Table 2.
Rapid nucleic acid extraction for pathogen detection in oral samples.
| Sample Type | Target Pathogen | Cell Lysis Method | Nucleic Acid Extraction Technique | Nucleic Acid Amplification Method | LOD/Extraction Efficiency | Total Sample-To-Answer/Sample Preparation time | Reference |
|---|---|---|---|---|---|---|---|
| Saliva | B.cereus, HIV-1 virus | On-chip chemical lysis | SPE using silica membrane | On-chip PCR using dry reagents | 104 copies/mL | 1 h (sample-to-answer) | (Chen et al., 2010; Qiu et al., 2011) |
| Saliva | Methicillin-susceptible S. aureus and methicillin-resistant S. aureus | Thermal lysis | Aluminum oxide membrane-based DNA extraction | Real-time RT-PCR | ~100 copies of bacterial DNA per sample | Less than 2.5 h (sample-to-answer) | Oblath et al. (2013) |
| Saliva | Mycobacterium tuberculosis (M.tb) | Chemical lysis | SPE using magnetic bead | Digital RPA using preloaded liquid reagents | 91.3% (extraction efficiency of M.tb) | ~45 min (sample-to-answer) | (H. Yang et al., 2018) |
| Saliva | Zika virus | Chemical lysis | Cellulose paper-based RNA extraction | RT-LAMP combined with colorimetric detection | 3.5 plaque-forming units (PFU)/mL | 50 min (sample-to-answer) | Jiang et al. (2018) |
| Saliva | Zika virus | Chemical lysis | SPE using magnetic bead | Real-time RT-RPA using preloaded liquid reagents | 5 PFU/mL | Less than 15 min (sample preparation) | Chan et al. (2018) |
| Saliva | Zika virus | Chemical lysis | Chitosan-modified silicon dioxide capillaries | In-situ RT-PCR | 50 transducing units (TU)/mL | 25 min (sample preparation) 90 min (sample-to-answer) | Zhu et al. (2020) |
| Sputum (artificial) | E. coli | Paper-based microfluidic origami device | Benchtop PCR | 33 CFU/mL | 1.5 h (sample preparation) | Govindarajan et al. (2012) | |
| Sputum | M. tb | On-chip chemical cell lysis | SPE using photoactivated polycarbonate micropillars | Continuous flow PCR | 50 cells/mL | 30 min (sample-to-answer) | Wang et al. (2012) |
| Sputum | M. tb | Chemical lysis and magnetic bead-based nucleic acid extraction into a tube | Real-time LAMP using prestored reagents | 1000 cells/mL | 15 min (sample preparation) | Creecy et al. (2015) | |
| Sputum | M. tb | Liquefied sputum with 4% NaOH was directly added to LAMP mixture | LAMP | 2 copies/μL | 60 min (sample-to-answer) | Bentaleb et al. (2016) | |
| Sputum | M. tb | Chemical cell lysis and SPE using silica membrane on a LabDisk | Real-time LAMP using prestored reagents | 103 CFU/mL | 2 h (sample-to-answer) | Loo et al. (2017) | |
| Oropharyngeal swabs | S. pneumoniae and M. pneumoniae | On-chip chemical lysis | SPE using magnetic particles | LAMP amplification using prestored primers | 20 fg DNA per reaction | ~15 min (sample preparation) | Wang et al. (2019) |
| Throat swab | H1N1 Influenza Virus from | Antibody-coated magnetic beads captured viral ribonucleoprotein | RT-PCR | 10 TCID50 | ~3.5 h (sample-to-answer) | Ferguson et al. (2011) | |