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Applied and Environmental Microbiology, February 2005, p. 898-903, Vol. 71, No. 2
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.2.898-903.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Division of Water Environment, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan1
Received 16 May 2004/ Accepted 21 September 2004
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The genus Cryptosporidium is composed of at least 13 species (23). In this genus, waterborne outbreaks are only known to be caused by C. parvum and C. hominis, which were previously classified into C. parvum bovine and human genotypes, respectively (13, 15, 16, 23). Only C. parvum and C. hominis have been confirmed to infect humans, though at least three species of Cryptosporidium, C. meleagridis, C. felis, and C. canis, have been detected and/or isolated from immunocompromised persons or children (12, 21). Thus, C. parvum and C. hominis are the most notable species to be controlled for safe drinking water as well as the water environment. In addition, discrimination between C. parvum and C. hominis is useful for elucidation of the contamination source by the pathogens in the water environment.
In the present study, we aimed to develop nested PCR which specifically detects the gene derived from C. parvum and C. hominis and discriminates the amplified product between these species. The Cpgp40/15 gene, which encodes the sporozoite membrane glycoproteins and shows high diversity between species (18), was suggested to be suitable as the amplification target. The generated product was analyzed by restriction fragment length polymorphism (RFLP) for discrimination between C. parvum and C. hominis. To investigate the sensitivity of nested PCR, the detection method was applied to oocyst inoculation experiments with concentrates of suspended solids recovered from river water, in which PCR inhibitors would be present (4). C. parvum oocysts inoculated into water samples of two different turbidities were recovered by immunomagnetic separation (IMS). The recovered oocysts were detected by both nested PCR and fluorescent antibody assays (FA). By comparison of the results, we discuss the evaluation of nested PCR for detection of C. parvum from an environmental sample.
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DNA extraction.
Chromosomal DNA was extracted and purified from 3 x 106 oocysts of the C. parvum Iowa strain as described by Maniatis et al. (10). The resulting DNA, which was 1.7 x 106 g in weight, was resolved in 100 µl of Tris-EDTA buffer. The chromosomal DNA was diluted with 10-fold serial dilutions to determine the sensitivity of nested PCR.
Chromosomal DNA of the C. parvum NHJ-1 strain, C. hominis, C. muris, G. lamblia, and G. muris was extracted as described by Johnson et al. (5) with some modifications. Briefly, the oocysts or cysts of the parasites were pelleted by centrifugation (1,200 x g at room temperature for 10 min) and then suspended in 50 µl of Tris-EDTA buffer. The suspension was frozen at 20°C for 15 min followed by thawing in boiling water for 3 min. These manipulations were performed for six cycles. The resultant was centrifuged at 20,000 x g for 1 min. The supernatant was recovered and then used as a template for the first PCR.
Nested PCR-RFLP analysis.
Design of the primers was referenced to the nucleotide sequences of the Cpgp40/15 genes as determined by Strong et al. (18). The GenBank accession numbers for the sequences cited in the present study are AF022929, AF164487 to AF164505, AF164508, AF164509, AF178690 to AF178697, and AF224462 to AF224464. The primers for the amplification of the Cpgp40/15 gene used in the present study are listed in Table 1. In order to amplify the Cpgp40/15 gene, the first PCR was performed with the primer set gp40/15-51 and gp40/15-31, and nested PCR was carried out with a pair of primers, gp40/15-52 and gp40/15-32. The first and nested PCR was performed in a 50-µl reaction system of 1x buffer, 0.2 mM deoxynucleoside triphosphate mix, 0.5 µM each of the primers, 0.2 units of Ex Taq polymerase (Takara Shuzo, Shiga, Japan), and 1 µl of the template. The reaction of the first and nested amplification for the Cpgp40/15 gene was programmed at initial denaturation at 94°C for 3 min, 30 cycles of denaturation at 94°C for 1 min, annealing at 60°C for 1 min, and extension at 72°C for 1 min, and a final extension at 72°C for 7 min. Nested PCR for the small-subunit (SSU) rRNA gene was performed as described by Xiao et al. (22, 24). The amplified product was separated by electrophoresis on 3% agarose gel, stained with ethidium bromide, and visualized under a UV transilluminator.
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TABLE 1. Primers used in this study
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Recovery of inoculated C. parvum oocysts from turbid water by IMS.
River water was collected on a rainy day in January 2002 from Tama River, Tokyo. The river water was filtrated with hydrophilic polytetrafluoroethylene (PTFE) membrane filters (pore size, 5 µm; Advantec, Inc., Tokyo, Japan). The membrane-trapped solids were eluted by ultrasonication into phosphate-buffered saline and centrifuged at 1,500 x g for 10 min. The recovered pellet was suspended into phosphate-buffered saline and stored at 4°C before use.
The concentrates recovered from 0.24 and 1.2 liters of the original river water, which were 0.05 and 0.3 g in wet weight, respectively, were washed three times with distilled water. The concentrates obtained were resuspended into 50 ml of distilled water, which resulted in turbidities of about 200 and 1,000 nephelometric turbidity units (NTU), respectively. These turbid water samples were prepared in two tubes, and each pair of tubes was inoculated with 50, 100, 200, and 600 oocysts of the C. parvum Iowa strain. The mixtures of turbid water and oocysts in 50-ml polypropylene tubes were agitated with a vertical rotator overnight. After overnight agitation, the samples were centrifuged at 1,500 x g for 10 min, and the pellets were used for the oocyst recovery procedure. The inoculated oocysts in the two tubes were separately recovered by IMS from each tube with a commercial kit (Dynabeads GC-combo; Dynal Biotech, Oslo, Norway). The recovered oocysts from one of the two tubes were detected with the Cpgp40/15 gene by nested PCR and that from another was investigated for the number of Cryptosporidium oocysts by FA. For nested PCR, chromosomal DNA from the recovered oocysts was extracted by the freeze-thaw method as described above, and three reaction systems were prepared for each trial. The inoculation trial was performed in duplicate or triplicate.
FA staining of the recovered oocysts.
The purified oocysts were stained on hydrophilic PTFE membrane filters (diameter, 25 mm; pore size, 0.2 µm; Advantec, Inc.) with a vacuum filtration unit (Advantec, Inc.). Staining of the oocysts was performed with a commercial kit according to the instructions (Hydrofluoro Combo Kit; Strategic Diagnostics Inc., Newark, Del.). The stained samples were observed with an epifluorescence differential-interference microscope (BX-50; Olympus, Tokyo, Japan) at a magnification of x400. The confirmed oocysts, which are 4 to 6 µm in diameter with a specific fluorescence at the edge of the spherical bodies, were counted on each membrane filter.
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FIG. 1. Nested PCR for the Cpgp40/15 gene and the SSU rRNA. (A) Nested PCR with templates of four kinds of parasites. Nested PCRs for the SSU rRNA gene and the Cpgp40/15 gene are shown in lanes 1 to 4 and 5 to 8, respectively. Lanes 1 and 5, C. muris RN66 strain; lanes 2 and 6, C. parvum Iowa strain; lanes 3 and 7, G. lamblia H3 strain; lanes 4 and 8, G. muris Roberts-Thompson strain. (B) Nested PCR with templates of C. parvum and C. hominis strains. Nested PCRs for the Cpgp40/15 and SSU rRNA are shown in lanes 1 to 3 and 4 to 6, respectively. Lanes 1 and 4, C. parvum Iowa strain; lanes 2 and 5, C. parvum HNJ-1 strain; lanes 3 and 6, C. hominis Ogose strain. Lanes M and N show DNA size standards (100-bp DNA ladder; Takara Shuzo) and the PCR negative control, respectively.
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FIG. 2. RFLP of the Cpgp40/15 PCR product generated from three C. parvum and C. hominis strains. The products digested with HindIII (A), MflI (B), and RsaI (C) are in lanes 1 to 3, 4 to 6, and 7 to 9, respectively. Lanes 1, 4, and 7, C. parvum Iowa strain; lanes 2, 5, and 8, C. parvum HNJ-1 strain; lanes 3, 6, and 9, C. hominis Ogose strain. Lane M shows a 100-bp DNA ladder. The lower band of the Ogose strain digested with RsaI (lane 9) consists of two fragments of 160 and 170 bp.
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FIG. 3. Detectable limit of nested PCR. Nested PCR was performed with 10-fold serially diluted chromosomal DNA template of the C. parvum Iowa strain ranging from 5 x 109 g (lane 1) to 5 x 1014 g (lane 6).
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The results obtained from the inoculation trials are shown in Table 2. In the trials in low turbidity water of about 200 NTU, the amplified product was detected from all trials with the 600 oocyst-inoculated water samples and two of three trials with the 100 and 200 oocyst-inoculated samples. In these trials, the PCR product of the 200 and 600 oocyst-inoculated trials was obtained from all three reaction systems, whereas that of the 100 oocyst-inoculated trials was obtained from one or two of the three reaction systems in each trial. In the trials with high turbidity water of about 1,000 NTU, amplified products were detected from one trial inoculated with 200 and 600 oocysts, in which the product was obtained from one and two of the three reaction systems.
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TABLE 2. Recovery and detection of C. parvum by IMS-PCR and IMS-FA from oocyst-inoculated turbid water samples
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Detection of oocysts from inoculated water sample without overnight agitation.
The IMS-PCR and IMS-FA assays were also applied to the oocyst-inoculated turbid water samples without the overnight agitation procedure to evaluate the effect of agitation on the recovery step by IMS followed by nested PCR and FA. One hundred oocysts were inoculated into water samples of two different turbidities at about 200 and 1,000 NTU. The trial was performed in duplicate for each turbid water sample and the results are shown in Table 3. PCR products were detected from all trials of both turbidities, and the product was obtained from all three reaction systems except for a single trial of high turbidity. The oocyst recovery rates confirmed by FA were 87 to 91% for the trials with the low-turbidity water sample and 52 to 71% for those of the high-turbidity water sample.
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TABLE 3. Recovery and detection of C. parvum by IMS-PCR and IMS-FA from oocyst-inoculated turbid water samples without agitationa
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A specific investigation showed that the nested PCR-RFLP developed in the present study detects only the C. parvum and C. hominis genes. The PCR product of C. hominis was digested with RsaI and MflI but not with HindIII, whereas that of C. parvum was digested with all the enzymes. A distinct RFLP patterns were obtained between the PCR products of C. parvum and C. hominis digested with MflI and RsaI. In addition, the combination of the PCR product length and RFLP patterns of MflI and RsaI is likely to enable to classification of C. hominis into four subtypes (Ia to Id), which was suggested by Strong et al. (18). The Ogose strain was found to be classified as genotype Ia.
In order to evaluate the application of nested PCR for environmental water samples, all the results obtained from the oocyst inoculation experiments using water samples of two different turbidities are shown in Fig. 4. The comparison between the genetic detection by nested PCR and oocyst numbers confirmed by FA suggests that the detection of C. parvum by nested PCR depends on the recovered oocyst number and that the detectable limit of nested PCR is about 50 oocysts in one trial. In the present study, however, one µl in 50 µl of DNA solution extracted from all the recovered oocysts was used as the template of the first PCR, whereas all the recovered sample was investigated for oocyst number by FA. Thus, nested PCR combined with IMS is suggested to have the ability to detect a single oocyst in an environmental sample. The detectable limit of nested PCR with purified C. parvum chromosomal DNA was 5 x 1013 g and was found to correspond to a single oocyst. Thus, the detection limit of nested PCR with oocysts recovered from a water sample by IMS was suggested to be almost equivalent to that with the purified DNA sample.
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FIG. 4. Relationship between genetic detection by nested PCR and oocyst number confirmed by FA from application experiments with oocyst-inoculated turbid water samples. Circles show successful detection by nested PCR. Solid circles show successful detection in all three reaction systems, and open circles show detection in at least one of the reaction systems. Crosses show failed detection by nested PCR.
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In conclusion, we showed that the nested PCR developed in the present study was able to specifically detect a selected gene of C. parvum and C. hominis and that the resulting product has the ability to discriminate between the two Cryptosporidium species by RFLP analysis. Our data also suggest that gene amplification in combination with IMS has the ability to detect the gene from a single oocyst in an environmental water sample. However, the application experiments showed that association of the oocysts with the suspended solids, which must also occur in environmental water, is a cause of the decrease in the oocyst recovery by IMS. We propose that the agitation procedure, which allows the oocysts to associate with suspended solids, should be performed in the application experiments for evaluation of the recovery and detection methods of the pathogens from environmental water samples.
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