Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis
Abstract
:1. Introduction
2. Materials and Methods
- Accelerate Pheno (Accelerate Diagnostics, Inc., Tucson, AZ, USA)
- Verigene (Nanosphere, Northbrook, IL, USA)
- ePlex BCID (Roche Diagnostics, Rotkreuz, Switzerland)
- Biofire Blood Culture Identification (bioMérieux SA, Marcy-l’Etoile, France)
- T2 Magnetic Resonance (T2 Biosystems, Lexington, MA, USA)
- Karius (Karius, Redwood City, California)
- DISQVER (Noscendo GmbH, Duisburg, Germany)
- Alfred 60/AST (Alifax®, Polverara, Italy)
- VITEK® REVEALTM (bioMérieux SA, Marcy-l’Etoile, France) (Formerly Specific Reveal)
- dRAST (QuantaMatrix, Seoul, Republic of Korea)
- ASTar (Q-linea AB, Uppsala, Sweden)
- Fastinov (Fastinov, Matosinhos, Portugal)
- Septicyte (Immunexpress, Seattle, WA, USA)
- Acuitas (OpGen, Rockville, MD, USA) (discontinued)
- SepsiTest (Molzym, Bremen, Germany) (no studies after 2016)
- Micro-Dx (Molzym, Bremen, Germany) (no studies with blood)
- Hybcell Pathogen DNA assay (Cube Dx, St. Valentin, Austria) (1 study from2016)
- iDTECT Dx Blood test (PathoQuest, Paris, France) (discontinued)
- Magicplex (Seegene, Seoul, Republic of Korea) (discontinued)
- Lightcycler SeptiFast (Roche Diagnostics, Rotkreuz, Switzerland) (discontinued)
- VYOO (SIRS-Lab, Jena, Germany) (discontinued)
- IRIDICA system (Abbott, Chicago, IL, USA) (discontinued)
- iCubate (iCubate, Huntsville, AL, USA) (no study after 2019)
- PNA FISH ADVANDX (OpGen, Rockville, MD, USA) (no studies after 2020)
3. Blood Culture-Dependent Methods
3.1. Fluorescence In Situ Hybridization with Peptide Nucleic Acid Probes (PNA-FISH)
Accelerate PhenoTM
3.2. Microarray-Based Assay
Verigene®
3.3. Multiplex Polymerase Chain Reaction
3.3.1. Cobas® Eplex System (Formerly ePlex® System) [43]
3.3.2. BioFire® Blood Culture Identification
3.3.3. Rapid MBT Sepsityper®
4. Culture Independent Methods
4.1. T2 Magnetic Resonance
4.2. Next Generation Sequencing
4.2.1. Karius®
4.2.2. DISQVER®
5. Rapid Antimicrobial Susceptibility Testing
5.1. Alfred 60/ASTTM
Standard of Care | N | CA (%) | VME | ME | mE | Ref. | |||||
---|---|---|---|---|---|---|---|---|---|---|---|
Barnini Italy, 2016 | Vitek2/SensiTitre | 1296 | 62.1 | - | - | - | [121] | ||||
Giordano Italy, 2018 | SensiTitre | 405 | 91.6 | 14.5% | 4.5% | 1.2% | [117] | ||||
Sánchez-Carrillo Spain, 2019 | MicroScan Walkaway | 828 | 97.1 | 1 | 22 | 1 | [122] | ||||
Boland Belgium, 2019 | Phoenix system | 679 (109 Gram Pos/570 Gram Neg) | Gram Pos | Gram Neg | Gram Pos | Gram Neg | Gram Pos | Gram Neg | Gram Pos | Gram Neg | [123] |
88.1 | 92.2 | 2.3% | 0 | 13.8% | - | 12% | - | ||||
Anton-Vazquez London, 2019 | Phoenix system | 2196 (333 Gram Pos/1863 Gram Neg) | 89 | 95 | 7 | 31 | 29 | 55 | 2 | 5 | [116] |
Poel Belgium, 2020 | Vitek2 or disk diffusion * | 595 | 93.4 | 8 | 18 | 13 | [120] | ||||
Mantzana Greece, 2021 | Vitek2 ** | 690 | 94.5 | 1.45% | 3.33% | 1.16% | [124] | ||||
Cupaiolo Belgium, 2022 | Vitek2 or disk diffusion *** | 1008 | 94.9 | 7.4% | 3% | 1.8% | [118] | ||||
Anton-Vazquez London, 2022 | BD Phoenix | 709 | 94 | 1 | 7 | 35 | [119] | ||||
Curtoni Italy, 2023 | Microscan Walkaway | 437 | 94.7 | 1 | 10 | 12 | [125] |
5.2. VITEK® REVEALTM (Formerly Specific Reveal®)
5.3. dRASTTM
5.4. ASTar®
5.5. Fastinov®
6. Other Tests and Emerging Technologies
7. Host Transcriptomics
Septicyte®
8. Discussion
9. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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System (Company) | Technology | Regulatory Status (for Bacteria) | Sample | Gram Stain Dependent | ID Targets | Type of AMR Testing | Resistance Markers or Antibiotics Tested |
---|---|---|---|---|---|---|---|
Accelete PhenoTM (Accelerate Diagnostics, Tucson, AZ, USA) | PNA-FISH and morphokinetic cellular analysis | CE marked/FDA cleared | BC | No | 6 g-positive 8 g-negative 2 yeasts | Phenotypic | gram-pos: ampicilin, ceftaroline, daptomycin, linezolid, vancomycin, and cefoxitin gram-neg: ampicilin-sulbactam, ciprofloxacin, gentamicin, tobramycin piperacillin-tazobactam, aztreonam cefepime, ceftazidime, ceftriaxone ertapenem, meropenem, and amikacin |
Verigene® (Nanosphere, Northbrook, IL, USA) | PCR + microarray | CE marked/FDA cleared | BC | Yes | 13 g-positive 9 g-negative | Genotypic | mecA, vanA/B, CTX-M, KPC, NDM, VIM, IMP, and OXA |
cobas® eplex (Roche Diagnostics, Rotkreuz, Switzerland) | PCR + microarray | CE marked/FDA cleared | BC | Yes | 20 g-positive 21 g-negative 16 fungal | Genotypic | mecA, mecC, vanA, vanB CTX-M, IMP, KPC NDM, VIM OXA (OXA-23 and OXA-48) |
BioFire® FilmArray® (bioMérieux, Marcy-l’Étoile, France) | PCR + microarray | CE marked/FDA cleared | BC | No | 8 g-positive 11 g-negative 5 Candida species | Genotypic | IMP, KPC, OXA-48-like NDM, VIM, mcr-1, ESBL CTX-M, mecA/C mecA/C and MREJ (MRSA), vanA/B |
Rapid MBT Sepsityper® (Bruker Daltonik, Bremen, Germany) | MALDI-TOF MS | CE marked/FDA cleared | BC | No | >425 organisms (including bacteria and yeasts) | - | - |
T2Bacteria Panel (T2Dx®, T2 Biosystems, Lexington, MA, USA) | Miniaturized magnetic resonance | CE marked/FDA cleared | WB | No | E. faecium S. aureus K. pneumoniae A. baumannii P. aeruginosa E. coli | - | - |
Karius® (Karius®, Redwood City, CA, USA) | Metagenomics | - ¥ | WB | No | >1000 pathogens (bacteria, DNA viruses, fungi and parasites) | - | - |
DISQVER® (Noscendo GmbH, Duisburg, Germany) | Metagenomics | CE marked | WB | No | 5621 bacteria | - | - |
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Liborio, M.P.; Harris, P.N.A.; Ravi, C.; Irwin, A.D. Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis. Microorganisms 2024, 12, 1824. https://doi.org/10.3390/microorganisms12091824
Liborio MP, Harris PNA, Ravi C, Irwin AD. Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis. Microorganisms. 2024; 12(9):1824. https://doi.org/10.3390/microorganisms12091824
Chicago/Turabian StyleLiborio, Mariana P., Patrick N. A. Harris, Chitra Ravi, and Adam D. Irwin. 2024. "Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis" Microorganisms 12, no. 9: 1824. https://doi.org/10.3390/microorganisms12091824