Abstract
A hydrophobic grid membrane filter-colony hybridization (HGMF-CH) method for the enumeration and isolation of cpe gene-carrying (cpe-positive) Clostridium perfringens spores from feces was developed. A 425-bp DNA probe specific for the cpe gene was sensitive and specific when tested with bacterial DNA and pure cultures. The enumeration of cpe-positive C. perfringens by the HGMF-CH method proved to be as sensitive as nested PCR combined with the most-probable number technique when tested with fecal samples from healthy individuals. With the aid of the HGMF-CH method, positive hybridization signals were detected from two out of seven fecal samples obtained from healthy individuals. Furthermore, cpe-positive C. perfringens was successfully isolated from both of these samples. The detection of cpe-positive C. perfringens by the HGMF-CH method is dependent on the ratio of cpe-positive C. perfringens colonies to total C. perfringens colonies growing on the HGMF-tryptose-sulfite-cycloserine plate. cpe-positive C. perfringens could be isolated if the ratio of cpe-positive C. perfringens spores to total C. perfringens spores was 6 × 10−5 or higher. The HGMF-CH method provides an aid in the investigation of fecal samples of patients suffering from food poisoning or other diseases caused by cpe-positive C. perfringens. The method also offers a new approach in the investigation of the epidemiology of cpe-positive C. perfringens strains.
Clostridium perfringens food poisoning is caused by the ingestion of food that contains large numbers of vegetative cells of cpe gene-positive C. perfringens strains, usually belonging to type A. These cpe-positive cells sporulate in the intestinal tract, producing enterotoxin (CPE), which is responsible for the diarrheal symptoms of the disease (12). When confirming a food poisoning outbreak caused by C. perfringens, isolation of the same cpe-positive strain from suspect food and from stools of affected individuals is advisable. However, conventional isolation of cpe-positive C. perfringens from the feces of affected individuals is occasionally complicated by the presence of cpe-negative C. perfringens as part of the normal fecal microbial population (5, 11, 16, 20, 22, 26). The isolation of the causative agent from fecal samples by direct plating is challenging, particularly if several days have passed since the onset of the illness (16).
The widespread distribution of C. perfringens in the environment has been considered to be an important factor in the frequent occurrence of C. perfringens type A food poisoning. However, only a small minority of C. perfringens strains isolated from humans and animals have been demonstrated to carry the cpe gene (1, 4, 8, 10, 24, 27). Studies by Miwa et al. have strengthened the hypothesis that, in fecal samples of animals, a small number of cpe-positive C. perfringens cells coexist with a large number of cpe-negative C. perfringens cells (14, 15). It has been shown that the ratio of cpe-positive strains to total C. perfringens strains in the intestinal contents of cattle, swine, and chickens may be as low as 10−4 to 10−5 (14, 15).
Due to the low ratio of cpe-positive C. perfringens strains to total C. perfringens strains in clinical samples, the isolation of cpe-positive C. perfringens strains is difficult and laborious. Thus, due to the lack of a specific method to isolate cpe-positive C. perfringens from clinical and environmental samples, the present knowledge of the epidemiology of the cpe-positive strains is deficient. Several PCR methods for the detection of cpe-positive C. perfringens from fecal samples have been described (6, 8, 13, 21, 23). The enumeration of cpe-positive C. perfringens is obtained by nested PCR combined with the most-probable number (MPN) technique (14). Furthermore, there are reports of the use of DNA probe hybridization and PCR-enzyme-linked immunosorbent assay for the detection of the cpe gene from food samples (2, 3). Compared to conventional methods, these techniques provide rapid and sensitive detection of the cpe gene, but the weakness of the methods is that none of them facilitate the isolation of cpe-positive C. perfringens. This study describes the design of a hydrophobic grid membrane filter-colony hybridization (HGMF-CH) method for the enumeration and isolation of cpe-positive C. perfringens spores from fecal samples.
MATERIALS AND METHODS
Bacterial strains.
A total of 11 cpe-positive and 19 cpe-negative C. perfringens strains, 38 strains of other clostridia, and 9 strains of other bacterial species were included in the study (Table 1).
TABLE 1.
Bacterial strains tested by cpe gene-specific PCR and DNA probe
| Species | Strain | Sourcea | PCRb | CHc | DNA-Hd |
|---|---|---|---|---|---|
| Clostridium aerotolerans | 108 | DFEH | NT | − | − |
| Clostridium botulinum (group I) | ATCC 25763 | ATCC | NT | − | − |
| ATCC 3502 | ATCC | NT | − | NT | |
| 62A | Riemann-Lindrothe | NT | − | NT | |
| 69A | Riemann-Lindroth | NT | − | NT | |
| Langeland | ATCC | NT | − | NT | |
| SL-2A | Lindroth | NT | − | − | |
| SL-3A | Lindroth | NT | − | NT | |
| SL-4A | Lindroth | NT | − | NT | |
| SL-6A | Lindroth | NT | − | NT | |
| SL-1B | Lindroth | NT | − | NT | |
| RS-3A | Lindroth | NT | − | NT | |
| RS-4A | Lindroth | NT | − | NT | |
| NCTC 7272 | NCTC | NT | − | NT | |
| ATCC 17841 | ATCC | NT | − | NT | |
| ATCC 7949 | ATCC | NT | − | NT | |
| ATCC 25764 | ATCC | NT | − | NT | |
| 126B | IP | NT | − | NT | |
| Crab F | Lindroth | NT | − | NT | |
| 133-4803 | McClung-Lindroth | NT | − | NT | |
| Clostridium botulinum (group II) | K45E | DFEH | NT | − | NT |
| 17B | ATCC | NT | − | NT | |
| ATCC 23387 | ATCC | NT | − | NT | |
| 2B | Eklund-Lindroth | NT | NT | − | |
| 250E | Crowther-Lindroth | NT | NT | − | |
| FT10F | Hobbs-Lindroth | NT | − | − | |
| K115E | DFEH | NT | − | − | |
| K44E | DFEH | NT | − | − | |
| BelugaE | Dolman-Lindroth | NT | − | − | |
| Clostridium chauvoei | 41 | DFEH | NT | − | − |
| 103 | DFEH | NT | − | − | |
| Clostridium histolyticum | 102 | DFEH | NT | − | − |
| Clostridium perfringens | ATCC 3624 | ATCC | − | − | − |
| ATCC 3626 | ATCC | − | − | − | |
| CCUG 2036 | CCUG | − | − | − | |
| CCUG 2037 | CCUG | − | − | − | |
| NCTC 8239 | NCTC | + | + | + | |
| NCTC 10239 | NCTC | + | + | + | |
| F 3686 | Notermansf | + | + | + | |
| 4732 | DFEH | − | − | NT | |
| 10204 | DFEH | − | − | NT | |
| D9030 | DFEH | + | + | + | |
| D9031 | DFEH | + | + | + | |
| D9032 | DFEH | + | + | + | |
| D9033 | DFEH | − | − | − | |
| D9063 | DFEH | − | − | − | |
| T8 | DFEH | − | − | NT | |
| T9 | DFEH | + | + | NT | |
| T16 | DFEH | + | + | NT | |
| T19 | DFEH | − | − | NT | |
| T20 | DFEH | − | − | NT | |
| T21 | DFEH | − | − | NT | |
| T22 | DFEH | − | − | NT | |
| T25 | DFEH | − | − | NT | |
| T28 | DFEH | + | + | NT | |
| T35 | DFEH | + | + | NT | |
| T37 | DFEH | + | + | NT | |
| T39 | DFEH | − | − | NT | |
| T42 | DFEH | − | − | NT | |
| T43 | DFEH | − | − | NT | |
| T44 | DFEH | − | − | NT | |
| T48 | DFEH | − | − | NT | |
| Clostridium putrefaciens | 104 | DFEH | NT | − | NT |
| Clostridium septicum | 43 | DFEH | NT | − | NT |
| Clostridium sporogenes | ATCC 19404 | ATCC | NT | − | − |
| Lang | DFEH | NT | − | NT | |
| 472A | DFEH | NT | − | NT | |
| 29A | DFEH | NT | − | NT | |
| Listeria monocytogenes | TT7E | DFEH | NT | NT | − |
| HT47E | DFEH | NT | NT | − | |
| AT12E | DFEH | NT | NT | − | |
| HT33E | DFEH | NT | NT | − | |
| LT15E | DFEH | NT | NT | − | |
| RT2E | DFEH | NT | NT | − | |
| Proteus vulgaris | 33 | DFEH | NT | − | NT |
| Serratia marcescens | 37 | DFEH | NT | − | NT |
| Streptococcus lactis | 12 | DFEH | NT | − | NT |
ATCC, American Type Culture Collection, Manossas, Va.; IP, Institute Pasteur, Paris, France; DFEH, Department of Food and Environmental Hygiene, University of Helsinki, Helsinki, Finland; CCUG, Culture Collection, University of Gothenburg, Gothenburg, Sweden; NCTC, National Collection of Type Cultures, London, United Kingdom.
PCR, detection of the cpe gene by PCR (20) from the bacterial cell lysate. +, positive PCR result; −, negative PCR result; NT, not tested.
CH, colony hybridization with cpe gene-specific DNA probe from pure cultures growing on HGMF- TSC plates. +, positive signal obtained by hybridization; −, no signal obtained by hybridization; NT, not tested.
DNA-H, hybridization with cpe gene-specific DNA probe. +, positive signal obtained by hybridization; −, no signal obtained by hybridization; NT, not tested.
Collected from various sources by the late Seppo Lindroth (University of California, Davis). The first name in each pair is the original source.
Obtained from Serve Notermans (Laboratory for Water and Food Microbiology, Bilthoven, The Netherlands).
DNA isolation.
The DNAs from all clostridial and Listeria strains used in the study were isolated as described by Hyytiä et al. (7) and Keto-Timonen et al. (9), respectively. All bacterial DNA was stored at −70°C prior to use.
Preparation of digoxigenin-labeled DNA probe specific for cpe gene.
In order to generate probes for detection of the cpe gene, 425-bp fragments were amplified by PCR (13). Purified DNAs of strains NCTC 8239 and NCTC 10239 were used as templates for PCR. The PCR products obtained with the two strains were combined, purified (High Pure PCR Product Purification kit; Roche, Mannheim, Germany) and labeled (DIG High Prime DNA Labeling and Detection Starter kit I; Roche). The efficiency of the labeling reaction was determined as recommended by the manufacturer.
Detection of the cpe gene from bacterial DNA with the DNA probe.
In order to determine the specificity of the probe, bacterial DNA was denatured at 95°C for 5 min and spotted on a positively charged nylon membrane (Roche). The bacterial DNA was fixed to the membrane with a UV cross-linker (Spectroline; Spectronics Corp., Westbury, N.Y.). Subsequently, the membrane was placed in a roller bottle containing hybridization solution (DIG Easy Hyb; Roche) and prehybridized at 41°C for 1 h. The hybridization solution was discarded and replaced with fresh solution containing 25 ng of denatured probe/ml, and incubation was continued at 41°C overnight. Thereafter, the hybridization solution was discarded and the membrane was washed twice (2× SSC [1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate] plus 0.1% sodium dodecyl sulfate) in roller bottles at room temperature for 5 min each time, followed by two 15-min washes in the same buffer at 65°C. The hybrids were detected with a chromogenic assay using the protocol provided by the DIG Application Manual (Roche).
Detection of cpe gene from pure bacterial cultures with DNA probe.
Tryptose-sulfite-cycloserine (TSC) agar was prepared by adding 1% d-cycloserine (Sigma-Aldrich, St. Louis, Mo.) to Shahidi-Ferguson Perfringens agar (Difco Laboratories, Detroit, Mich.). HGMFs (Iso-Grid; Neogen, Baltimore, Md.) were placed on freshly prepared TSC agar plates, and the bacterial strains were streaked onto HGMF-TSC plates with a sterile loop. After the plates were incubated under anaerobic conditions at 37°C for 24 h, colonies on the HGMF-TSC plates were replicated by placing a nylon membrane aseptically on top of the HGMF. The membranes carrying the colony lifts were laid colony side up on Whatman (Kent, United Kingdom) 3MM blotting paper soaked in the denaturation solution (0.5 M NaOH, 1.5 M NaCl) for 15 min, in neutralization solution (1.0 M Tris-HCl, 1.5 M NaCl, pH 7.4) for 15 min, and in 2× SSC for 10 min. The membranes were briefly air dried after each step and then were thoroughly dried after the 2× SSC treatment. Volumes of 1 μl of positive and negative control DNAs were spotted on dry membranes before the DNA was fixed to the membranes as described above. To remove cell debris, the membranes were treated at 37°C for 1 h with 0.5 ml of proteinase K (Finnzymes, Espoo, Finland) diluted 1:9 in 2× SSC. The debris was removed from the membranes by tightly pressing a sheet of blotting paper soaked with sterile distilled water onto the membranes. This procedure was repeated until all visible debris was removed. Subsequently, the membranes were prehybridized and hybridized as described above. Washing procedures and the chromogenic detection of the hybrids were carried out as described above.
Detection and enumeration of cpe-positive C. perfringens spores from fecal samples using the HGMF-CH method.
In order to test the applicability of the HGMF-CH method in the investigation of fecal specimens, seven fecal samples from healthy individuals were included in the study. Each fecal sample was diluted 10-fold in 0.1% peptone water and heated at 75°C for 20 min in order to kill vegetative cells and to promote spore germination. A total of 0.1 g per sample was filtered using 10 HGMFs in a membrane filtration system (Iso-Grid). After filtration, the HGMFs were placed on TSC plates and incubated for 36 to 42 h at 37°C. Bacterial colonies grown on HGMF-TSC agar plates were replicated by placing a nylon membrane disk aseptically onto the HGMF. The disk was marked in order to orient the replica in relation to the HGMF. The nylon replicas were transferred to a dry sheet of blotting paper and prepared for hybridization as described above. After chromogenic detection, the nylon membranes were examined carefully in order to enumerate the positive hybridization signals corresponding to cpe-positive colonies on the original HGMF-TSC plate. As each HGMF allows the growth of 1,600 bacterial colonies, the theoretical detection limit of the method is 1 cpe-positive C. perfringens colony per 1,600 total C. perfringens colonies, provided that no more than one filter is investigated. When investigating 10 HGMFs, it is theoretically possible to detect and isolate 1 cpe-positive colony among 1.6 × 104 cpe-negative colonies.
As a reference to the quantification obtained by the HGMF-CH method, the number of cpe-positive C. perfringens spores in the fecal samples was estimated using nested PCR combined with the MPN technique (MPN-PCR) (13, 18), and the total number of C. perfringens spores was determined by plating fecal dilutions onto TSC agar (17). A total of three or four colonies from each sample containing typical colonies on TSC agar were confirmed by culture methods to be C. perfringens (17).
Isolation of cpe-positive C. perfringens spores from fecal samples using HGMF-CH method.
During the hybridization procedure of the nylon membranes, the HGMF-TSC plates were kept under anaerobic conditions at room temperature in order to maintain the bacterial growth on the plates. The colonies yielding a positive signal on the nylon membranes were localized on the original HGMF-TSC plates. Several probe-positive colonies were picked from the original plates, streaked onto blood agar, and incubated for 24 h at 37°C. These isolates were further analyzed for the presence of the cpe gene by PCR (20).
RESULTS
Detection of the cpe gene from bacterial DNA and pure bacterial cultures with the DNA probe.
DNA and pure cultures of all cpe-positive C. perfringens strains tested were positive as determined by the hybridization method (Table 1). The positive hybridization signals were seen as clearly visible purple spots on the nylon membrane after chromogenic detection. All cpe-negative C. perfringens strains and the other bacterial strains tested yielded no hybridization signals (Table 1).
Enumeration and isolation of cpe-positive C. perfringens spores from fecal samples using the HGMF-CH method.
The HGMF-CH method proved to be as sensitive as MPN-PCR in detecting cpe-positive C. perfringens spores in fecal samples (Table 2). Positive hybridization signals were detected from two fecal samples, N1 and N4 (Table 2). These signals were strong, purple, round or square spots on the nylon membrane (Fig. 1). The numbers of cpe-positive C. perfringens spores in the samples were 60 and 1,500 CFU/g. The other five samples revealed no positive hybridization signals (Table 2). The total number of C. perfringens spores on the HGMFs was similar to the results obtained by the plate count on TSC agar.
TABLE 2.
Enumeration and isolation of cpe-positive C. perfringens from fecal samplesa
| Sample no. | Ageb (yr) | No. of cpe-positive C. perfringens spores/gc | Total no. of C. perfringens spores/gd | No. of cpe-positive C. perfringens spores/total no. of C. perfringens sporese | HGMF-CH
|
|
|---|---|---|---|---|---|---|
| No. of cpe-positive C. perfringens spores/gf | Isolation of cpe-positive C. perfringensg | |||||
| N1 | 30 | 74 | 5.8 × 105 | 1 × 10−4 | 60 | + |
| N2 | 57 | <3 | 2.1 × 106 | ND | <10 | − |
| N3 | 17 | <3 | 1.5 × 104 | ND | <10 | − |
| N4 | 55 | 7,500 | 1.3 × 105 | 6 × 10−2 | 1,500 | + |
| N5 | 24 | 3.6 | 3.2 × 103 | 1 × 10−3 | <10 | − |
| N6 | 51 | <3 | 2.3 × 102 | ND | <10 | − |
| N7 | 24 | 9.2 | 2.5 × 105 | 4 × 10−5 | <10 | − |
Sample heated at 75°C for 20 min.
Age of donor.
Number of cpe-positive C. perfringens spores in the sample determined by nested PCR combined with MPN technique. A value of <3/g was assigned when no positive PCR results were obtained.
Determined by plate count on TSC agar and confirming three or four counts of typical colonies by culture methods.
Ratio of number of cpe-positive C. perfringens spores determined by nested PCR combined with MPN technique to total number of C. perfringens spores obtained by plate count on TSC agar. ND, no ratio for cpe-positive C. perfringens and total C. perfringens spore numbers could be determined.
Number of cpe-positive C. perfringens spores determined by HGMF-CH method. A value of <10/g was assigned when no hybridization signals were obtained.
+, cpe-positive C. perfringens isolates obtained; −, no cpe-positive C. perfringens isolates obtained.
FIG. 1.
(A) HGMF containing C. perfringens growth after incubation on TSC agar plate. cpe-positive colonies detected later with hybridization are circled. (B) Nylon membrane replica of growth on HGMF-TSC plate, hybridized with cpe gene-specific DNA probe. The circles indicate positive hybridization signals corresponding to cpe-positive colonies on the original HGMF membrane.
The cpe-positive C. perfringens isolates were obtained from both of the samples revealing positive hybridization signals. The isolates were confirmed to be cpe positive by PCR.
DISCUSSION
An HGMF-CH method for the enumeration and isolation of cpe-positive C. perfringens spores from feces was developed. The method provides a marked improvement in the investigation of cpe-positive C. perfringens from feces, since none of the previously reported detection methods facilitates the isolation of cpe-positive C. perfringens (2, 3, 6, 8, 13, 14, 21, 23). With the HGMF-CH method, up to 1,600 separate colonies on a single membrane can be simultaneously screened for the presence of the cpe gene. The method thus provides the possibility of enumerating and isolating cpe-positive colonies.
When tested with bacterial DNA and pure cultures, the DNA probe proved to be specific and sensitive, revealing strong hybridization signals with all cpe-positive C. perfringens strains. Stringent hybridization and washing conditions ensured high specificity, and none of the cpe-negative bacterial strains revealed positive signals. Even a 2-h hybridization period was sufficient to provide a strong hybridization signal, but for practical purposes the hybridization was continued overnight.
When the HGMF-CH method was applied to the investigation of feces from healthy individuals, the method was shown to be as sensitive as the MPN-PCR employed for detecting cpe-positive C. perfringens spores in fecal samples. The detection limit of the method was dependent on at least two factors. First, the size of the sample filtered defines the lowest level of cpe-positive C. perfringens spores detected. Thus, when a total of 0.1 g of a sample was filtered, the limit of detection was 10 CFU/g. However, a lower detection limit would be achieved by studying a larger amount of sample. Secondly, the detection limit of the HGMF-CH method is dependent on the ratio of cpe-positive C. perfringens strains to total C. perfringens strains growing on the HGMF-TSC. By studying 10 HGMFs, the lowest detectable ratio is 6 × 10−5. When the HGMF-CH method was applied in the investigation of feces from healthy individuals, positive hybridization signals were detected from two samples, N1 and N4 (Table 2). When 0.1 g of sample was filtered, totals of 6 and 150 cpe-positive colonies were detected from samples N1 and N4, respectively. cpe-positive C. perfringens was successfully isolated from both of these samples. However, cpe-positive colonies could not be detected or isolated from samples N5 and N7, which contained cpe-positive C. perfringens according to the results obtained by MPN-PCR. This is explained by the fact that the numbers of cpe-positive C. perfringens spores in these two samples were below the detection limit of the HGMF-CH method (Table 2). In sample N7, the number of cpe-positive C. perfringens spores was 9.2/g, which is close to the 10 CFU/g detection limit. The ratio of cpe-positive C. perfringens strains to total C. perfringens strains in this sample was 4 × 10−5, which is also close to the detection limit of the method. Thus, detection of cpe-positive C. perfringens spores from sample N7 should have been possible by examining a greater number of membranes and/or filtering a larger amount of feces.
As the number of cpe-positive C. perfringens spores and the ratio of cpe-positive spores to total C. perfringens spores in the intestinal contents of humans and animals seem to be extremely low, the HGMF-CH method offers a powerful tool in the investigation of the reservoirs for cpe-positive C. perfringens. By initial screening of samples for the presence of the cpe gene by PCR and choosing only the PCR-positive samples for HGMF-CH, the diagnostics cost would be reduced and studying of reservoirs for the cpe-positive strains would be more effective. As indicated by the results of this study, a larger sample size and a higher number of membranes hybridized are recommended when positive hybridization signals are not found from PCR-positive samples.
The total time required to detect the cpe-positive C. perfringens spores in a sample was 3 to 4 days. The filtration of a fecal sample was laborious due to the occasional obstruction of the filtration apparatus and the membrane. Sample enrichment has been used in previous studies of the HGMF technique combined with DNA hybridization (19, 25). Enriching the sample would probably prevent the filtration apparatus and the membrane from becoming obstructed and improve the filtration rate. However, enrichment procedures would naturally hamper the quantitative analysis and therefore other sample preparation methods should be considered in order to improve the efficacy of the method.
The samples were heated in order to kill the vegetative cells and to increase spore germination. However, without heating the sample, the vegetative cells could be detected and enumerated. Thus, in C. perfringens food poisoning outbreaks, the HGMF-CH method could also be applied to the investigation of the suspected food, since the disease is caused by food containing a large number of vegetative cells of cpe-positive C. perfringens.
The HGMF-CH method provides a new approach in the diagnostics of food poisoning caused by cpe-positive C. perfringens, since the conventional isolation of cpe-positive C. perfringens from the feces of affected individuals is occasionally complicated by the presence of cpe-negative C. perfringens (5, 11, 16, 20, 22, 26). As the HGMF-CH method provides a means to determine the presence of the cpe gene in a large number of isolates simultaneously and to enumerate and further isolate the cpe-positive strain, the method markedly improves the investigation of the epidemiology of cpe-positive C. perfringens strains. The method may also help in the diagnostics of food poisoning and other gastrointestinal diseases caused by cpe-positive C. perfringens, especially if the samples are collected several days after the onset of the disease (16).
Acknowledgments
We are grateful to Kirsi Ristkari, Anu Seppänen, and Maria Stark for technical assistance.
Financial support was provided by the Walter Ehrström Foundation, Finnish Veterinary Foundation and Research Training Programme of Veterinary Medicine, University of Helsinki.
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