Validation and optimization of C. difficile TcdA and TcdB specific PLA using Canine faeces

Development of a PLA using pure antigen is not representative of the clinical setting so TcdA and TcdB specific PLAs were performed with the antigen spiked into canine faeces sample as a model of human faecal samples. Previous studies have shown the isolation of pathogenic C. difficile toxins from the diarrhoeic and non-pathogenic C. difficile from non-diarrhoeic dogs, therefore, the canine faecal sample was used (Chouicha and Marks, 2006). Initially, the canine faeces sample was prepared by spiking 10ng/mL of TcdA toxin (methods section 5.6) into 50mg of canine faeces and further diluted to 1ng/mL and 0.5ng/mL in 1X Serum Dilution Buffer II. The non-spiked faecal sample was also used as the negative control or no protein control assay. Two independent PLA s were carried out in duplicates using the standard PLA conditions (methods 5.4.2). The results in table 3.1 show that the assay did not work as no amplification was seen in the neat TcdA spiked faecal sample. But when the neat TcdA spiked faecal sample was diluted in Serum Dilution Buffer II the working of the assay was restored.

107 of the sample with 1XSDB restored the working of the assay in both PLAs.

108 Even with this dilution the neat sample still did not amplify which was most likely due to the presence of PCR inhibitors such as bile salts and other complex polysaccharides in the faeces sample (Oikarinen et al., 2009). Therefore in order to remove any potential inhibitors of the qPCR, canine faeces sample for PLA were dialysed in the 1X TE buffer and further diluted in order to remove any leftover PCR inhibitors (methods 5.6.2). PLAs were performed using five replicates of each concentration. The results in Table 3.3 show that the dialysis and dilution of the spiked canine faeces helped to partially restore the sensitivity of the assay to the levels of the ELISA assay which has the detection of 0.5ng/mL.

109 TcdA

Concentation

10ng/mL(Neat) 1ng/mL 1:10 of

Neat

0.5ng/mL 1:20 of

Neat

NPC (Neat)

Replicate 1 38.04 34.26 33.02 NA

Replicate 2 38.14 36.63 33.20 NA

Replicate 3 NA NA 33.45 NA

Replicate 4 NA NA 33.38 NA

Replicate 5 NA NA 33.28 NA

Table 3.3: Result for TcdA spiked canine faecal PLA with dialysis and dilution of the sample. Five replicates of each concentration (10ng/mL (Neat: no dilution), 1ng/mL(1:10 dilution) and 0.5ng/mL (1:20 dilution)) were used. Dialysis of faecal samples resulted in restoring the sensitivity of PLA with the spiked faecal sample.

110 Although dialysis and dilution of the spiked canine faeces helped to partially restore the sensitivity of the assay this additional step increased both the time of the assay by 24 hours as well as its complexity (with additional dialysis), which would limit its use as a diagnostic test. Therefore, to overcome the inhibitory elements in the spiked faecal sample the Perfecta qPCR Toughmix (Quanta) was used to perform the qPCR step of the PLA instead of the ABI mastermix (Life Technologies, USA). The Perfecta qPCR Toughmix (Quanta) contains additives which prevent inhibition of PCR by common PCR inhibitors.

Initially, PLAs were performed using purified TcdA toxin. Figure 21 shows that replacing the ABI mastermix with Perfecta qPCR master mix did not change the LOD of the assay and gave the similar results as the ABI mastermix when performed with the purified TcdA.

Interestingly, Perfecta qPCR Toughmix did not allow amplification for the NPCs which shows that Toughmix inhibits the non-specific ligation of the free oligonucleotides in the NPC whereas background ligation was seen in the case of PLA using ABI mastermix.

111

C q

Toxin A concentration

Figure 21: Purified TcdA specific PLA using ABI mastermix and Perfecta qPCR Toughmix.

Quantification cycle (Cq) obtained at each concentration of purified TcdA is plotted. PLA was carried out in duplicate. The error bars shows the standard deviation of the three PLA replicates. The graph shows no bar for toughmix NPC because toughmix inhibits the non-specific binding of oligonucleotides. Statistical analysis shows no significant difference between the Cqs of the PLA using ABI mastermix and Perfecta ToughMix (p-value = 0.8571 and n=3. T-test (Mann-Whitney U)).

112 These results showed that Perfecta qPCR Toughmix worked successfully in the PLA using purified toxin. Therefore, further PLAs was carried out using canine faeces sample spiked with the purified TcdA and TcdB giving a final concentration of 250ng/mL. The spiked sample was further diluted to 25 and 2.5ng/mL and 0.625ng/mL in 1X SDB. The non-spiked faecal sample was also used with the NPC (method section 5.6.3). Two replicate of PLAs were carried out in duplicate using the above-said concentration for both TcdA and TcdB spiked sample. The results in Table 3.4 show that the dilution of the sample in 1X SDB and performing PLA with Toughmix overcame the inhibitors in the faecal sample. The 250ng/mL (neat) for both TcdA and TcdB did not show any amplification, but the further dilution of the sample showed the amplification of the samples giving the LOD of 0.625ng/mL for both TcdA and TcdB spiked canine faeces. Finally, the use of Toughmix partially restores the partial sensitivity of the assay without requiring dialysis thus reduces the time and complexity of the assay.

113

TcdA spiked ∆Cq

Canine Faeces ∆Cq 250ng/mL ∆Cq 25ng/mL ∆Cq 2.5ng/mL

0.625ng/mL

Canine Faeces ∆Cq 250ng/mL ∆Cq 25ng/mL ∆Cq 2.5ng/mL

0.625ng/mL

TcdB Concentration 250ng/mL(NEAT) 25ng/mL 1:10 of neat

Table 3.4: Two independent PLAs were carried out in duplicate with Perfecta qPCR Toughmix using canine faeces sample spiked with TcdA and TcdB antigen at the concentration of 250ng/mL. The spiked sample was further diluted in 1X SDB to the concentration of 25ng/mL, 2.5ng/mL and 0.625ng/mL along with their NPCs. The neat 250ng/mL of the sample showed no amplification (NA) for both TcdA and TcdB. But dilution of the faecal sample in 1xSDB shows the ∆Cq range of concentration samples used in the PLA for TcdA spiked canine faeces and TcdB spiked canine faeces.

114

6.4 Validation of C. difficile TcdA and TcdB specific PLA using clinical faeces