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1 From the Departments of Molecular Virology and Microbiology and 2 Ophthalmology, Baylor College of Medicine, Houston, Texas.
| Abstract |
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METHODS. PCR primers were designed for either the broad-spectrum detection of fungal DNA or the specific detection of C. albicans DNA. Their sequences were based on rDNA regions highly conserved among and specific to fungi and C. albicans, respectively. PCR conditions with the two primer sets were optimized and tested for sensitivity using purified C. albicans genomic DNA and a plasmid containing the relevant region of C. albicans DNA. The specificity of the primer sets was established using higher eukaryotic, fungal, prokaryotic, and viral DNAs as PCR templates. Donor eye swab specimens were collected before corneal excision. DNA was extracted from the specimens and tested by both PCR assays.
RESULTS. The lower limit of detection for both primer sets was consistently 103 genome equivalents, when using genomic DNA as a template and 102 copies of plasmid. The fungal PCR assay amplified DNA from all fungal species tested but did not amplify any of the selected mammalian, bacterial, or viral DNA. The C. albicans PCR detected the C. albicans DNA but was negative for all other DNA substrates, including the other fungal templates. Thirty-five percent of the donor eye samples tested were positive for fungus, and 19% were positive for C. albicans DNA.
CONCLUSIONS. The PCR assays allowed the rapid screening of DNA extracted from specimens collected from corneal donors for potential fungal contamination. The assay was highly sensitive and specific for screening corneal surfaces. The results suggest that approximately one-third of donor eyes tested harbor fungi on the ocular surface.
| Introduction |
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PCR technology has allowed the rapid detection of low copy numbers of DNA in clinical samples of small volume. The purpose of this study was to develop effective PCR-based techniques for the detection of a broad spectrum of fungal DNA and C. albicans DNA specifically from donor eye specimens. The development of these assays resulted in a highly sensitive and specific method for screening corneal donors and has the advantage of rapid detection of fungi from ocular surfaces compared with standard culture methods. Our results indicate a higher prevalence of fungi on the ocular surface of donor eyes than has been previously reported in eyes of healthy individuals. These findings may have implications for the monitoring of mycologic contamination of donor corneas before or during storage in corneal preservation medium.
| Materials and Methods |
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DNA Extraction
Candida albicans strain 32354 was obtained from the
American Type Culture Collection (ATCC; Rockville, MD), and other
control fungal and prokaryotic cultures and clinical samples were
obtained from the Sid W. Richardson Ocular Microbiology Laboratory
collection, Baylor College of Medicine (Houston, TX).
Overnight cultures of C. albicans, Candida parapsilosis, Candida tropicalis, Candida guilliermondii, Candida lipolytica, and Saccharomyces cerevisiae at more than 108 cells/ml were processed for DNA extraction by standard yeast genomic DNA methods,7 with modifications. Briefly, 30-ml cultures were pelleted by centrifugation (10,000g), resuspended in 10 ml sorbitol-EDTA buffer, and incubated with 1.25 mg/ml Lyticase (Sigma, St. Louis, MO) for 3 hours to induce spheroplast formation. The spheroplasts were resuspended in 3 ml Tris-EDTA (TE) buffer and incubated with 10% SDS, and the proteins were precipitated with 5 M potassium acetate. The nucleic acidcontaining supernatant was precipitated with 100% ethanol, resuspended in 4 ml TE buffer, and incubated in the presence of 1 mg/ml RNase A (Roche Diagnostics, Indianapolis, IN). The DNA was extracted three times with phenol-chloroform-isoamyl alcohol (25:24:1), ethanol precipitated, and resuspended in 1 ml TE. Aspergillus flavus was processed for DNA extraction by standard methods.8 For the processing of the donor eye swab pellets and the C. albicansspiked control samples, each pellet was resuspended in 1 ml PBS, and the standard yeast genomic preparation was used with the volumes of all reagents reduced proportionately. Glycogen was used as a carrier.9 10 11
Human DNA was extracted from a human lung fibroblast cell line (MRC-5 cells, CCL-171; ATCC), and murine DNA was extracted from a mouse embryo fibroblast cell line (NIH 3T3 cells, CCL-1658; ATCC). The nucleic acids were extracted, and the DNA was isolated from confluent cell monolayers with an RNA extraction reagent (TRIzol; Gibco BRL, Gaithersburg, MD), as previously described.9 10 11 Calf thymus DNA was obtained from Sigma. One to 3 µg of each DNA template, which corresponds to more than 106 copies of genomic DNA, was used in the PCR reactions.
Escherichia coli and Pseudomonas aeruginosa overnight cultures were processed for genomic DNA extraction by selective precipitation of polysaccharides with hexadecyltrimethyl ammonium bromide (CTAB).7 Herpes simplex virus genomic DNA was extracted according to published methods.12 Purified adenovirus DNA was a generous gift from Ronald Javier, Department of Molecular Virology and Microbiology, Baylor College of Medicine.
Cloning of C. albicans rDNA Region
Total genomic DNA was isolated from C. albicans
strain 32354 and digested with EcoRI. The digested fragments
were separated on a 0.7% agarose gel and transferred to a nylon
membrane for Southern blot analysis.7
A 200-bp
double-stranded DNA probe was generated, by using C.
albicansspecific primers in a PCR containing
32P-dATP.13
An EcoRI
fragment approximately 4 kb in size was identified, isolated, and used
in a ligation reaction with an EcoRI-digested pUC19 plasmid.
The clone pCA1 was identified by colony lift using the 200-bp
probe.7
The plasmid was purified with a kit (Concert
Midiprep; Gibco BRL), and the concentration was adjusted to 1 x
108 copies/µl.
Polymerase Chain Reaction
PCR primers were designed for the detection of broad-spectrum
fungal DNA (F-fwd and F-rev) or C. albicansspecific DNA
(Ca-fwd and Ca-rev). Their sequences were based on BLAST (provided in
the public domain by the National Center for Biotechnology Information
and available at http://www.ncbi.nlm.nih.gov) searches of rDNA regions
highly conserved among and specific to fungi and C.
albicans, respectively. The forward fungal PCR primer (5'-GCA TCG
ATG AAG AAC GCA GC-3') and reverse fungal PCR primer (5'-TCC TCC GCT
TAT TGA TAT GC-3') encompass the highly conserved 5.8s rRNA, internal
transcribed sequence-2 (ITS-2), and 28s rRNA regions and were designed
to amplify a variety of different fungal DNA templates. Although
genetic variation is expected for different fungal species, the fungal
PCR was predicted to amplify a 328-bp region of C. albicans
DNA. The C. albicans forward primer (5'-TCA TCG AAT CTT TGA
ACG CAC A-3') and the reverse primer (5'-GAC GTT ACC GCC GCA AGC A-3')
were designed to specifically amplify C. albicans DNA. The
C. albicansspecific primers were predicted to produce a
200-bp product. PCR conditions previously described10
11
were optimized for the two primer sets, which included 1 pmol of
forward and reverse primers and 5 mM MgCl2 in
50-µl reactions. The cycling was performed at 94°C, 58°C, and
72°C, 3 minutes each for 1 cycle, and 94°C, 58°C, and 72°C, 1
minute each for 30 cycles. Thirty percent of each PCR product was
resolved on a 1.8% agarose Tris-borate-EDTA (TBE) gel and was
visualized using ethidium bromide and ultraviolet excitation.
In addition to size differentiation, the PCR products were confirmed by
Southern blot analysis, using standard methods.7
In
general, the PCR products were immobilized on a nylon membrane by
capillary transfer and hybridized with a probe end labeled with
-[32P]ATP. The probe (5'-GCA TGC CTG TTT GAG
CGT CGT TTC T-3') was designed from internal sequence of the predicted
PCR product of the C. albicansspecific PCR. The
hybridization was performed at 60°C for 16 hours and washed, using
standard methods.7
Autoradiography with the use of
intensifying screens was used for visualization of the blot analysis
results.
| Results |
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PCR Analysis of Donor Eye Swab Specimens
The panfungal and C. albicansspecific PCR assays were
used on pre-excision swab specimens to determine the prevalence of
fungal flora from donor eyes that were to be excised for corneal
transplantation. The samples were systematically collected during a
3-month period and analyzed in a masked fashion. Pellets from 111 swabs
were processed for DNA extraction and tested in both the fungal and
C. albicans PCR assays. Representative results are shown in
Figure 5 . Thirty-five percent (39/111) of the samples tested were positive in
the fungal PCR with 50% of those testing positive in both eyes
(Table 1)
. Several of the samples may have contained more than one organism, as
indicated by the amplification of more than one PCR product (Fig. 5A
,
lanes H and N). Analysis using the C. albicans PCR showed
that 19% (21/111) of the swab specimens were positive for C.
albicans DNA, with 25% of the positive cadavers testing positive
in both eyes. All 21 (100%) of the C. albicanspositive
specimens were positive in the fungal PCR, with at least one band of
the appropriate size (328 bp) for amplification of C.
albicans by the fungal PCR. Multivariable logistic regression,
which controlled for the effects of donor age, gender, and cause of
death, was performed on the PCR data. The odds of having a positive
panfungal PCR was 3.66 times greater when the time of death to time of
collection was 12 hours or more (P = 0.03, 95% confidence
limits, 1.44 and 9.31). Similarly, the odds of PCR showing a positive
C. albicans was 4.67 times greater (P = 0.01,
95% confidence limits, 1.20 and 18.12).
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| Discussion |
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The sensitivity and specificity of the panfungal and C. albicansspecific PCR assays is advantageous, because it makes it possible to rapidly screen specimens from ocular surfaces for mycologic contamination. This allowed the screening of DNA extracted from samples collected from corneal donors for potential fungal contamination. The prevalence of positive samples (35%) determined with our panfungal primers was slightly higher than the range reported previously for ocular fungal flora by culture analysis in the United States (3%28%).3 4 5 However, the prevalence in our study is within the range of the overall carrier rate of fungi reported from various parts of the world in healthy individuals, which varies from 2.5% to 52%. The reasons for the variations in prevalence are not known, but warm moist climates, rural agricultural environments, or advanced age may be associated with an increase in positive fungal cultures.17 A likely reason for the relatively high prevalence observed in our study is the differences between healthy individuals and cadavers. Physiological changes such as differences in tear film or a reduction in eye movements or blinking could feasibly contribute to the amount of fungi present or the ability for the organisms to grow. Other factors that may have contributed to our detection rates include the increased sensitivity of the PCR over standard culture methods and the geographic location of specimens collected. Based on logistic regression analysis, the chance of detecting C. albicans and other fungi in our study was significantly greater when the time between death and donation was prolonged. Yeasts and hyphae may proliferate on the ocular surface after death, migrate from the periocular skin, or reach the decedents eyes from the environment.
Of interest, the broad-spectrum fungal PCR amplified multiple bands of varying sizes in several of the positive samples, indicating more than one organism was present in the swab specimen. This is not necessarily surprising, because many species of fungi are found in the conjunctival sac of a healthy population and because several of these, which are transient colonizers, are also known to be associated with ocular mycoses.17 Table 2 lists several common fungal ocular pathogens and their predicted PCR product size when using our panfungal primers. Some of the nonC. albicans bands we observed were consistent with the predicted sizes of other ocular fungi. For instance, several positive samples had signals corresponding to the predicted size of Aspergillus sp., a common ocular fungus. Analysis of the PCR products by Southern blot or sequencing could be used for genera-specific identification. Regardless, the broad-spectrum PCR was a good indicator of the prevalence of fungi-positive ocular surfaces and a general indication of the diversity in the organisms present. It is also noteworthy that although the C. albicans primers were species specific, 10 different isolates of C. albicans were readily detected with the C. albicans primers, including seven different clinical isolates. This suggests that negative findings with the C. albicansspecific PCR for any of the specimens tested were not negative because of genetic diversity of a particular C. albicans strain.
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| Acknowledgements |
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| Footnotes |
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Submitted for publication June 4, 2001; accepted July 11, 2001.
Commercial relationships policy: N.
The publication costs of this article were defrayed in part by page
charge payment. This article must therefore be marked
"advertisement" in accordance with 18 U.S.C.
1734
solely to indicate this fact.
Corresponding author: Bradley M. Mitchell, Department of Ophthalmology, Baylor College of Medicine, 6565 Fannin Street, NC205, Houston, TX 77030.bmm{at}bcm.tmc.edu
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