1/OXA-51-like (3), ISAba1/OXA-51-like + SHV-5, ISAba1/OXA-51-like + GES-12 (4) | - | - | - | - | - | - | 4/4 | - | 3/3 | 1/1 | - | - | 2/8 | - | ||
A. baumannii (7) | OXA-23 (5), OXA-23 + GES-1, OXA-23 +GES-14 | - | - | - | - | - | - | 1/1 | - | 4/4 | - | 6/6 | 6/6 | - | |||
A. baumannii (11) | NDM-1 (4), NDM-1 + OXA-23, NDM-1 (4) + ISAba1/OXA-51-like, NDM-2, NDM-9 | - | - | 11/11 | - | - | - | - | - | 2/2 | - | - | 6/6 | 11/11 | - | ||
A. baumannii (3) | IMP-1 (2), IMP-4 + OXA-58 | - | - | - | - | 3/3 | - | - | - | - | 3/3 | - | - | - | - | 0/3 | |
A. genomospecies 16 | VIM-4 | - | - | - | 1/1 | - | - | - | - | - | - | - | - | - | - | 0/1 | - |
Total | - | - | 11/11 | 1/1 | 3/3 | - | - | 13/13 c | 2/2 | 23/23 d | 2/2 e | - | - | 13/13 | 37/55 f | ||
Sensitivity | 100% (71.5% to 100%) | 100% (2.5% to 100%) | 100% (29.2% to 100%) | 100% (63.1% to 100%) | 100% (15.8% to 100%) | 100% (75.3% to 100%) | 67.3% (53.3% to 79.3%) | ||||||||||
Specificity | 100% (93.6% to 100%) | 100% (93.6% to 100%) | 100% (92.1% to 100%) | 100% (93.5% to 100%) | 100% (93.3% to 100%) | 100% (93.6% to 100%) | 100% (93.6% to 100%) | 89.6% (77.3% to 96.5%) | 100% (93.4% to 100%) | 64.6% (51.7% to 76.1%) | 96.9% 8(9.3% to 99.6%) | 100% (93.6% to 100%) | 100% (93.6% to 100%) | 100% (91.8% to 100%) | 100% (93.6% to 100%) |
EasyScreenTM ESBL/CPO Detection Kit | |||
---|---|---|---|
Global French CPE Epidemiology a | Global French CP-Pa Epidemiology b | Global French CP-Ab Epidemiology c | |
(2012–2018) | 2018 | 2018 | |
Isolates received at the F-NRCs | 19,600 | 678 | 379 |
Carbapenemase positive isolates | 9468 (6798 OXA-48, 284 KPC, 1676 NDM, 492 VIM, 123 IMP, 54 IMI; 1 FRI-1; 2 GES; 10 OXA-23; 2 TMB-1; and 1 SME-4) | 169 (127 VIM, 1 NDM, 0 KPC, 18 IMP, 20 GES, 3 DIM) | 366 (284 OXA-23, 38 OXA-24/40 et 5 OXA-58; 65 NDM) |
Sensitivity | 99.97% (95%CI: 99.91–99.99) | 98.22% (95%CI: 94.9–99.6) | 88.25% (95%CI: 84.5–91.4) |
Specificity | 99.99% (95%CI: 99.95–100) | 100% (95%CI: 99.3–100) | 100% (95%CI: 75.3–100) |
Expected False positive | 1 OXA-405 | None | None |
Expected False negative | 1 FRI, 2 TMB-1 => 3 isolates | 3 DIM, =>3 isolates | 38 OXA-24/40 and 5 OXA-58-producers => 43 isolates |
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Gonzalez, C.; Oueslati, S.; Biez, L.; Dortet, L.; Naas, T. Evaluation of the EasyScreen™ ESBL/CPO Detection Kit for the Detection of ß-Lactam Resistance Genes. Diagnostics 2022, 12, 2223. https://doi.org/10.3390/diagnostics12092223
Gonzalez C, Oueslati S, Biez L, Dortet L, Naas T. Evaluation of the EasyScreen™ ESBL/CPO Detection Kit for the Detection of ß-Lactam Resistance Genes. Diagnostics. 2022; 12(9):2223. https://doi.org/10.3390/diagnostics12092223
Chicago/Turabian StyleGonzalez, Camille, Saoussen Oueslati, Laura Biez, Laurent Dortet, and Thierry Naas. 2022. "Evaluation of the EasyScreen™ ESBL/CPO Detection Kit for the Detection of ß-Lactam Resistance Genes" Diagnostics 12, no. 9: 2223. https://doi.org/10.3390/diagnostics12092223