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CFSAN
June 9, 1997
Cyclospora cayetanensis Protocol:
Concentration and Preparation of Oocysts from Produce for the
Polymerase Chain Reaction (PCR) and Microscopy
NOTE: This methodology is still evolving. Updates may be issued
at any time. Laboratories unable to undertake the miscroscopic and
PCR analyses should proceed with the wash method (Section II) and
ship the wash sediment (1 ml supernatant plus pellet: Section II,
Step 6) to a lab that can follow up. This works better than
shipping the produce. Brand names and suppliers of reagents are
provided as a convenience and comparable substitutions may be made.
The use of brand names in this protocol does not constitute an
endorsement of that product.
- Reagents & Materials
- Water
- Deionized Water (for washing produce)
- Sterile Deionized Water (for PCR)
- Glass Beads (Sigma #G-9139, TMS silicanized, 140-270 mesh).
- Sterile 1X TE, pH 7.4. (Digene catalog #3400-139 or equivalent product.)
- 50 ml Centrifuge Tubes (eg., 50 ml polypropylene
centrifuge tubes with caps, Gibco #925-4900XT) or 250 ml centrifuge
tubes (Sorvall Instruments #03939 or equivalent) depending on the
centrifuge and rotor used. Reusable tubes are thoroughly washed in
detergent, rinsed 5X (including at least 2X in deionized water) and
drained.
- Epifluoresence Microscope equiped with a UV 1A filter
block (Excitation Filter, EX 365/10; Dichroic mirror,
DM 400; Barrier Filter, BA-400; or equivalent).
- GeneAmp PCR Core Reagent Kit II (Perkin Elmer Catalog
#N808-0009) (no MgCl2)
- Components: AmpliTaq polymerase, 250 Units, 5U/microliter
- GeneAmp dNTPs, set of four, consists of dATP, dTTP, dGTP and
dCTP, each vial containing 320 microliters of a 10 mM solution of
the specified deoxynucleoside triphosphate.
- GeneAmp 10X PCR Buffer II, 1.5 ml, consisting of 500 mM KCl and
100 mM Tris-HCl, pH 8.3.
- MgCl2 solution, 1.5 ml, 25 mM
- Primers: CYCF1E, CYCR2B, CYCF3E and CYCR4B are described
in Relman et al., (J. Infect. Dis. 173:440-445, 1996) and in Table
1. Primers can be commercially prepared (e.g. Midland Certified
Reagent Co.), and the primers are stored at -20°C as a stock
solution of 100 micromolar in deionized water. Prepare a working
solution of 10 micromolar in sterile deionized water and store at
-20°C (in a non-frostfree freezer if possible).
Table 1: PCR Primer Sequences
Primer |
Sequence (5' - 3') |
Use |
CYCF1E |
GGAATTCCTACCCAATGAAAACAGTTT |
1st PCR - forward |
CYCR2B |
CGGGATCCAGGAGAAGCCAAGGTAGG |
1st PCR - reverse |
CYCF3E |
GGAATTCCTTCCGCGCTTCGCTGCGT |
2nd PCR - forward |
CYCR4B |
CGGGATCCCGTCTTCAAACCCCCTACTG |
2nd PCR - reverse |
- Agarose (SeaKem LE Agarose FMC BioProducts catalog
#50004 or equivalent product).
- Ethidium Bromide (Sigma Chemical Co. catalog #E-8751 or equivalent product).
- 1X TBE.
- 100 ml 10X TBE (Digene catalog #3400-1036 or equivalent product).
- 900 ml deionized water.
- Gel Loading Buffer.
- 1 ml Reconstituted Bromphenol blue-Xylene Cyanole Dye Solution
(Sigma catalog #B-3269 or equivalent product).
- 0.6 ml Sterile Glycerol (J.T. Baker Inc. catalog #4043-00 or
equivalent product).
- qs to 2 ml with sterile deionized water.
- 100 bp Molecular Weight Ladder (BioMarker Low,
BioVentures 101, catalog #M-1 or equivalent product).
- Polaroid Type 667 and Type 665 film. Polaroid
Corporation, Cambridge, MA.
- Restriction Endonuclease Enzyme Mnl I
- (Amersham Life Sciences Inc., Arlington Heights, IL) comes with
Buffer M (catalog #E0215Y)
- 4% Nusieve 3:1 agarose or GTG agarose, FMC, Rockland, ME (catalog #50091 or #50081).
- Recovery of Oocysts
Wash Method for Fresh Produce (Berries, Lettuce, ...) or Puree (For Vinaigrette, Proceed to Step 4)
- Prepare a ziplock or stomacher bag containing 250 ml of deionized water (Reagent #1).
- Add 250-500 grams of produce (berries ± 1 berry; USE ONLY
INTACT BERRIES, because the juice from cut or broken berries may be
inhibitory to PCR and debris may interfere with microscopy). Use
250 grams of puree (because this consists of mashed berries, juice
and debris are unavoidable).
- Agitate gently for 20 minutes by placing on a platform shaker
set at 60 to 150 cycles per minute, depending on the condition of
the produce (especially the berries). Invert the bag at 10 minutes
to ensure thorough washing.
- Pour liquid suspension into the centrifuge tubes.
- Centrifuge the 50 ml tubes at 1500 X g for 10 minutes.
Centrifuge the 250 ml tubes at 1500 X g for 20 minutes.
- Decant or aspirate supernatant and discard, leaving
approximately 1 ml of supernatant and pellet fraction. If the 50 ml
tubes are used for centrifugation, all pellet material and residual
supernatant should be combined into one tube. The volume of the
residual supernatant and pellet fraction varies, depending on the
type and condition of samples, and the volume should be recorded.
Appropriate aliquots will be removed from this tube for microscopy
(Section III) and PCR (Section IV). The remaining portion should be
stored at 40°C for up to one month. After one month, the remaining
material should be diluted with an equal volume of 2.5% potassium
dichromate, mixed and stored at 40°C.
NOTE:
If the sediment for the puree is too gelatinous, dilute
one to one with deionized water.
When decanting or aspirating samples with small pellets (e.g. from
lettuce), adjust the volume of supernatant to less than one ml.
Leaving more than one ml of supernatant on top of small pellets may
make microscopy difficult.
- Slide Preparation and Microscopic Analysis
Cyclospora oocysts autofluoresce cobalt blue with the
UV-1A emission filter or blue-green with broader emission spectra
filters under ultraviolet illumination. Prepare slides in
duplicate, and examine slides under ultraviolet illumination as
described below.
Laboratories should use a microscope reticle capable of
measuring 8 - 10 micrometers to check on cyst size when organisms
are recovered. Compare presumptive oocysts to those in a known standard.
- Slide Preparation
- Cover slip should be ringed with silicone vacuum grease.
- Apply 10 microliters of sediment to a clean glass slide and
prepare a wet mount using the pre-greased cover slip.
- Microscopy
- Examine slide under UV light at 400 X. Cyclospora
oocysts fluoresce. Check cyst size and compare to a standard.
- Switch from epifluorescence microscopy to bright field
microscopy or differential interference contrast microscopy to
confirm internal structures of presumptive Cyclospora
oocysts. Recheck size and again compare to a standard.
- Presumptive positive results should be
- preserved by sealing the cover slips to the glass slides using
fingernail polish, slide compound or paraffin wax,
- documented with photographs at multiple planes, and
- confirmed by an expert laboratory.
- PCR Analysis
- Template Extraction and Preparation:
- Remove 100 microliters of produce sediment prepared in Section
II, Step 6 and transfer to a sterile cryo-microcentrifuge tube
(Sarstedt #72.694.006 or equivalent tube should be screw capped and
durable enough to withstand the freeze/thaw procedure). Remove the
end of small bore pipet tips to facilitate pipeting of produce
sediment.
- Centrifuge at 14,000 RPM (15,800 X g) for 3 minutes and discard
supernatant.
- Wash the pellet once with 500 microliters of TE (Section I,
Reagent #3) and centrifuge at 14,000 RPM for 3 minutes.
- Resuspend in 100 microliters TE (Section I, Reagent 3).
- Vortex to resuspend pellet, approximately 10-30 sec.
- Complete 3 freeze/thaw cycles, each 2 min. in liquid nitrogen
or a dry ice-ethanol bath followed by 2 min in a 98°C
waterbath.
- Add 0.1 ± 0.02 g. glass beads (Sigma #G-9139) to
extract.
- Agitate the suspension with a vortex mixer or thermomixer, set
at full speed, for 5 minutes and then chill on ice for 5 minutes. A
mixer attachment for holding multiple samples is useful at this
step.
- Centrifuge sample extract at 14,000 RPM (15,800 X g) for 3
minutes.
- Transfer the supernatant to new sterile microcentrifuge tube.
This extract can be stored frozen (-20°C) until ready for the PCR
analysis, or if needed as reserve in the case of template
inhibition problems.
- Combine 20 microliters of sample extract and 2 microliters of
Non-fat Milk Solution (50 mg instant nonfat dried milk, [Janet Lee
Brand or any food-grade equivalent] in 1 ml sterile deionized
water, prepared fresh the day of the analysis). The entire 22
microliter volume will be used as template in a 100 microliter PCR
amplification.
- PCR Conditions:
- Reagents: Perkin Elmer Kit II (no MgCl2 in 10X buffer)
- Primers: CYCF1E, CYCR2B, CYCF3E and CYCR4B are described in Relman
et al., (J. Infect. Dis. 173:440-445, 1996) and in Table 1 (above).
Primers can be commercially prepared (e.g. Midland Certified
Reagent Co.), and the primers are stored at -20°C as a stock
solution of 100 micromolar in sterile deionized water. Prepare a
working solution of 10 micromolar in sterile deionized water and
store at -20°C (in a non-frostfree freezer if possible).
- Prepare reaction mix as indicated in Table 2:
Table 2: First PCR Reaction Components
Component |
microliters |
Final concentration |
sterile deionized water |
43.5 |
|
10X PCR Buffer II |
10.0 |
50 mM KCl, 10 mM Tris-HCl, pH 8.3 |
dATP, dCTP, dGTP, dTTP 10 mM
each dNTP mixed to give a final concentration of 2.5 mM |
8.0 |
200 micromolar each dNTP |
MgCl2; 25 mM |
8.0 |
2.0 mM |
Primer CYCF1E (10 micromolar) |
4.0 |
0.4 micromolar |
Primer CYCR2B (10 micromolar) |
4.0 |
0.4 micromolar |
AmpliTaq polymerase, 5U/microliter |
0.5 |
2.5 Units |
Template DNA |
22 |
Sample extract prepared above |
- Mix tubes by gently tapping and add 50 microliters (or 2 drops)
sterile mineral oil if required by thermal cycler model.
- All PCR analyses should include positive and negative controls
for each experiment. Positive control DNA template can be prepared
by the extraction of DNA from Eimeria tenella or
Cyclospora cayetanensis oocysts using the method described
above. The positive control reaction should use extracted DNA
equivalent to 25 to 50 oocysts as a template. In a separate
reaction 20 microliters of produce extract spiked with extracted
DNA equivalent to 25 to 50 oocysts should be included as a control
for detecting inhibition by produce extracts. If inhibition by 20
microliters of produce extract is observed, a smaller volume (1 to
10 microliters) of the produce extract should be assayed in a
attempt to overcome the inhibition (appropriate controls should be
included).
- PCR cycling protocol is as shown in Table 3:
Table 3: First PCR thermal cycling parameters
Step |
Temperature/Duration |
Initial Inactivation/Denaturation: 1 cycle |
94°C/3 min |
Amplification: 45 cycles |
|
Denaturation |
94°C/30 sec |
Annealing |
55°C/30 sec |
Extension |
72°C/90 sec |
Final extension: 1 cycle |
72°C/9 min |
Hold (until next PCR round) |
40°C |
- For the second round of PCR add 2 microliters of the first PCR
product to 48 microliters of new reaction mix containing no
template or test fraction. Refer to Table 4 for individual reaction components:
Table 4: Second PCR Reaction Components
Component |
microliters |
Final concentration |
sterile deionized water |
30.75 |
|
10X PCR Buffer II |
5.0 |
50 mM KCl,
10 mM Tris-HCl, pH 8.3 |
dATP, dCTP, dGTP, dTTP 10 mM each dNTP mixed to give a final
concentration of 2.5 mM |
4.0 |
200 micromolar each dNTP |
MgCl2; 25 mM |
4.0 |
2.0 mM |
Primer CYCF3E, 10 micromolar |
2.0 |
0.4 micromolar |
Primer CYCR4B, 10 micromolar |
2.0 |
0.4 micromolar |
AmpliTaq polymerase, 5U/microliter |
0.25 |
1.25 Units |
Template DNA |
2.0 |
From first PCR |
- The second PCR cycling conditions are identical to the first
except that the annealing temperature is 60°C.
- Gel Electrophoresis:
- Mix 10 microliters of the amplification product from the second
round of PCR with 2 microliters gel loading buffer (0.25%
bromphenol blue, 0.25% xylene cyanole and 30% glycerol or
equivalent). If mineral oil has been used, wipe the pipet tip
before mixing reaction material with loading buffer.
- Load the entire volume into a well of a 1.2% agarose gel
prepared with Tris Borate EDTA (TBE) buffer and 0.5 micrograms/ml
ethidium bromide. Alternatively the gel (without ethidium bromide)
can be post stained for 15 minutes with ethidium bromide (1.0
microgram/ml) in TBE. A 100 bp ladder Molecular Weight marker
(BioMarker Low, BioVentures 101, Murfreesboro, TN or equivalent) is
very useful for distinguishing the 308 bp DNA amplification
product, especially because primer-dependent material that is not
Cyclospora DNA is visible at around 100 bp.
- Electrophorese the gel at 8-V/cm for approximately 1 hour.
- PCR products are visualized by UV transillumination and
photographed using Polaroid Type 667 film. The predicted size after
F1E/R2B, is 651 bp; after F3E/R4B is 308 bp. Note: The amplified
product after the first round may not be visible; therefore, only
product from the second round of PCR should be electrophoresed.
- Restriction Endonuclease Fragment Length Polymorphism (RFLP)
Analysis of PCR Amplified Products:
- A PCR product of 308 bp after the second PCR round in the
nested PCR is a presumptive positive for Cyclospora or
Eimeria. The band pattern resulting from digestion of the
amplification product with the restriction enzyme Mnl I
can be used to distinguish between Cyclospora and
Eimeria amplification products.
Combine 10 microliters of amplification product from the second
round of PCR with one unit of the restriction endonuclease enzyme
Mnl I (Amersham Life Sciences Inc., Arlington Heights, IL)
and 5 microliters 10X Buffer M supplied with the restriction enzyme
and bring the final reaction volume up to 50 microliters with
sterile deionized water.
Prepare a separate restriction digest for each presumptive
positive PCR amplification, and amplification products from control
Cyclospora cayetanensis and Eimeria tenella
strains. A digest including 1 microgram lambda DNA should also be
prepared to demonstate complete digestion by the enzyme.
- Incubate the restriction digests 1 hr in a 37°C waterbath.
- Mix 10 microliters of each restriction endonuclease digest with
2 microliters of loading buffer (0.25% bromphenol blue, 0.25%
xylene cyanole and 30% glycerol). Load the entire volume into a
well on a 4% NuSieve 3:1 or GTG agarose (FMC, Rockland, ME) gel
prepared with Tris Borate EDTA (TBE) buffer. Alternate lanes should
contain a molecular size standard ladder (BioMarker Low,
BioVentures 101, Murfreesboro, TN).
- Electrophorese the gel at 5 volts/cm for 3 hr or until the
first dye front is approximately 1 cm from the end of the gel.
- Post-stain the gel in 1X TBE containing 1 microgram/ml ethidium
bromide (Sigma Chemicals, St. Louis, MO) for 10 to 15 min and
destain in deionized water for 1 to 5 min.
- Place the gel on a UV transilluminator and photograph with Type
667 (1 second at f4.5) and/or Type 665 film (50-60 seconds at
f4.5). Develop the negatives from Type 665 film as per
manufacturer's instructions (Polaroid Corp., Cambridge, MA).
- Acquire images by transmission densitometry from the Polaroid
Type 665 film negatives with gel scanner (Sharp JX-325 with film
scan unit or equivalent) as *.tif bitmap images (Adobe Photoshop v.
3.0 or equivalent). Gel analysis software (RFLPScan 3.0 (beta)
Scanalytics Inc., Billerica MA or equivalent) can be used to
analyze gels with user interactive algorithms for the band (peak)
detection and relative peak area (% integrated optical density, OD)
calculations. Band detection parameters of lane width of 39-29.66,
band height threshold of 6-4, and smoothing operator pixel length
of 2-50, allow for the automatic detection of all peaks. The
molecular size standards are entered and properly associated with
the standard peaks for the lanes containing the standards. The
lanes are calibrated using the RFLPScan "de-smile" method with
external lane standards and log piecewise linear regression. Band
data may then be exported to a spreadsheet program (EXCEL 5.0,
Microsoft, Redmond, WA or equivalent).
The band position analysis can also be performed by measuring
the band migration distances from the bottom of the gel wells to
the nearest 0.25 mm with a ruler and using the SeqAid II program
ver. 3.81 (D.J. Roufa, Manhattan, KS or equivalent), or generating
a calibration curve by plotting the logarithm of the number of base
pairs of each standard band versus the migration distance. Table 5
lists the predicted fragment sizes for Cyclospora and
Eimeria amplified products, observed fragment sizes should be
within 5% of the predicted bp sizes.
Table 5: Predicted Restriction Endonuclease
Mnl I Fragment Sizes.
|
Predicted Fragment Sizes |
Organism |
Fragment 1 |
Fragment 2 |
Fragment 3 |
Cyclospora sp. |
146 |
114 |
48 |
Eimeria sp. |
132 |
114 |
62 |
- References
- Chambers, J., Somerfeldt, S., Mackey, L., Nichols, S., Ball, R.,
Roberts, D., Dufford, N., Reddick, A., Gibson, J. (1996). Outbreaks
of Cyclospora cayetanensis infection -- United States,
1996. MMWR 45: 549-551.
- De Boer, S.H., Ward, L.J., Li, X., and Chittaranjan, S. (1995).
Attenuation of PCR inhibition in the presence of plant compounds by
addition of Blotto. Nuc. Acids Res. 23:2567-2568.
- Herwaldt, B.L., Ackers, M-L., and Cyclospora Working
Group (1997). An outbreak of cyclosporiasis associated with
imported raspberries. New England Journal of Medicine. May 29,
1997:1548-1556.
- Huang, P., Weber, J.T., Sosin, D.M., Griffin, P.M., Long, E.G.,
Murphy, J.J., Kocka, F., Peters, C. and Kallick, K.C. (1995). The
first reported outbreak of diarrheal illness associated with
Cyclospora in the United States. Ann. Intern. Med. 123:
409-414.
- Jackson, G.J., Leclerc, J.E., Bier, J.W. and Madden, J.M.
(1997). Cyclospora - Still Another New Foodborne Pathogen.
Food Technology 51:120.
- Jinneman, K.C., Wetherington, J.W., Adams, A.M., Johnson, J. M.
Tenge, B.J., Dang, N.L. and Hill W.E. (1996).
Differentiation of Cyclospora sp. and Eimeria spp.
by Using the Polymerase Chain Reaction Amplification Products and
Restriction Fragment Length Polymorphisms.
FDA Laboratory Information Bulletin 4044
(Web page accessed on February 22, 2008).
Note: For a more recent method for Cyclospora, see the BAM method by Orlandi, et al.
(Reference #10).
- Johnson, D.W., Pieniazek, N.J., Griffin, D.W., Misener, L. and
Rose, J.B. (1995) Development of a PCR protocol for sensitive
detection of Cryptosporidium oocysts in water samples.
Appl. Environ. Microbiol. 61: 3849-3855.
- Levine, N.D. (1985) Phylum II: Apicomplexa. In Illustrated
Guide to the Protozoa, J.J. Lee, S.H. Hunter, and G.C. Boure,
(eds.), Society of Protozoologist, Lawrence, KS, pp. 319-350.
- Noble, E.R., and Noble, G.A. (1971) Parasitology: The
Biology of Animal Parasitology, 3rd ed., Lee and Febiger,
Philadelphia. PA, pp. 84-86.
- Orlandi, P., Frazar, C., Carter, L., Chu, D.,
CFSAN Biological Analytical Methods (BAM) Online, Chapter 19A,
"
Detection of Cyclospora and Cryptosporidium from Fresh
Produce: Isolation and Identification by Polymerase Chain
Reaction (PCR) and Microscopic Analysis", October 2004,
(web page acessed on February 21, 2008).
- Ortega, Y., Sterling, C.R., Gilman, R.H, Cama, V.A, and Diaz, F.
(1993) Cyclospora species -- a new protozoan pathogen of
humans. N. Engl. J. Med. 328: 1308-1312.
- Relman, D.A., Schmidt, T.M., Gajadhar, A., Sogin, M., Cross, J.,
Yoder, K.l., Sethabutr, O., and Echeverria, P. (1996) Molecular
phylogenetic analysis of Cyclospora, the human intestinal
pathogen, suggests that it is closely related to Eimeria
species. J. Infect. Dis. 173:440-445.
- Roxas, C., Miller, N., Cabrera, L., Ortega, Y., Gilman, R., and
Sterling, D. (1996) Vegetables as a potential transmission route
for Cyclospora and Cryptosporidium. Abstracts of
the Annual Meeting of the American Society for Microbiology, C-102,
p.19.
- Yoder, K.E., Sethabutr, O., and Relman, D.A. (1996) PCR-based
detect ion of the intestinal pathogen Cyclospora in
PCR Protocols for Emerging Infectious Diseases, a supplement
to Diagnostic Molecular Microbiology: Principles and
Applications. D.H. Persing (ed.), ASM Press, Washington, DC,
pp.169-176.