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Journal of Clinical Microbiology, July 2002, p. 2466-2471, Vol. 40, No. 7
0095-1137/02/$04.00+0 DOI: 10.1128/JCM.40.7.2466-2471.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
and Martin Altwegg
Department of Medical Microbiology, University of Zurich, 8028 Zürich, Switzerland
Received 8 February 2002/ Returned for modification 18 March 2002/ Accepted 29 April 2002
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To avoid invasive procedures for obtaining suitable specimens, e.g., duodenal biopsies, we have investigated the use of stool specimens for the detection of T. whipplei DNA by PCR. Because multiple PCR inhibitors, such as hemoglobin, bilirubin, bile salts, urea, and heparin, may be present in stool samples (27), a suitable DNA extraction protocol which efficiently eliminates these inhibitors had to be established. For this purpose we have adapted a method previously described by Mangiapan et al. (16) which removes the inhibitors by capturing target DNA with specific probes. Large amounts of other DNA (human, bacterial) which may also reduce the sensitivity of PCR can simultaneously be removed with this method. In addition, we tested a new commercially available kit (Invisorb Spin Stool DNA Kit; Invitek, Berlin, Germany) and compared the results to those of the target capture method. The simplified stool extraction method is based on removing PCR inhibitors with InviAdsorb using a single centrifugation step, followed by the adsorption of the DNA to a column matrix and elution with a low-salt buffer.
(Parts of this study were presented at the 101st General Meeting of the American Society for Microbiology, Orlando, Florida, 20 to 24 May 2001 [R. C. Maibach, F. Dutly, and M. Altwegg, Abstr. 101st Gen. Meet. Am. Soc. Microbiol., abstr. C-456, p. 257, 2001]).
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TABLE 1. Compilation of all results for patients with confirmed (group I) and suspected (group II) Whipple's diseasej
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TABLE 2. Patients without Whipple's disease (group III)a
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Extraction of DNA. One milliliter of stool was suspended in 1 ml of 0.85% NaCl and then centrifuged at low speed (500 x g) for 10 min. The pellet was discarded, and the supernatant was again centrifuged at high speed (10,000 x g) for 10 min to pellet the bacteria. The pellet was then washed once with 1 ml of 0.85% NaCl, resuspended in 200 µl of digestion buffer (50 mM Tris-HCl [pH 8.5], 1 mM EDTA, 0.5% sodium dodecyl sulfate) containing 400 µg of proteinase K/ml and incubated at 55°C for 1 to 2 h with agitation. Total DNA was extracted with QIAamp DNA binding columns (QIAGEN, Basel, Switzerland) according to the manufacturer's protocol except that in the final step only 100 µl (instead of 200 µl) of elution buffer AE was used.
Oligonucleotides. For sequence capturing of the T. whipplei DNA, 5'-biotinylated oligonucleotides TW963f (5'-GTAGAGATACGCCCCCCGCAAGGT) and TW1084r (5'-GTCTCCTGTGAGTCCCCGCCATTAC) designed using the software Oligo 4.1 (Wojciech Rychlik, National Biosciences) were used. These oligonucleotides are complementary to the 16S rDNA specific for T. whipplei in the area between primers TW1 and TW3 (Fig. 1). For amplification of the 16S rRNA, primers TW-1 and TW-2 were used, resulting in a 267-bp fragment, whereas seminested reamplification with TW-4 and TW-2 produced a 229-bp fragment (2). For amplification of the hypervariable region of domain III of the 23S rDNA, primers HGC-23InsF and TW-23InsR1 and for nested reamplification TW-23InsF and TW-23InsR2 were used (13). All primers and capture oligonucleotides were synthesized by Microsynth (Balgach, Switzerland).
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FIG. 1. Schematic overview of the positions of primers and probes used for amplification and capturing, respectively. Positions are shown according to the rRNA genes of E. coli.
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Invisorb Spin Stool DNA kit. DNA was extracted from 15 PCR-positive and 22 PCR-negative stool specimens (180 to 300 mg) according to the manufacturer's protocol (Invitek, Berlin, Germany), except that in the final step only 100 µl (instead of 200 µl) of elution buffer was used. Again, 5 µl of the eluate was used for PCR.
Amplification of T. whipplei DNA. PCR was performed on a Gene Amp PCR System 9600 (Perkin-Elmer) and included an initial activation-denaturation step of 9 min at 95°C and 2 min at 96°C. Amplification and reamplification were both done in a volume of 50 µl containing dATP, dCTP, dGTP, and dUTP at a concentration of 200 µM each, 25 pmol of the corresponding primers, 2.5 U of AmpliTaq Gold polymerase including the appropriate amount of its optimized buffer (Perkin-Elmer, Norwalk, Conn.), and 5 µl of DNA template. For amplification, but not for reamplification, 0.25 U of thermolabile uracil-N-glycosylase (Epicentre Technologies, Madison, Wis.) was added to prevent carryover contamination from previous amplifications. For reamplification, 5 µl of the first amplification mixture was used as a template. Amplification consisted of 40 cycles at 95°C for 1 min, at 60°C for 1 min, and at 72°C for 1 min. Seminested reamplification was performed for 15 cycles at 95°C for 1 min, at 60°C for 1 min, and at 72°C for 1 min. To avoid degradation of the amplified products because of the uracil-N-glycosylase (24), reaction tubes were held at 72 or -20°C after cycling and then stored at -20°C. Amplifications and reamplifications with primers targeting the hypervariable region of domain III of the 23S rDNA were performed as previously described (13). PCR products were separated by electrophoresis on a 2% (wt/vol) agarose gel (UltraPure agarose; Life Technologies, Paisley, Scotland), stained with ethidium bromide, and visualized under UV light.
Amplification control. All PCR-negative DNA extracts were tested for inhibition of the Taq polymerase by adding positive control DNA to the amplification mix. When still negative, extracts were diluted 1:5 and both PCR and amplification control were repeated.
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Patients with suspected Whipple's disease (group II). For two of these four patients, the duodenal biopsy as well as the stool specimen had a positive PCR result. These two patients also tested positive in the stool by the 23S rRNA PCR system. For the other two patients, all specimens were negative with the 16S rRNA PCR system. However, patient 10 tested positive in the duodenal biopsy with the 23S rRNA and the ITS PCR systems (Table 1).
Patients without Whipple's disease (group III). Of the 84 patients with elective gastroscopy (Ehrbar et al., letter) but no clinical signs suggestive of Whipple's disease, 70 tested PCR negative in the duodenal biopsy, in the gastric aspirate, and in the stool, whereas for 14, at least one of the specimens analyzed was positive (Table 2). All results of the 23S rRNA PCR system corresponded to those of the 16S rRNA PCR system except for the following three patients: (i) the two patients with positive results only for the stool but not for the biopsy or the gastric aspirate were considered as false positive, although they were again positive after reextraction and PCR with the 16S rRNA PCR system but were negative with the 23S rRNA PCR system; (ii) one of the three patients testing PCR positive with the 16S rRNA PCR system for the stool and the gastric aspirate but not for the duodenal biopsy was also negative with the 23S rRNA PCR system for the stool.
Amplification control. Among all 96 stool samples analyzed, 10 were shown to be inhibited when DNA extracts were tested undiluted. At a dilution of 1:5, all these samples showed a positive amplification control.
Sensitivity and specificity. Based on the above-described results, the sensitivity of the stool PCR in combination with the target capture DNA extraction method is 100% compared to PCR-positive results in the duodenal biopsies irrespective of the presence of Whipple's disease (Table 3). For calculation of the specificity of the assay, only specimens from patients without clinical evidence of Whipple's disease and negative PCR results in duodenal biopsies and gastric aspirates were included. Only 2 of 72 stool results were considered false positive, resulting in a specificity of 97.3%. However, both these specimens again tested positive upon repeat analysis (including a new DNA extraction from the same stool specimen) (see above).
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TABLE 3. Performance of stool PCR using the target capture methoda
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A total of 12 patients with confirmed or suspected Whipple's disease and 84 persons undergoing elective endoscopy but without symptoms suggestive for Whipple's disease (e.g., absence of diarrhea, weight loss, and arthralgias) (Ehrbar et al., letter) were included in the study. Results of the stool PCR were primarily compared to PCR results from duodenal biopsies and gastric juice, data available not only for most patients (Table 1) but also for all controls.
As shown in Table 3, all persons for whom duodenal biopsies were PCR positive were also positive by 16S rRNA PCR with their stool specimens irrespective of the presence or absence of Whipple's disease. In addition, PCR targeting domain III of the 23S rDNA was also positive with all these specimens. Thus, the sensitivity of our stool PCR is 100% if compared to PCR from duodenal biopsies (Table 3). However, the clinical sensitivity, i.e., the sensitivity with regard to the detection of patients with Whipple's disease, is only 63% but still significantly higher than that of histopathology (4, 17, 19, 23), with a clinical sensitivity of only 12.5% in our small series. This confirms that PCR from duodenal biopsies and stool specimens is significantly more sensitive than histopathology and that a number of patients with Whipple's disease show no gastrointestinal evidence (clinical or laboratory) whatsoever for the presence of this disease (9, 11, 20).
In contrast, there are persons without Whipple's disease who carry T. whipplei DNA in their gastrointestinal tract. All seven patients without Whipple's disease but PCR positive in their duodenal biopsies were also positive by 16S rRNA stool PCR. This and the fact that these specimens were also positive by 23S rRNA PCR support the view that asymptomatic carriage of T. whipplei, or at least its DNA, indeed exists, as suggested previously (7, 26; Ehrbar et al., letter). Among the eight persons without Whipple's disease that were PCR positive with gastric juice but not with duodenal biopsies, only three were positive by stool PCR as well. This may reflect a quantitative phenomenon influenced by whether or not the organism penetrates the intestinal mucosa.
To circumvent problems with asymptomatic carriage, the specificity of the stool PCR was analyzed with reference to those persons without evidence for Whipple's disease who were PCR negative with both gastric juice and duodenal biopsy and was calculated to be 97.3%. However, both false-positive specimens were again positive when the entire procedure, i.e., including DNA extraction, was repeated. In contrast, both were negative by 23S rRNA PCR. However, when the DNA extraction was performed with the Invisorb kit, one of the two was also positive. If this sample is considered as being correctly positive, the specificity of the 16S rRNA stool PCR rises to 98.6%. Whether or not very low amounts of T. whipplei DNA at the limits of its detectability for the 23S but not the 16S rRNA PCR system or true false positivity is responsible for these contradictory results remains unsolved.
We were astonished that the results of the 23S rRNA PCR system are comparable to those of the 16S rRNA PCR system, because T. whipplei DNA was captured after column purification with a probe targeting the 16S rRNA gene. The hypervariable region in domain III of the 23S rDNA, where the 23S rRNA primers anneal, is located approximately 2,000 bp downstream from the capturing positions within the 16S rRNA gene. This shows that the captured sequences are at least 2,000 bp long. Thus, the capturing method is suitable for the extraction of long DNA sequences out of difficult samples such as stool or possibly also environmental samples.
The results with the Invisorb kit are comparable to those with the target capture method. One of the two false-negative stool samples using this simplified procedure was positive with the capture method but had been classified as false positive because the duodenal biopsy, the gastric aspirate, and the 23S rRNA PCR from stool were PCR negative. Thus, the result with the Invisorb kit is probably correctly negative. The other sample which was considered false positive with the capture method was also positive with the Invisorb kit (see above). Therefore, the sample has to be considered a true positive. A third sample only weakly positive with the capture method was negative with the Invisorb kit. This may be a problem of storing the stool samples for months at -20°C with a concomitant deterioration of the DNA quality. Another sample negative with the capture method but positive with the Invisorb kit was considered a true positive because the gastric aspirate of the same patient had been positive with the TW1-TW3 PCR system (23) as well as the TW4-TW2 PCR system (2). The last discrepancy involved a specimen which was negative with the capture method but weakly positive with the Invisorb kit. Since no information is available that would suggest otherwise, the Invisorb result has to be considered a true false positive. These adjustments result in a sensitivity of 93.3% and a specificity of 95.5% for PCR from Invisorb-treated stool specimens. Due to the easier handling and because it is less time consuming (i.e., 3 to 4 h for extraction time, versus 9 h for the capturing method), the Invisorb kit is a suitable alternative for use in the routine diagnostic laboratory.
Based on the above-described results, we conclude that PCR from stool specimens is more sensitive than histopathology and about as sensitive as PCR from duodenal biopsies for patients with Whipple's disease. However, positive results do not confirm Whipple's disease and require further evaluation of the patients, as is the case for PCR results from duodenal biopsies and gastric juice. Similar results have meanwhile been obtained with healthy control persons, with a prevalence of positive PCR assays in stool specimens of about 7% (L. Amsler, P. Bauerfeind, Ch. Nigg, R. C. Maibach, R. Steffen, and M. Altwegg, unpublished data). Finally, DNA extraction from stool specimens with the Invisorb kit is a suitable alternative to target capturing in a diagnostic laboratory.
Present address: IMD, Institut für medizinische und molekulare Diagnostik AG, CH-8047 Zürich, Switzerland. ![]()
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