Table 1.
Comparison of methods applicable for pathogen detection. (RD: Resistance Determination, AST: Antimicrobial susceptibility testing, POC: Point-of-Care).
| Method | Pathogen Identification (ID) | Time | RD | AST | Advantages and Disadvantages | POC | Ref |
|---|---|---|---|---|---|---|---|
| Cell culture | Growth based; all culturable bacteria | 24–72 h cultivation + 18–24 h for biochemical ID | - | √ | + Cost-effective + Good specificity − Long turnaround times − Lacking sensitivity − Prone to errors in workflow − Difficulties with fastidious organisms − Unculturable organisms not detectable |
- | [5,6,13,14,16,21,27,133,134,135] |
| PCR-analysis and real-time PCR | Sequence dependent amplification of bacterial genes > pathogen-specific | One to several hours | √ | - | + No cultivation + Good performance − Expensive − A priori knowledge on suspected pathogens necessary − Turnaround time − High-end instrumentation |
- | [8,13,16,17,19,21,27,136,137,138,139,140,141,142] |
| Next-generation sequencing | Simultaneous sequencing of billions of nucleic acid fragments contained in heterogenous samples > identification on subspecies or strain level based on SNPs | 14–20 h | √ | - | + Primer independent + Identification without a priori knowledge or suspicion + Faster adaption to new resistance mechanisms − Complex workflow with experimental pitfalls and biases − High overall error rate − Differentiation between colonization and infection critical |
(√) | [5,22,23,24,27,28,29,31,32,33,136,143,144,145,146] |
| MALDI-TOF; Direct sample testing | Generated mass spectrum of molecular sample composition compared to spectral database containing spectra from pure colonies (pre-cultivation); Cell enrichment followed by specific isolation | 2–50 h | (√) | (√) | + Automatable + Low costs per test + Fast analysis − Pre-cultivation necessary − Several resistance mechanisms not detectable − Identification of subspecies limited − Polymicrobial analysis difficult + No pre-cultivation − A priori knowledge necessary |
- | [15,38,39,41,43,44,45,46,47,48,49,50,51,52,53,54,55,147,148,149,150,151,152] |
| HPLC-MS | Separation of proteolytic digests of cell extracts via HPLC and identification of unique peptide markers | ~4 h | - | - | − Transferability to routine lab remains limited | - | [38,56,57,58] |
| Biosensors | Recognition of pathogen presence or their metabolic activity via biological recognition elements in intimate contact to transducers and detection systems | √ | - | + (Semi-) quantitative measurement + No or few additional reagents, pre-enrichment or processing steps |
(√) | [60,61,62,63] | |
| Mass transduction (e.g., QCM, SAW) | Detection of mass changes on the sensor (e.g., piezoelectric crystals) | variable | (-) | (-) | + Results comparable to ELISA, PCR + Target selectivity better than SPR − Affordability (QCM) − Long incubation times (SAW) − High packing costs (SAW) |
- | |
| Electrochemical transduction (e.g., EIS) | Variable (e.g., screen-printed electrodes with antibiotic-seeded hydrogel or bacterial growth in electrode containing micro-wells in presence of antibiotics) | 1–3 h | √ | √ | + Unaffected of samples optical properties + Low-power instrumentation − Limited in sensitivity and specificity than optical-based sensors |
(√) | [60,68,98,153,154] |
| Optical transduction (e.g., SPR) | Variable (e.g., digital time-lapse microscopy, SPR) | variable | √ | √ | + High sensitivities and specificities + Sensors small and cost effective + Fast real-time detection − Label-based detection requires additional steps − Label-free detection often not easily accessible − Interference of non-specific binding − Trouble analyzing turbid samples − Interference in complex matrices |
(√) | [60,68,77,78,98,155] |
| Whispering gallery mode (optical) | Label-free detection via capturing of pathogens and pathogen compounds with biological recognition molecules | ~15–30 min | √ | - | + Label-free and real-time + Detection of single molecules and atoms + No prior purification or amplification + Low manufacturing costs + Small test volume − Sensor stability and specificity |
(√) | [85,86,89,90,91,92,93] |
| Lateral Flow Assays | detection via capturing of pathogens and pathogen compounds with biological recognition molecules, detection with colorimetric and optical detection molecules | Several minutes | √ | - | + Broad range of biological samples + Results confirmed by naked eye − Low accuracy − Limited sensitivities − Cross-reactivity in multiplexing − Interpretation of weakly positive tests difficult |
√ | [99,100,102,103,104,109,110,111,112,156,157,158,159] |
| Low-cost paper-based NAT | Containing all three key steps of NAT for pathogen detection | 45 min–120 min | √ | - | + Higher sensitivities and specificities than immunoassays + Capability for multiplex detection |
(√) | [19,114,115,116] |
| Micro-fluidic systems | Variable (e.g., NAT-based micro-fluidic systems, chip-based isothermal nano calorimetry, micro-fluidic channels with gold-micro-electrodes, nanoliter-sized-micro-chamber and micro-array based micro-fluidic) | 15 min–3 h | (√) | (√) | + faster and better LOD by simple adaption to micro-fluidic format − sensitive to air bubbles − Sample preparation necessary (RPA) |
(√) | [106,160,161,162,163] |
| Biochemical tests (e.g., CarbaNP, BYG Carba test) | No pathogen identification | Several minutes | √ | - | − Applied amount of bacteria critical − Limitations in sensitivity for some lactamases |
- | [164,165,166,167] |