Table 4. Quantification of the effect of incubating strawberry tissues with or without X. fragariae in the sample preparation procedure on downstream DNA amplification.
| Incubation without X. fragariaea | Incubation with X. fragariaeb | Effect of incubation on detectionc | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| qPCR | LAMP | qPCR | LAMP | qPCR t-test | LAMP t-test | |||||||||
| Media | LS-means | LS-means | LS-means | LS-means | Mean | SE | P value | Mean | SE | P value | ||||
| H2O | 35.2 | A | 33.4 | B | 35.9 | A | 38.8 | A | -0.7 | 0.650 | 0.260 | -5.4 | 2.950 | 0.097 |
| SPB | 37.2 | A | 40.0 | A | 35.7 | A | 33.8 | A | 1.4 | 0.661 | 0.051 | 6.2 | 3.154 | 0.076 |
| R2A | 32.0 | B | 14.2 | C | 31.3 | B | 16.4 | B | 0.7 | 0.426 | 0.112 | -2.2 | 2.047 | 0.308 |
| PBS | 31.6 | B | 13.1 | C | 30.4 | B | 11.9 | B | 1.2 | 0.448 | <0.001 | 1.2 | 0.295 | 0.002 |
a Shown are the effect of incubated strawberry tissue suspension (without added bacteria) in each media on DNA amplification. The data presented are the LS-means of the Ct (qPCR) and Tt (LAMP) values of samples prepared from X. fragariae (104 CFU/mL) freshly mixed with each media suspension (incubated with healthy strawberry tissues alone for 21 h) (Fig 1). The standard errors are 0.731 and 1.77 for qPCR and LAMP, respectively.
b Shown are the detection results of the bacteria-spiked strawberry tissues in each media. The data are presented as the LS-means of the Ct (qPCR) and Tt (LAMP) values of each media at 21 h after incubating 104 CFU/mL of X. fragariae with healthy strawberry tissues. The standard errors are 0.473 and 3.17 for qPCR and LAMP, respectively.
c The effect of incubation of strawberry tissues with X. fragariae on detection is represented by the differences of the corresponding Ct (qPCR) or Tt (LAMP) values between (a) and (b).