Phenotypic and genotypic characterization of Cryptosporidium species and isolates.

Recent outbreaks of cryptosporidiosis from contaminated water supplies have led to a need for the detection of Cryptosporidium oocysts from various hosts and contaminating sources. The presence of nonpathogenic species or strains of Cryptosporidium is important for diagnostic purposes as there is a potential for false- positive detection of pathogenic parasites. The present review focuses on phenotypic differences and recent advances in genotypic analyses of the genus Cryptosporidium with an emphasis on detecting various isolates and identifying differences in Cryptosporidium parvum and other species in this genus. The information currently available demonstrates important patterns in DNA sequences of Cryptosporidium, and our understanding of macro- and microevolutionary patterns has increased in recent years. However, current knowledge of Cryptosporidium genetic diversity is far from complete, and the large amount of both phenotypic and genotypic data has led to problems in our understanding of the systematics of this genus.

DNA fingerprinting of Cryptosporidium parvum isolates using amplified fragment length polymorphism (AFLP).

The genetic variability of 10 Cryptosporidium parvum isolates of human and animal origin was investigated using amplified fragment length polymorphism (AFLP). Analysis of fluorescent dye-labeled amplified products was carried out using an ABI PRISMS 377 DNA sequencer and ABI PRISMS GeneScan software. One-hundred and twelve primer combinations were evaluated using a single C. parvum isolate. The patterns generated were highly reproducible. For subsequent study, a subset of 9 primer pairs that yielded 30-90 DNA fragments after the polymerase chain reaction, within the size range of 50-500 bp, was used to screen the 10 C. parvum isolates, including 7 bovine, 1 equine, and 2 of human origin. The animal isolates produced identical fingerprint patterns with every primer combination tested. Of the 2 human isolates tested, 1 of the isolates, passaged in calves, generated the same AFLP DNA banding patterns as the animal isolates, whereas the other isolate, obtained directly from human feces, produced unique patterns. Polymorphism, detected by comparison of the fingerprint patterns of the latter human isolate with the common pattern shared by all other isolates, ranged from 17 to 35% for the 9 primer pairs. The results show that AFLP is a useful method for differentiating C. parvum isolates into 2 distinct genotypes.

Evaluation of the Reveal and SafePath rapid Escherichia coli O157 detection tests for use on bovine feces and carcasses.

The Reveal (Neogen Corp., Lansing, Mich.) and SafePath (SafePath Laboratories LLC, St. Paul, Minn.) tests were evaluated for their performance as beef fecal and beef carcass Escherichia coli O157:H7 monitoring tests. Agreement between these tests and a reference test system was determined using naturally contaminated bovine feces and beef carcasses. The reference system utilized immunomagnetic separation with plating onto cefixime, tellurite, sorbitol MacConkey agar, followed by colony testing using a serum agglutination test for the O157 antigen. Relative to this reference method, the Reveal test showed a sensitivity of 46% and a specificity of 82% on bovine feces and a specificity of 99% on carcass samples. The SafePath test, demonstrated a significantly higher sensitivity at 79% and a similar specificity of 79%. On carcass samples the SafePath test performed similarly to the Reveal test, demonstrating a specificity of 100% relative to the reference system. There was an insufficient number of E. coli O157-positive carcass samples to estimate precisely the sensitivity of these two methods. Both methods show promise as rapid carcass monitoring tests, but further field testing to estimate sensitivity is needed to complete their evaluation. The proportion of positive fecal samples for E. coli O157:H7 by the reference method ranged from 10.2% to 36% in 10 lots of cattle with an overall mean of 17.3% (39/225). Quarter carcass sponging of 125 carcasses revealed 1.6% positive for the pathogen (2/125).

PCR-based quantitation of Cryptosporidium parvum in municipal water samples.

A PCR method for the quantitation of Cryptosporidium parvum oocysts in municipal drinking water samples was investigated. Quantitative PCR uses an internal standard (IS) template with unknown target numbers to compare to standards of known concentrations in a standard curve. The IS template was amplified using the same primers used to amplify a portion of a 358 bp gene fragment that encodes a repetitive oocyst wall protein in C. parvum. Municipal water samples spiked with known numbers of C. parvum oocysts were tested by quantitative PCR using the IS and the Digene SHARP Signal System Assay for PCR product detection. The absorbance readings for target DNA and IS templates versus the number of molecules of the target DNA were plotted to generate standard curves for estimating oocyst numbers. The method allowed the quantitation of oocysts from log 3 to log 5 spiked into municipal water samples.

Three sample preparation protocols for polymerase chain reaction based detection of Cryptosporidium parvum in environmental samples.

Cryptosporidium parvum is a protozoan parasite responsible for an increasing number of outbreaks of gastrointestinal illness worldwide. In this report, we describe development of sample preparation protocols for polymerase chain reaction (PCR)-based detection of C. parvum in fecal material and environmental water samples. Two of these methods were found adequate for isolation of Cryptosporidium DNA from filtered water pellet suspensions. The first involved several filtration steps, immunomagnetic separation and freeze-thaw cycles. The second method involved filtration, addition of EnviroAmp lysis reagent, freeze-thaw cycles and precipitation of the DNA with isopropanol. Using nested PCR, we detected 100 oocysts/ml of filtered water pellet suspension, with either of the above sample preparation procedures. Nested PCR increased sensitivity of the assay by two to three orders of magnitude as compared to the primary PCR. The detection limit for seeded fecal samples was 10-fold higher than for filtered environmental water pellet suspension. Nested PCR results showed 62.4 and 91.1% correlation with immunofluorescence assay (IFA) for fecal samples and filtered environmental water pellet suspensions, respectively. This correlation decreased to 47.2% and 44.4%, respectively, when only IFA positive samples were analyzed. However, in fecal samples contaminated with a high number (> 10(5)/g) of C. parvum oocysts, this correlation was 100%.

An automated fluorescent PCR method for detection of shiga toxin-producing Escherichia coli in foods.

An automated fluorescence-based PCR system (a model AG-9600 AmpliSensor analyzer) was investigated to determine whether it could detect Shiga toxin-producing Escherichia coli (STEC). The AmpliSensor PCR assay involves amplification-mediated disruption of a fluorogenic DNA signal duplex (AmpliSensor) that is homologous to conserved target sequences in a 323-bp amplified fragment of Shiga toxin genes stx1, stx2, and stxe. Using the Amplisensor assay, we detected 113 strains of STEC belonging to 50 different serotypes, while 18 strains of non-Shiga-toxin-producing E. coli and 68 strains of other bacteria were not detected. The detection limits of the assay were less than 1 to 5 CFU per PCR mixture when pure cultures of five reference strains were used and 3 CFU per 25 g of food when spiked ground beef samples that were preenriched overnight were used. The performance of the assay was also evaluated by using 53 naturally contaminated meat samples and 48 raw milk samples. Thirty-two STEC-positive samples that were confirmed to be positive by the culture assay were found to be positive when the AmpliSensor assay was used. Nine samples that were found to be positive when the PCR assay was used were culture negative. The system described here is an automated PCR-based system that can be used for detection of all serotypes of STEC in food or clinical samples.

Repeatability of the Petrifilm HEC test and agreement with a hydrophobic grid membrane filtration method for the enumeration of Escherichia coli O157:H7 on beef carcasses.

The Petrifilm HEC test (3M Canada Inc., London, Ontario), a quantitative microbiological test for Escherichia coli O157:H7, was evaluated for its performance as a beef-carcass monitoring test. Test repeatability and agreement and agreement with an E. coli O157:H7 detection method using a hydrophobic grid membrane filter (HGMF) overlaid onto cefixime-tellurite-sorbitol MacConkey agar (CT-SMAC) followed by a latex agglutination test for the O157 antigen were determined by using pure cultures of E. coli O157:H7, beef samples experimentally contaminated with bovine feces containing E. coli O157:H7, and naturally contaminated beef carcasses of unknown E. coli O157:H7 status from a local abattoir. The Petrifilm HEC test showed excellent repeatability and excellent agreement with the HGMF-CT-SMAC method when test samples were obtained from pure cultures and experimentally contaminated meat. All 125 naturally contaminated beef carcasses surveyed were negative for E. coli O157:H7 with both microbial methods. The Petrifilm HEC test, however, demonstrated a significantly lower proportion of cross-reactive organisms (false-positive reactions) than the HGMF-CT-SMAC method. Given the performance of this test coupled with its ease of use and compact size, it shows considerable promise for carcass testing where abattoir laboratory facilities are limited and as a substitute for more complex laboratory testing methods used in established laboratories.

A rapid, sensitive and automated method for detection of Salmonella species in foods using AG-9600 AmpliSensor Analyzer.

The AG-9600 AmpliSensor Analyzer is an automated fluorescence-based system for detection of polymerase chain reaction (PCR) products. The principle of the AmpliSensor PCR assay involves amplification-mediated disruption of a fluorogenic DNA signal duplex (AmpliSensor) that is homologous to a target sequence within a 284-bp amplified fragment of the Salmonella invA gene. Since the assay is homogenous, the data can be obtained by direct measurement of fluorescence of the amplification mixture. The accumulation of the amplified product, reflected by the fluorescence index, is monitored cycle by cycle by the AG-9600 Analyzer. The detection limit of the assay was less than 2 colony-forming units (cfu) per PCR reaction using a pure culture of Salmonella typhimurium. In post-spiking experiments in which Salmonella was added to the overnight pre-enriched samples (chicken carcass rinses, ground beef, ground pork and raw milk), the detection limit of the assay was 2-6 cfu per PCR reaction. In pre-spiking experiments in which Salmonella was added to the samples prior to overnight pre-enrichment, the detection limit was less than 3 cfu per 25 g or 25 ml of food. The assay was up to 2 orders of magnitude more sensitive than detection by ethidium bromide-stained agarose gel electrophoresis. To further evaluate assay performance, 54 naturally contaminated chicken carcass rinses, 65 raw milk and six ground pork samples were tested in the study. Thirty-eight Salmonella-positive samples confirmed by the Modified Semi-solid Rappaport-Vassiliadis (MSRV) culture assay were found positive using the AmpliSensor assay. Two chicken carcass rinses found positive using the assay were MSRV-negative. In addition, relative quantification using the AmpliSensor assay was linear up to 3 logs of initial target concentration in artificially contaminated food samples.

The evaluation of a fluorogenic polymerase chain reaction assay for the detection of Salmonella species in food commodities.

The TaqMan LS-50B PCR Detection System facilitates the automated and direct detection of polymerase chain reaction (PCR) products. The system employs the 5' nuclease activity of Taq DNA polymerase to hydrolyse a Salmonella specific internal fluorogenic probe for monitoring the amplification of a 287-bp region of the Salmonella invA gene. Using the fluorogenic 5' nuclease assay, 164 Salmonella strains representing all the subspecies of Salmonella enterica were detected while over 50 non-Salmonella strains were not detected. The detection limit of the assay was two colony forming units (cfu) per PCR reaction when a pure culture of S. typhimurium was used. Six protocols for the isolation of PCR-amplifiable DNA were evaluated using chicken carcass rinses, ground beef, ground pork and raw milk contaminated with Salmonella. Of the six DNA isolation protocols, a modified sample preparation protocol using the EnviroAmp kit was chosen for subsequent studies because it was reliable, easy to use and efficient for the isolation of PCR-amplifiable DNA from foods. A detection limit of 3-7 cfu per PCR reaction was obtained using food samples that were pre-enriched overnight and then inoculated with Salmonella. The detection limit was below 3 cfu/25 g or 25 ml when foods inoculated with Salmonella were pre-enriched overnight. Naturally contaminated foods (50 chicken carcass rinses and 60 raw milk samples) were examined using both the fluorogenic 5' nuclease assay and a modified semi-solid rappaport vassiliadis (MSRV) culture method. Thirty four of the 110 samples tested were Salmonella-positive and 74 were Salmonella-negative by both the 5' nuclease assay and the MSRV method. Two samples were Salmonella-positive by the 5' nuclease assay, but negative by the MSRV method. The correlation between the 5' nuclease assay and the MSRV method was over 98%.

Development of competitive PCR and the QPCR system 5000 as a transcription-based screen.

We describe the use of the quantitative PCR (QPCR) system 5000 (Perkin-Elmer) and competitive PCR in a simple and reproducible assay format for use in establishing a screen for the discovery of compounds that affect gene regulation. Insulin-like growth factor 1 (IGF-1) mRNA was chosen as an initial target to test the sensitivity and reproducibility of the QPCR System 5000 in the quantitation of PCR products generated in competitive PCR reactions. We found that with the use of sequence-specific probes, the QPCR 5000 could be used easily to distinguish between internal standard (IS) and wild-type products in PCR reactions. We were able to detect as little as twofold changes in cDNA amounts by using dilutions of total rat liver cDNA as a source of IGF-1 message. The QPCR system 5000 could be used to analyze 24 competitive PCR reactions (48 samples), single determinations, in approximately 1 hr. The flexibility, automation, and sensitivity of the QPCR System 5000 makes it a useful tool to measure the transcriptional regulation of various mRNAs.

Amplification of an invA gene sequence of Salmonella typhimurium by polymerase chain reaction as a specific method of detection of Salmonella.

Amplification of nucleotide sequences within the invA gene of Salmonella typhimurium was evaluated as a means of detecting Salmonella. A collection of 630 strains of Salmonella comprising over 100 serovars, including the 20 most prevalent serovars isolated from animals and humans in Canada, was examined. Controls consisted of 142 non-Salmonella strains comprising 21 genera of bacteria. Cultures were screened by inoculating a single colony of bacteria directly into a polymerase chain reaction (PCR) mixture which contained a pair of primers specific for the invA gene. The specific PCR product was a 284 bp DNA fragment which was visualized in 2% agarose gels. With the exception of two S. litchfield and two S. senftenberg strains, all Salmonella strains were detected. In contrast, none of the non-Salmonella strains yielded the specific amplification product. Non-specific amplification of a few non-Salmonella strains resulted in a product that was distinctly different in size from the specific 284 bp product. Specificity of amplification was further confirmed by demonstration of hybridization of a 32P-labelled invA gene fragment only to the specific 284 bp product. The detection of 99.4% of Salmonella strains tested and the failure to specifically amplify DNA from non-Salmonella strains confirm that the invA gene contains sequences unique to Salmonella and demonstrate that this gene is a suitable PCR target, with potential diagnostic applications.

Polymerase chain reaction for detection of verocytotoxigenic Escherichia coli isolated from animal and food sources.

Animals and their by-products have been implicated as important sources of verocytotoxigenic Escherichia coli (VTEC) associated with disease in humans. VTEC comprise a wide range of serotypes and produce a variety of closely related verocytotoxins (VT). A pair of oligonucleotide primers, targeting conserved sequences found in VT1, VT2 and VTE genes, was used to develop a polymerase chain reaction (PCR) procedure to detect all types of VTEC. Supernatants of boiled broth cultures of VTEC (223 strains) isolated from ground beef, ground pork, raw milk, bovine faeces and porcine faeces; non-VTEC E. coli (72 strains); and other enteric and food bacteria (76 strains) were tested by PCR. The verocytotoxigenicity of these strains was verified by the Vero cell assay. All 223 VTEC isolates, comprising over 50 different serotypes, were detected by the PCR procedure. Shigella dysenteriae type 1 was the only other bacterium that was positive in this assay. As little as 1 pg of VTEC DNA and as few as 17 cfu of VTEC could be detected with this method. The results indicate that these primers detect VTEC over a wide range of serotypes. This method may be applicable as a screening procedure for the detection of VTEC in samples of foods and faeces.

Cloning and nucleotide sequence analysis of the genes determining verocytotoxin production in a porcine edema disease isolate of Escherichia coli.

The structural genes determining the edema disease principle were cloned from the total cellular DNA of Escherichia coli strain 412 (O139:K82) isolated from a case of porcine edema disease. An assay for cytotoxicity in Vero cells was used to detect the edema disease principle. A 7.5 kb EcoRI-SalI fragment specifying cytotoxin production was subcloned in pUC18. Sequences which specified production of cytotoxin were localized to a 0.9 kb region by transposon Tn5 mutagenesis. A 2.4 kb EcoRI-BglII fragment encompassing this region was subcloned into pUC18. Using nucleotide sequence analysis, two open reading frames separated by 12 bp were identified. They encoded proteins of 319 (A subunit) and 87 (B subunit) amino acids which both had N-terminal sequences typical of E. coli signal peptides. Comparison of these with the published sequence for the Shiga-like toxin II (SLT-II) showed 91% overall nucleotide sequence similarity. The nucleotide sequence similarity extended to 200 base pairs upstream of the putative A subunit translational start site suggesting a common regulatory mechanism. The deduced amino acid sequences of the processed A and B subunits had 94% and 84% similarity, respectively. These findings confirm the close genetic relationship between SLT-II and edema disease principle.

Antimicrobial susceptibility patterns and R plasmid-mediated resistance of the fish pathogen Yersinia ruckeri.

Fifty strains of Yersinia ruckeri, the causative agent of enteric redmouth disease of salmonid fish, were tested for susceptibility to 23 antimicrobial agents by using an agar dilution procedure. The MICs were generally uniform for all serological varieties. Two of the 50 strains carried a 36-megadalton plasmid which determined resistance to tetracyclines and sulfonamides and was transferable to both Escherichia coli and Y. ruckeri recipients. The serovars did differ in their response to polymyxin B. Strains of serovars II, III, and V were highly resistant (MICs of 128 to 512 micrograms/ml), whereas most serovar I strains were susceptible to less than or equal to 2.0 micrograms/ml. Of 33 serovar I strains, 6 were highly resistant to polymyxin B, which is a characteristic that may divide serovar I (Hagerman) strains into two distinct subgroups.

Transmissible plasmids from Campylobacter jejuni.

Tetracycline resistance in clinical isolates of Campylobacter jejuni was shown to be plasmid mediated. Intra- and interspecies transfers to C. fetus subsp. fetus were demonstrated. The frequency of transfer was increased by approximately 100-fold on a solid surface by using a plate- or filter-mating procedure, as compared with a liquid-mating method. Results of experiments in which cell-free filtrates were used to replace the donor strain in mating experiments tend to rule out bacteriophage-mediated transduction in the transfer of tetracycline resistance. The plasmid-transfer frequency was not affected when deoxyribonuclease was added to the agar used in the mating experiments, indicating that transformation was not involved. Four transmissible plasmids from different tetracycline-resistant strains of C. jejuni each had a molecular weight of 38 x 10(6). Transfer of these plasmids to Escherichia coli was not demonstrated.