Table 2.
Comparison of five point‐of‐care DNA extraction methods: NaOH, QuickExtract, KOH, KAPA Express Extract and Buccalyse DNA release with a reference laboratory method (EZ1 Biorobot) for the LAMP detection of Neoparamoeba perurans using cultured amoeba‐soaked Isohelix swabs
| DNA extraction method | DNA ng/ul | Ratio 260/280 | LAMP | TaqMan™ qPCR | ||
|---|---|---|---|---|---|---|
| Tp (mm:ss) | +ve | Ct | +ve | |||
| EZ1 Biorobot | 0.5 ± 1.2 | 1.8 | 12:45 ± 0:50 | 5/5 | 30.7 ± 3.1 | 5/5 |
| NaOH | 28.1 | 1.5 | Undetectable | 0/5 | Undetectable | 0/5 |
| QuickExtract | 38.8 ± 14.6 | 1.7 | 18:45 ± 4:35 | 5/5 | 36.5 ± 1.4 | 5/5 |
| KOH | 200.9 ± 38.3 | 1.5 | 33:15 ± 4:15 | 3/5 | Undetectable | 0/5 |
| KAPA Express Extract | 32.3 ± 3.6 | 1.3 | 22:45 ± 3:00 | 5/5 | Undetectable | 0/5 |
| Buccalyse DNA release | 52.7 ± 6.5 | 1.1 | 20:50 ± 2:10 | 3/5 | 36.5 ± 0.5 | 3/5 |
Number of positive samples (+ve) expressed as number of positive swabs/total number of swabs analysed per method. LAMP amplification expressed as the time of positivity Tp (mm:ss). TaqMan™ qPCR detection expressed as cycle threshold (Ct) values.