Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Reexamination Certificate
1999-07-12
2001-05-22
Zitomer, Stephanie W. (Department: 1655)
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
C536S024300, C536S024320, C536S023740, C536S023100, C435S006120, C435S091100, C435S091200
Reexamination Certificate
active
06235890
ABSTRACT:
FIELD OF THE INVENTION
This invention relates to diagnostic assays for the detection and differentiation of the genus Candida and different species of Candida as well as other microorganisms, and compositions and kits for performing the assays.
BACKGROUND OF THE INVENTION
Candida albicans
is a commensal of the gastrointestinal tract.
C. albicans,
and to a lesser extent several other related species, are of increasing importance as opportunistic pathogens in immunocompromised hosts. A dimorphic, diploid yeast with no known sexual cycle,
C. albicans
is an endogenous organism that can be isolated from skin and mucosal tissues of persons whose immune systems are intact. However, perturbations of the immune or endocrine systems can create opportunities for Candida species to convert from a commensal state to invade tissues either locally or systemically. An example of this opportunism is the oral-esophageal or vaginal candidiasis that is encountered in association with HIV infection.
In
C. albicans
, the nuclear rDNA genes encoding the 5S, 18S, 5.8S, and 28S rRNAs are found as 50-100 copy tandem repeats of approximately 10 kb unit length on chromosome seven (Magee et al., 1987, Thrash-Bingham and Gorman, 1992). The 5S rDNA gene (121 bp) is flanked by two nontranscribed regions located between the small and large subunits, and collectively termed the intergenic spacer (IGS). Ribosomal 5.8S sequences have been compiled from a variety of eukaryotes (Dams et al., 1988). In addition, sequence analysis of the 5.8/28S internally transcribed spacer (ITS) region has shown strain variation within at least one fungal species (O'Donnell, 1992), while other species have demonstrated complete conservation (Mitchell et al., 1992). Strain-specific restriction polymorphisms (RFLPs) have previously been observed in the IGS region for
C. albicans
(Magee et al., 1987).
An opportunistic fungus,
C. albicans
also causes systemic disease in severely immunocompromised hosts. It is the most causative species of disseminated candidiasis followed by
C. tropicalis, C. parapsilosis,
and
C. glabrata
(Odds, 1988). Dissemination occurs when Candida is spread via the bloodstream or by invasion of mucosal surfaces to internal organs (Odds, 1988). High-risk patient populations include individuals with malignancy or neutropenia, those receiving chemotherapy and/or multiple antibiotics, and those with indwelling catheters or low birth weight infants (Armstrong, 1989).
Diagnosis of systemic candidiasis is complicated by the absence of clinically distinguishing signs, frequently negative blood cultures, and the absence of a reliable serological test to detect infection. Currently, disseminated candidiasis is often diagnosed by a minimum of at least two positive blood cultures (Odds, 1988). However, blood culture alone is clearly not sufficient for the diagnosis of disseminated candidiasis since as many as 50% of disseminated candidiasis cases are diagnosed at autopsy (Telenti, et al. 1989). The nephrotoxicity of amphotericin B, the drug of choice for immunocompromised patients with disseminated disease, precludes its use for prophylaxis.
The incidence of disseminated candidiasis has increased in recent years due to the rising number of immunosuppressed and post-operative patients. The advent of new anti-fungal drugs has improved the prospects for management of this disease; however, diagnosis remains difficult. In addition, although fluconazole prophylaxis of bone marrow transplant patients has reduced the incidence of disseminated disease caused by
Candida albicans,
other Candida species which are innately resistant to fluconazole, most notably
C. krusei
and
C. glabrata
, have increased as the primary causative agent. Early detection and identification of Candida species is therefore essential for the proper targeting of antifungal therapy.
These facts, in conjunction with the difficulty of reliably culturing Candida from the blood and the lack of a sensitive and specific serological test to detect disease, underscore the need to develop alternative diagnostic approaches.
Technology has been developed for the detection of bacterial and viral DNA from the bloodstream of infected patients through the use of the polymerase chain reaction (PCR). The PCR amplifies genomic DNA geometrically so that it may be detected by agarose gel electrophoresis, Southern blotting, or dot blot hybridization (Miyakawa et al. 1992, Kafatos et al. 1979, Lasker et al. 1992).
PCR-based diagnostic methods may provide increased sensitivity relative to blood culture techniques since viable organisms are not required for amplification or detection. There has only been one report to date describing the detection of
C. albicans
cells in infected patient blood through the use of PCR-amplified DNA (Buckman et al. 1990). Buchman et al. lysed
C. albicans
cells with ZYMOLYASE and proteinase K and extracted the DNA with phenol and chloroform. The limit of sensitivity by this method was 120 cells per ml of whole blood. As described, this method was time consuming, labor-intensive, repeatedly used toxic chemicals (phenol and chloroform), and has not been shown to be readily reproducible. In addition, a single copy gene, the cytochrome P-450 gene, was the target for DNA amplification, thus making the method much less sensitive. Miyakawa et al. described improved sensitivity by use of Southern blot hybridization for the detection of PCR products from Candida DNA (Miyakawa et al. 1991). The limit of sensitivity by Southern blot in their study was 10 cells per ml of urine and did not address detection in blood.
Use of polymerase chain reaction (PCR)-based tests to detect
C. albicans
DNA in body fluids has produced some encouraging results. However, routine application of these tests for the detection of candidemia remains difficult. Current methods require labor-intensive sample preparation, costly enzymes for liberation of Candida DNA, and phenol-chloroform extraction to purify DNA before PCR amplification. After amplification, detection of PCR products by gel electrophoresis or Southern blotting is often not practical in a clinical laboratory setting. Sensitivity has been variable and false positive as well as false negative results have been reported. Also, most studies have concentrated on the detection of
C. albicans
DNA but not on DNA from non-albicans Candida species.
On the other hand, routine, culture-based identification of Candida species requires at least one day following initial positive results to obtain a pure culture, another day to identify
C. albicans
isolates by germ tube formation, and two or more additional days to identify non-albicans Candida isolates by API-20C sugar assimilation strip tests and cornmeal agar morphology. Therefore, a test to rapidly and accurately identify Candida isolates to the species level would be both clinically and epidemiologically useful.
The ability to detect Candida in blood is crucial for the rapid and accurate diagnosis of systemic candidiasis, because detection from urine or mucosal secretions can be confused with the normal commensal status of the organism or a localized non-disseminated infection.
SUMMARY OF THE INVENTION
The invention provides a rapid approach to species identification through the use of non-conserved regions of the ITS2 flanked by highly conserved, functional domains. Genus and other related organism identification is also enhanced by detection of “genus”-specific regions of the 5.8S rRNA gene. It was surprising to find a region of this gene which enabled us to selectively retrieve the organisms described here.
The present invention provides an isolated double-stranded nucleic acid consisting essentially of the nucleotide sequence defined in the Sequence Listing by SEQ ID NO:5. This is the
C. albicans
ITS2 sequence and includes a nucleic acid comprising a nucleotide sequence that is specific for
C. albicans.
Further examples of an isolated double stranded nucleic acid of the present invention consist essentially of the nucleotide sequences defined i
Holloway Brian
Morrison Christine J.
Reiss Errol
Shin Jong Hee
Klarquist Sparkman Campbell & Leigh & Whinston, LLP
The United States of America as represented by the Department of
Wilder Cynthia
Zitomer Stephanie W.
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