WO1996021741A1 - Nucleic acid probes for the detection and identification of fungi - Google Patents
Nucleic acid probes for the detection and identification of fungi Download PDFInfo
- Publication number
- WO1996021741A1 WO1996021741A1 PCT/IB1996/000026 IB9600026W WO9621741A1 WO 1996021741 A1 WO1996021741 A1 WO 1996021741A1 IB 9600026 W IB9600026 W IB 9600026W WO 9621741 A1 WO9621741 A1 WO 9621741A1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- seq
- aspergillus
- candida
- cryptococcus
- probes
- Prior art date
Links
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/37—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from fungi
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
- C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/913—Aspergillus
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/921—Candida
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/921—Candida
- Y10S435/922—Candida albicans
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/921—Candida
- Y10S435/924—Candida tropicalis
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/929—Fusarium
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/931—Mucor
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/933—Penicillium
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/939—Rhizopus
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/94—Saccharomyces
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/8215—Microorganisms
- Y10S435/911—Microorganisms using fungi
- Y10S435/94—Saccharomyces
- Y10S435/942—Saccharomyces cerevisiae
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
- Y10T436/00—Chemistry: analytical and immunological testing
- Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
- Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
- Y10T436/143333—Saccharide [e.g., DNA, etc.]
Definitions
- the inventions described and claimed herein relate to the design and composition of two nucleic acid probes capable of detecting many different fungal organisms in clinical, food, environmental and other samples.
- the inventions described and claimed herein also relate to the design and composition of probes capable of specifically detecting and identifying Acremonium sp., Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigat s, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus terreus, Aspergillus unguis, Aspergillus ustus, Beauveria sp., Bipolaris sp., Blastoschizomyces sp., Blastomyces dermatitidis, Candida albicans, Candida glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida
- Fungi are eukaryotic microorganisms that are universally distributed. While in nature fungi play a major role in the decomposition of plant materials, they are also responsible for spoilage of food, beverage and pharmaceutical preparations. Out of an estimated 100,000 species of fungi described by mycologists, approximately 150 species are pathogenic to man and animals. The increasing incidence of AIDS and the development of newer treatments for hematologic malignancies and organ transplants has lead to an increase in the number of immunocompromised patients. These patients have a high risk of developing fungal infections, which if not rapidly diagnosed and treated are capable of causing death in a matter of days. The number of antifungal drugs is limited and their toxic side effects on the patient are much higher than that of comparable antibacterial therapy. A rapid diagnosis of fungal infection and start of treatment is critical in these patients. Books by Kwon-Chung and Bennett, along with Sarosi and Davies, provide an overview into the medical importance of fungi.
- Fungi may take anywhere from two days to several weeks to grow in culture and often the same organism can take radically different forms depending on the growth conditions. This makes timely identification difficult even for the classically trained expert and impedes the treatment of patients where rapid identification of genus and species is of medical advantage.
- Aspergillus fumigatus is among the top three causes of systemic fungal infection treated in hospitals. It usually affects patients with organ transplants, acute leukemias and burns and can be rapidly fatal if not diagnosed quickly. With over 150 species of Aspergillus present in the soil, air and water, accurate detection of Aspergillus fumigatus becomes extremely important.
- Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus terreus, Aspergillus unguis and Aspergillus ustus represent a majority of Aspergillus species seen in clinical specimens and their presence can cause diagnostic difficulties.
- Aspergillus flavus, Aspergillus fumigatus and Aspergillus niger have been linked with disease in humans, with Aspergillus fumigatus being the predominant pathogen in North America.
- Blastomyces dermatitidis is present in the soil, usually in bird droppings and animal feces. Infections often occur at construction sites and the ensuing lung infiltration and pneumonitis are usually fatal in immunocompromised patients. Diagnosis by culture may take weeks, and the organism is occasionally mistaken for other fungi. Existing immunological diagnostic tests are unreliable, and there is a need for rapid and reliable DNA based diagnostic tests. Similarly, Histoplasma capsulatum exists in the soil and is known to have infected at least 20% of the population of North America. Most infections start in the lung and resolve spontaneously, but may occasionally spread to other organs. AIDS patients represent a growing number of cases of Histoplasmosis.
- Coccidioides immitis is found in abundance in the soil in Southeastern United States. Dust storms, farming, building construction, earthquakes and even hiking have been linked with outbreaks of disease. Lung infection followed by cavitation and disseminated miliary coccidioidomycosis are seen. Meningitis is usually lethal, and as with other fungi, mortality is highest in debilitated hosts.
- Four serotypes of Cryptococcus neoformans cause disease in humans.
- Cryptococcus neoformans serotype A Cryptococcus neoformans var gatti serotype B, Filobasidiella (Cryptococcus) neoformans var bacillispora serotype C and Filobasidiella (Cryptococcus) neoformans var. neoformans serotype D.
- the incidence of this disease is growing rapidly, with up to 10% of HIV infected people developing cryptococcosis.
- DNA probes capable of detecting all 4 serotypes are required for the early diagnosis and treatment for life threatening infections like cryptococcal meningitis.
- Candida albicans is one of the most common causes of fungal infection in humans. It is present in the respiratory, gastrointestinal and female genital tract of healthy individuals, and acts as an opportunistic pathogen in debilitated individuals on steroid or chemotherapy. Diabetes mellitus and indwelling catheters are other predisposing causes. Immunocompromised hosts show rapid hematogenous spread of fungi. Morbidity and mortality in untreated cases is high. Candida glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida lusitaniae, Candida parapsilosis and Candida tropicalis are also known to cause disease in humans. DNA probes capable of identifying these individual species would eliminate the need for multiple blood cultures and lengthy biochemical speciation.
- rDNA ribosomal DNA
- cDNA complementary DNA
- Ribosomes are composites of unique rRNA and protein species that function in the translation of messenger RNA into protein. Evolutionary studies are consistent with the interpretation that all extant life has evolved from a single organism. Thus, all cellular organisms contain rRNA and these rRNAs are related by evolution.
- nucleotide sequence is intended to include either DNA or RNA forms or modification thereof.
- primer sequences can be used as probes and vice versa.
- nucleic acid hybridization to detect specific nucleic acid sequences of interest is also described by Kohne (U.S. Patent 4,851,330, 7/1989).
- ribosomal RNA and the corresponding rDNA genes are identified by the size of the RNA.
- the sizes are related in terms of sedimentation velocity or S values.
- S values are 5S, 16S, and 23S; and for eukaryotes the values are 5S, 5.8S, 18S and 28S.
- all ribosomes perform the same function which is essential for cell viability, ribosomal sequences are largely conserved, yet certain regions of each ribosomal species are subject to more variation without consequence to function. It is these hypervariable regions that allow one to identify different species amongst members of the same genus.
- ITS2 5.8 S RNA and the internal transcribed spacer
- Makimura amplifies a 687 bp fragment from the 18S rDNA of 25 medically important fungi and uses these in the diagnosis of Candida albicans in clinical samples.
- Mitchell uses nested PCR to amplify 5.8S and internal transcribed spacer (ITS) to identify Cryptococcus neoformans. No subsequent testing is done to verify the identity of the amplified DNA.
- Nakamura et. al. use 18S primers to detect Aspergillus fumigatus infections of the lung. Most protocols given in these references can only be used to detect an extremely limited number of fungi from a clinical specimen. Hopfer et. al. and Maiwald et. al. can identify multiple organisms from pure cultures, but their utility for clinical specimens containing multiple fungal species is limited at best.
- United States patents have been issued to Weisburg et. al. for probes developed for the detection of 18S small subunit ribosomal RNA sequences in fungi. These probes will detect fungi from many species, but cannot be used easily to identify any single species. United States patents have also been issued to Milliman for probes developed for the specific detection of the bacteria Staphylococcus aureus based on the 16S ribosomal sequences. Hogan et. al. (European Pat. App. 0,272,009) describe one fungal probe for 18S rRNA and three fungal probes for 28S rRNA sequences.
- 28S probes detect several different fungi while the third probe detects Candida krusei from a limited panel of 10 fungi.
- None of the 28S probes described by Hogan et. al. is related to any of the probes described in our invention. All probes claimed in our invention can be mapped within the first 900 base pairs of a 28S gene. The probes described by Hogan et. al. are located further 3' on the 28S sequence, between base pairs 1000 and 2000 (these numbers are comparable to the primary sequence oi Saccharomyces cerevisiae 28S rRNA gene. Genbank accession number: J01355). Leclerc et. al.
- Leclerc have published reports analyzing the phylogenetic relationship between fungi based on partial DNA sequences of several fungal 28S genes sequenced by them. Some of the organisms claimed to have been sequenced by Leclerc are the same as some organisms sequenced by us. These are Sporothrix schenckii, Pseudallescheria boydii, Blastomyces dermatitidis, Histoplasma capsulatum and Chrysosporium sp. Leclerc et. al. have not published any sequence data in their report, and to the best of our knowledge, they have not made these sequences publically available in the GenBank.
- One aspect of this invention is to provide nucleic acid primers capable of detecting 28 S sequences from DNA or RNA of most fungi. These would be used as “Universal” primers in a polymerase chain reaction to amplify 28S sequences from any fungus present in clinical, food, environmental or other samples. These "Universal” primers would also be used to sequence the amplified DNA. The sequence obtained would be used to identify the fungus by comparing with a database of known fungal sequences.
- a second aspect of this invention is to provide nucleic acid probes capable of detecting and identifying, by nucleic acid hybridization, the pathogens
- nucleotide sequence information is provided to identify these pathogens and other fungi by DNA sequence comparison ( Figure 2) or by the construction of additional probes.
- Nucleic acid probes and primers are described for detecting fungi that cause disease in humans and animals, as well as spoilage of food and beverages. These probes can detect rRNA, rDNA or polymerase chain reaction products from a majority of fungi in clinical, environmental or food samples.
- Figure 1 represents the relative position of the sequences described on the 28S subunit of fungi.
- Figures 2 A, B, C and D together represent the multiple sequence alignment for (SEQ ID NO: 24) through (SEQ ID NO: 74).
- the first objective was to develop nucleic acid primers for use in a polymerase chain reaction to amplify 28S genes from all fungi likely to be present in a clinical sample. This amplified DNA would then be amenable to probing with several different species specific probes. Each one of these species specific probes would, under conditions of hybridization, anneal to 28S ribosomal DNA from only one species of fungus, thereby detecting and identifying the species of fungus present in the clinical sample.
- the 28S gene was selected as a target because it had regions that were conserved among fungi and these would provide potential annealing sites for "universal" fungal probes.
- the ribosomal 28S genes were also expected to have hypervariable regions that would be unique enough to provide sites for species specific probes.
- the large rRNA gene is called the 23 S rRNA gene in prokaryotes and 28S in eukaryotes. This designation is based on the length and therefore the sedimentation coefficient of these rRNA molecules.
- Fungal large subunit rRNAs vary in size among different organisms and are often referred to as being 25S, 26S or 28S. Since fungi are eukaryotes, and to maintain uniformity in this application, we shall refer to fungal large subunit rRNA as 28S rRNA.
- nucleic acid primers PI ATCAATAAGC GGAGGAAAAG
- P2 CTCTGGCTTC ACCCTATTC
- DNA was extracted from the fungi listed above by the following method.
- a loopful of fungal culture was scraped off a culture plate using a sterile inoculation loop.
- the fungus was added one milliliter of sterile water in a 1.5 ml Sarsted (Newton, North Carolina) screw cap microcentrifuge tube. This tube was placed in a boiling water bath for 20 minutes in order to lyse the fungus and release DNA from the cells. Two microliters of this whole cell lysate was used in a PCR to amplify 28S rDNA.
- PCR amplifications were carried out as hot-start reactions in a 50 ul reaction volume using Perkin-Elmer (Norwalk, CT) 0.5 ml thin-wall polypropylene tubes and a Perkin-Elmer thermal cycler.
- Reagents added to the tube initially were 2.5 ul of 10X PCR buffer (100 mM tris pH 8.3, 500 mM KCl, 15 mM gC_2), 5.0 ul of 50% glycerol/1 mM cresol red, 8.0 ul of dNTP mix (1.25 mM each of dATP, dGTP, dTTP and dCTP), 12 picomoles of each nucleic acid primer and sterile water to make up a volume of 25 ul.
- a wax bead (Ampliwax Gem- 100, Perkin-Elmer) was added and the tubes heated to 77°C for 1 minute and cooled to room temperature to form a wax barrier.
- the amplified DNA was electrophoresed and purified from a low melt agarose gel by tris buffered phenol pH 8.0, phenol/chloroform/isoamyl alcohol (25:24:1 by vol.) and 3 ether extractions, followed by isopropanol precipitation and 70% ethanol wash.
- Each probe sequence required an appropriate thermal profile, secondary structure and utility in a DNA amplification reaction.
- These probes were optimized to work for PCR amplification in pure cultures of fungus, as well as in the presence of DNA from multiple sources as in the case of clinical specimens.
- the probes were also designed to facilitate direct sequencing of the amplified DNA.
- Our analysis led to the discovery of the oligonucleotide probes listed in (SEQ ID NO:l) and (SEQ ID NO:2).
- Table 1 Presence of hybridization sites for probes SEQ ID NO: 1 and SEQ ID NO: 2 in 28S nucleic acid sequences.
- Probes SEQ ID NO: 1 and SEQ ID NO: 2 were used to successfully amplify (Table 2) and sequence DNA ( Figure 2) spanning this variable region from the following 49 organisms: Acremonium sp., Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus terreus, Aspergillus unguis, Aspergillus ustus, Beauvaria sp., Bipolaris sp., Blastomyces dermatitidis, Blastoschizomyces sp., Candida albicans, Candida glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida lusitaniae, Candida parapsilosis, Candida tropicalis, Chrysosporium sp.,
- gattii serotype B Cryptococcus terreus, Cryptococcus laurentii, Curvularia sp., Filobasidiella (Cryptococcus) neoformans var bacillispora serotype C, Filobasidiella (Cryptococcus) neoformans var neoformans serotype D, Filobasidium capsuligenum, Filobasidium uniguttulatum, Fusarium sp., Geotrichum sp., Histoplasma capsulatum, Malbranchea sp., Mucor sp., Paecilomyces sp., Penicillium sp., Pseudallescheria boydii, Rhizopus sp., Saccharomyces cerevisiae, Scopulariopsis brevicaulis, Scopulariopsis brumptii, Sporothrix schenkii and Tri
- This list contains all 4 serotypes (A, B, C and D) of Cryptococcus neoformans.
- This sequence information generated by the use of probes SEQ ID NO: 1 and SEQ ID NO: 2 expanded the size of our database consisting of fungal 28S sequences. All amplified DNA was sequenced across both strands from a minimum of two different isolates of each organism to ensure accuracy of the data generated. Table 2:
- This list of fungi sequenced by us represents organisms responsible for most cases of subcutaneous and deep mycotic infections in humans and also includes saprophytes (non-pathogenic fungi) commonly encountered in clinical isolates. Since the two probes (SEQ ID NO: 1 and SEQ ID NO: 2) hybridize to 28S rDNA from all the fungi listed above, they are capable of diagnosing the presence of a majority of fungi that are likely to be present in a clinical specimen. They are believed to be primers for universally detecting fungi.
- Probes listed in SEQ ID NO: 1 and SEQ ID NO: 2 were also checked for their potential ability to hybridize to, and amplify (in a polymerase chain reaction) 23 S sequences from bacteria by searching for hybridization sites among the 539 bacterial 23 S genes listed in GenBank. Bacterial 23 S rDNAs do not have suitable hybridization sites for SEQ ID NO: 1 and SEQ ID NO: 2 and these two probes should not be able to amplify bacterial DNA under stringent conditions.
- sequences incorporating modification of any of the moieties comprising the nucleic acid are functional equivalents of the sequence. It should also be recognized that these additional sequences can potentially serve as probes or primers. Finally, those versed in the art recognize that comparisons of extensive DNA sequences provides enough variability and uniqueness to speciate organisms (Figure 2). The nucleic acid sequences for these species specific synthetic probes are listed in SEQ ID NO: 3 to SEQ ID NO: 23.
- gattii serotype B Cryptococcus terreus, Cryptococcus laurentii, Filobasidiella (Cryptococcus) neoformans var bacillispora serotype C, Filobasidiella (Cryptococcus) neoformans var neoformans serotype D, Filobasidium capsuligenum and Filobasidium uniguttulatum before we were able to identify potential regions for the development of species specific probes for these two fungal organisms that would not cross react with the others listed above.
- the probes developed by us allow rapid species identification of a large number of pathogenic fungi by using multiple probes against only one PCR amplified fragment of DNA. Coupled with our modified DNA extraction technique and our ability to accurately diagnose in the case of mixed organisms, this strategy can provide the greatest amount of diagnostic information in the shortest amount of time. This diagnostic strategy is also amenable to automation, which can result in even greater savings in time, money and effort.
- sequences and the complement of the sequences claimed in this disclosure may potentially be utilized in assays for the identification of fungi based on several existing methodologies, as well as future improvements and alterations of this technology. These techniques include, but are not limited to, assays based on hybridization, ligation, polymerization, depolymerization, sequencing, chemical degradation, enzymatic digestion, electrophoresis, chromatography and amplification. Furthermore, all such variations ultimately are based in some selection or amplification process, some ligand or some nucleic acid moiety that recognizes or utilizes the sequences (SEQ ID NO: 1) to (SEQ ID NO:23) claimed in this application.
- Such variations include but are not limited to use of a variety of linear or exponential target amplification schemes, such as, any of the myriad forms of PCR, the ligase chain reaction, Q-beta repliase, etc.; direct detection of species- specific nucleic acid purified or extracted from pure fungal culture using a probe selected from the group (SEQ ID NO: 3) to (SEQ ID NO: 23); use of the complementary DNA forms of (SEQ ID NO: 1 ) to (SEQ ID NO:23); use of the RNA forms of these sequences and their complements; and use of derivatives of these DNA or RNA sequences by the addition of one or more reporter moieties from a variety of labels including nucleic acid sequences, proteins, signal generating ligands such as acridinium esters, and/or paramagnetic particles.
- These techniques may be utilized with DNA, RNA or modified derivatives used as either the target or the detection molecule.
- SEQ ID NO: 1 to SEQ ID NO: 23 we also describe an additional 51 sequences SEQ ID NO: 24 to SEQ ID NO: 74.
- These 51 sequences are inclusive of SEQ ID NO: 3 to SEQ ID NO: 23 and are shown as a multiple sequence alignment ( Figure 2) with coordinate 1 corresponding to base # 431 of a reference S. cerevisiae 28S rRNA gene. (The numbers are comparable to the primary sequence of S. cerevisiae 28S rRNA gene. Genbank accession number: J01355).
- SEQ ID NO: 1 corresponds to coordinates 403-422 and the SEQ ID NO: 2 corresponds to coordinates 645-662 of the reference S. cerevisiae gene).
- SEQ ID NO: 24 to SEQ ID NO: 74 may be specific for groups of fungi arranged phylogenetically at the level of genus or higher.
- SEQ ID NO: 24 to SEQ ID NO: 74, their complements, along with any modification to these sequences may also potentially be utilized in assays for the identification of fungi based on existing methodologies and future technologies as noted above for SEQ ID NO: 1 to SEQ ID NO: 23.
- the multiple sequence alignment shows the sequence of 28S ribosomal RNA genes amplified with primers SEQ ID NO: 1 and SEQ ID NO: 2. 21 species specific probes (SEQ ID NO: 3 to SEQ ID NO: 23) are shown underlined. Minor sequence variation among two isolate of the same organism are represented by the appropriate code (see key below). Major differences among Rhizopus species are depicted by including 3 separate Rhizopus sequences in the alignment. (The organisms in this figure are listed according to their sequence relatedness.)
- EXAMPLE 1 Testing probes SEQ ID NO: 3 to SEQ ID NO: 23 for hybridization specificity.
- Probes listed in SEQ ID NO: 3 to SEQ ID NO: 23 were tested for specificity against their target organisms.
- Probe SEQ ID NO: 5 for Candida albicans was the first one tested against a panel of fungi taken from the Mayo Clinic collection.
- 28S rDNA from Acremonium sp., Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus terreus, Aspergillus unguis, Aspergillus ustus, Aspergillus sp., Beauvaria sp., Bipolar is sp., Blastomyces dermatitidis, Candida albicans, Candida glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida lusit
- PCR amplifications were carried out as hot-start reactions in a 50 ul reaction volume using Perkin-Elmer (Norwalk, CT) 0.5 ml thin- wall polypropylene tubes and a Perkin-Elmer thermal cycler.
- Reagents added to the tube initially were 2.5 ul of 10X PCR buffer (100 mM tris pH 8.3, 500 mM KCl, 15 mM MgCl 2 ), 5.0 ul of 50% glycerol/1 mM cresol red, 8.0 ul of dNTP mix (1.25 mM each of dATP, dGTP, dTTP and dCTP), 11 picomoles of each nucleic acid primer and sterile water to make up a volume of 25 ul.
- the membrane was washed in hybridization buffer at 40°C for 15 minutes followed by a wash in 2X SSC at 40°C for 15 minutes. The membrane was then exposed on x-ray film for at least 1 hour.
- the oligonucleotide probe SEQ ID NO: 5 only hybridized to amplified 28S rDNA from Candida albicans (see Table 3) Under these hybridization conditions, probe SEQ ID NO: 5 is extremely specific for Candida albicans.
- the sequence of oligonucleotide probe SEQ ID NO: 5 differs from the sequences of other species of Candida by as few as 1 or 2 bases, but these mismatches are sufficient to prevent stable hybrids from forming with the other Candida species.
- Probes SEQ ID NO: 3 to SEQ ID NO: 23 were tested for specificity, as described above for the Candida albicans probe SEQ ID NO: 5, against the same panel of fungi listed in the preceding paragraph.
- the positively charged polysulphone based membrane probed with Candida albicans probe SEQ ID NO: 5 was washed in 0.5 N NaOH at 40°C for 10 minutes to remove all bound Candida albicans probe.
- the membrane was sequentially probed with all probes listed in SEQ ID NO: 3 to SEQ ID NO: 23. For each subsequently tested probe, the membrane was blocked for at least 30 minutes, probe hybridization was carried out at 40-42°C for at least 3 hours, and post-hybridization washes were done in 2X SSC for 20 minutes.
- each probe listed in SEQ ID NO: 3 to SEQ ID NO: 23 specifically hybridizes to only one target fungal 28S nucleic acid sequence. This specificity is essential for identifying a given species of fungus in clinical specimens containing mixed fungal organisms with a high level of reliability.
- the 39 organisms listed in these Tables represent a majority of organisms that are commonly isolated from clinical samples.
- GenBank search was carried out with all probes listed in SEQ ID NO: 3 to SEQ ID NO: 23 in order to determine whether similar gene sequences were present in the database.
- 28S sequences for Candida albicans and one serotype of Cryptococcus neoformans are already present in GenBank, and as expected, the probes for Candida albicans and Cryptococcus neoformans correctly identified the 28S sequences from these two organsims.
- Ten other probes also matched DNA sequences from a variety of genes not related to the 28S gene (Table 7). This was expected because short stretches of sequence identity can often be found for any query sequence in unrelated genes from the same or a different organism. This observation is known to those versed in this art.
- sequences that matched a probe sequence were not located within the 28S rRNA genes.
- Our probes are used to analyze 28S DNA that has been previously amplified in a polymerase chain reaction with our probes SEQ ID NO: 1 and SEQ ID NO: 2. Under stringent conditions, these two probes only amplify DNA from fungal 28S rRNA genes. Therefore no amplified DNA from the non-28S genes listed in Table 7 will be available for the hybridization of probes SEQ ID NO: 3 to SEQ ID NO: 23. The presence of related sequences in non-28S, unamplified genes will not be detected and will, thus, not have any effect on the sensitivity or the specificity of our detection and identification strategy.
- GenBank search results listing genes from other organisms having 100% identity to probes SEQ ID NO: 3 to SEQ ID NO: 23
- Candida albicans 5 Candida albicans 28S rRNA L28817
- Cryptococcus neoformans 7 Cryptococcus neoformans 28S rRNA LI 4067, LI 4068,
- Cryptococcus neoformans 8 Cryptococcus neoformans 28S rRNA LI 4067, LI 4068, L20964
- EXAMPLE 2 Use of method in example 1 to test clinical specimens for specific fungal organisms.
- DNA was extracted from all clinical samples by our modification of the technique of Chomczynski and Sacchi which originally described the use of acid guanidinium thiocyanate- phenol-chloroform to preferentially extract RNA from cells and tissues.
- 1.5 ml Sarsted (Newton, North Carolina) polypropylene screw cap tubes with o-ring seals were used for the extractions.
- the aqueous phase was mixed with 500 ul of 100% isopropanol and placed at -20°C for at least 1 hour. At the end of this period the tubes were centrifuged for 15 minutes and the supernatant removed without disturbing the nucleic acid pellet. The pellet was washed with 500 ul of ice-cold 70% ethanol to remove traces of GPT reagent by gently inverting 2 times and then centrifuged for 5 minutes. The ethanol was removed and the pellet dried in a speed vac for 10 minutes. The pellet was resuspended in 25 ul of sterile deionized water and 5 ul was used in a 50 ul PCR amplification.
- the PCR was carried out as a hot-start reaction using the thermal cycling conditions for probes SEQ ID NO: 1 and SEQ ID NO: 2 described in example 1. Gel electrophoresis showed that probes SEQ ID NO: 1 and SEQ ID NO: 2 successfully amplified DNA from all 44 specimens.
- the amplified DNA from each specimen was transferred to a positively charged polysulphone based membrane.
- Membrane blocking, probe hybridization and washes were done exactly as described in example 1. The results are shown in Table 8.
- EXAMPLE 3 DNA sequence based identification of unknown fungal organisms.
- Probes SEQ ID NO: 1 and SEQ ID NO: 2 are used in a polymerase chain reaction to amplify 28S rDNA from an unknown fungus. Probes SEQ ID NO: 1 or SEQ ID NO: 2 are then used as sequencing primers to obtain DNA sequence from this amplified 28S DNA belonging to the unknown fungus. This DNA sequence is compared to the fungal 28S DNA sequences in our database, and a sequence match at, or overlapping any one of the probe sequences in SEQ ID NO: 3 to SEQ ID NO: 74 will confirm the identity of the fungus.
- This technique cannot be used directly on clinical samples, as these usually contain DNA from more than one fungus, and the DNA sequence generated will consist of overlapping sequences of several organisms. This technique has utility in rapidly and reliably identifying colonies of a single fungus on culture plates, clinical specimens, food, pharmaceutical, environmental or other samples containing only one species of fungus.
- All primers and probes described in this invention disclosure may be labeled with any detectable reporter or signal moiety including, but not limited to radioisotopes, enzymes, antigens, antibodies, chemiluminescent reagents and fluorescent chemicals. Additionally, these probes may be modified without changing the substance of their purpose by terminal addition of nucleotides designed to incorporate restriction sites or other useful sequences. These probes may also be modified by the addition of a capture moiety (including, but not limited to para-magnetic particles, biotin, fluorescein, dioxigenin, antigens, antibodies) or attached to the walls of microtiter trays to assist in the solid phase capture and purification of these probes and any DNA or RNA hybridized to these probes.
- a capture moiety including, but not limited to para-magnetic particles, biotin, fluorescein, dioxigenin, antigens, antibodies
- Fluorescein may be used as a signal moiety as well as a capture moiety, the latter by interacting with an anti-fluorescein antibody.
- a typical utility of these modifications would be as follows.
- Primers SEQ ID NO: 1 and SEQ ID NO: 2 would be utilized to amplify 28S rDNA from a sample, if present, as described previously. Primers would be modified so as to contain a biotin moiety at their 5' ends.
- a streptavidin solid phase, such as a paramagnetic particle, would be used to separate PCR products, if present, from the reaction mixture.
- the amplified target may be subsequently hybridized to a third probe ((SEQ ID NO: 3) to (SEQ ID NO: 74) or their complements) attached to a detectable moiety to determine which species of fungus is present in the given sample.
- a third probe ((SEQ ID NO: 3) to (SEQ ID NO: 74) or their complements) attached to a detectable moiety to determine which species of fungus is present in the given sample.
- Multiple probes, each labeled with a different detectable moiety may be used at one time to analyze the amplified target.
- Primers SEQ ID NO: 1 and SEQ ID NO: 2 would be utilized to amplify 28S rDNA from a sample, if present, as above.
- SEQ ID NO: 1 or SEQ ID NO: 2 would be modified by attachment to a solid phase capture moiety, such as a paramagnetic particle, and SEQ ID NO: 3 to SEQ ID NO: 74 (or their complements) would be modified by addition of a detectable moiety.
- any sequences delimited by SEQ ID NO: 1 and SEQ ID NO: 2 including but not limited to SEQ ID NO: 3 to SEQ ID NO: 74, may be used in the design of a capture probe.
- One of the probes attached to a solid phase (SEQ ID NO: 1 and SEQ ID NO: 2) or any other appropriately designed sequences and one of the probes modified by attachment to a detectable moiety (SEQ ID NO: 3 to SEQ ID NO: 74 or their complements) would be hybridized together, in solution, to products of the PCR, if they had been generated.
- the hybrids, if present, would be captured from the solution, and analyzed by a method appropriate to the detection moiety. Detection of the hybridized probe would indicate which species of fungus was present in the given sample.
- Multiple probes, each labeled with a different detectable moiety may be used at one time to analyze the amplified target.
- EXAMPLE 5 Species-specific amplification of fungal DNA
- one primer is a universal one, such as (SEQ ID NO: 1 ) or (SEQ ID NO:2), and the other is a species-specific primer selected from the group consisting of (SEQ ID NO:3) to (SEQ ID NO: 23) or the complements thereof.
- SEQ ID NO:3 the substitution of (SEQ ID NO:l) or (SEQ ID NO:2) with any functional sequence located in proximity to the species-specific primer.
- SEQ ID NO: 14 substitution of (SEQ ID NO:l) or (SEQ ID NO:2) with any functional sequence located in proximity to the species-specific primer.
- Another variation of this approach is the selection of any appropriate species specific primer pair from SEQ ID NO: 24 to SEQ ID NO: 74.
- MOLECULE TYPE Nucleic acid probe for fungal organisms
- MOLECULE TYPE Nucleic acid probe for fungal organisms
- MOLECULE TYPE Nucleic acid probe for Aspergillus fumigatus
- MOLECULE TYPE Nucleic acid probe for Blastomyces dermatitidis
- MOLECULE TYPE Nucleic acid probe for Candida albicans
- MOLECULE TYPE Nucleic acid probe for Coccidioides immitis
- MOLECULE TYPE Nucleic acid probe for Cryptococcus neoformans
- MOLECULE TYPE Nucleic acid probe for Cryptococcus neoformans
- MOLECULE TYPE Nucleic acid probe for Histoplasma capsulatum
- MOLECULE TYPE Nucleic acid probe for Aspergillus glaucus
- HYPOTHETICAL No
- MOLECULE TYPE Nucleic acid probe for Aspergillus niger
- MOLECULE TYPE Nucleic acid probe for Aspergillus terreus
- MOLECULE TYPE Nucleic acid probe for Candida glabrata
- MOLECULE TYPE Nucleic acid probe for Candida guilliermondii
- MOLECULE TYPE Nucleic acid probe for Candida kefyr
- MOLECULE TYPE Nucleic acid probe for Candida krusei
- MOLECULE TYPE Nucleic acid probe for Candida lusitaniae
- MOLECULE TYPE Nucleic acid probe for Candida parapsilosis
- MOLECULE TYPE Nucleic acid probe for Candida tropicalis
- MOLECULE TYPE Nucleic acid probe for Aspergillus flavus
- MOLECULE TYPE Nucleic acid probe for Sporothrix schenckii
- HYPOTHETICAL No
- MOLECULE TYPE Nucleic acid probe for Sporothrix schenckii
- MOLECULE TYPE Acremonium species specific region of 28S gene.
- GGTGCACTTT GCCGTCCCAG GCCAGCATCA GTTCGCCG GGGGATAAAG GTTTCGGGAA TGTAGCTCCT TCGGGAGTGT TATAGCCCGT TGCGTAATAC CCTGGCGTGG ACTGAGGTCC GCGCTCTGCA AGGATGCTGG CGTAATGGTC ATCAGTGACC CGTCTTGA
- MOLECULE TYPE Aspergillus clavatus specific region of 28S gene.
- MOLECULE TYPE Aspergillus fumigatus specific region of 28S gene
- GACCAGACTC GCTTCCGGGG TTCAGCCGGC TTTCGGGCCG GTGTACTTCC CCGGGGGCGG GCCAGCGTCG GTTTGGGCGG CCGGTCAAAG GCCCCTGGAA TGTAACGCCT CTCGGGGCGC CTTATAGCCA GGGGTGTCAT GCGGCCAGCC TGGACCGAGG AACGCGCTTC GGCACGGACG CTGGCATAAT GGTCGTAAAC GACCCGTCTT GA
- MOLECULE TYPE Aspergillus nidulans specific region of 28S gene.
- SEQ ID NO: 29 GACCAGACTC GGCCCCGGGG TTCARCCAGC ACTCGTGCTG GTGTACTTCC CCGGGGGCGG GCCAGCGTCG GTTTGGGCGG CCGGTCAAAG GCCCCAGGAA TGTATCGCCC TCCGGGGTTG TCTTATAGCC TGGGGTGCAA TGCGGCCAGC CCGGACCGAG GAACGCGCTT CGGCACGGAC GCTGGCGTAA TGGTCGCAAA CGACCCGTCT TGA
- MOLECULE TYPE Aspergillus niger specific region of 28S gene.
- MOLECULE TYPE Aspergillus ochraceus specific region of 28S gene.
- MOLECULE TYPE Aspergillus unguis specific region of 28S gene
- MOLECULE TYPE Aspergillus ustus specific region of 28S gene.
- MOLECULE TYPE Beauveria species specific region of 28S gene
- MOLECULE TYPE Blastoschizomyces species specific region of 28S gene.
- MOLECULE TYPE Blastomyces dermatitidis specific region of 28S gene.
- MOLECULE TYPE Chrysosporium species specific region of 28S gene.
- AACCAGACTT GCGCGCGGCC GATCATCCGG TGTTCTCACC
- GGTGCACTCG GCCGTGCTCA GGCCAGCATC GGTTTTGGCG
- GCTGGATAAA GGCCCTAGGA ATGTGGCTCC TCTCGGGGAG TGTTATAGCC TAGGGTGCAA TGCAGCCTGC TGGGACCGAG
- GACCGCTT CGGCTAGGAT GCTGGCGTAA TGGTTGTAAG CGGCCCGTCT TGA
- MOLECULE TYPE Cladosporium species specific region of 28S gene
- MOLECULE TYPE Curvularia species specific region of 28S gene.
- MOLECULE TYPE Candida albicans specific region of 28S gene.
- MOLECULE TYPE Candida glabrata specific region of 28S gene
- MOLECULE TYPE Candida guilliermondii specific region of 28S gene
- GATCAGACTC GATATTTTGT GAGCCTTGCC TTCGTGGCGG GGTGACCCGC AGCTTATCGG GCCAGCATCG GTTTGGGCGG TAGGATAATG GCGTAGGAAT GTGACTTTRC TTCGGTGAAG TGTTATAGCC TGCGTTGATG CTGCCTGCCT AGACCGAGGA CTGCGATTTT ATCAAGGATG CTGGCATAAT GATCCCAAAC CGCCCGTCTT GA
- MOLECULE TYPE Coccidioides immitis specific region of 28S gene.
- MOLECULE TYPE Candida kefyr specific region of 28S gene.
- MOLECULE TYPE Candida krusei specific region of 28S gene
- MOLECULE TYPE Cryptococcus laurentii specific region of 28 S gene.
- MOLECULE TYPE Candida lusitaniae specific region of 28S gene.
- MOLECULE TYPE Cryptococcus neoformans var gattii (serotype B) specific region of 28S gene.
- MOLECULE TYPE Cryptococcus neoformans (serotype A) specific region of 28S gene.
- MOLECULE TYPE Candida parapsilosis specific region of 28S gene.
Abstract
Description
Claims
Priority Applications (5)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
JP8521540A JPH11500305A (en) | 1995-01-13 | 1996-01-12 | Nucleic acid probes for detection and identification of fungi |
BR9607497A BR9607497A (en) | 1995-01-13 | 1996-01-12 | Nucleic acid probes for the detection and identification of fungi |
EP96900051A EP0804619A1 (en) | 1995-01-13 | 1996-01-12 | Nucleic acid probes for the detection and identification of fungi |
AU43138/96A AU693625B2 (en) | 1995-01-13 | 1996-01-12 | Nucleic acid probes for the detection and identification of fungi |
MXPA/A/1997/005292A MXPA97005292A (en) | 1995-01-13 | 1997-07-11 | Nucleic acid ps for the detection and identification of hon |
Applications Claiming Priority (4)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US08/373,127 US5763169A (en) | 1995-01-13 | 1995-01-13 | Nucleic acid probes for the detection and identification of fungi |
US08/373,127 | 1995-01-13 | ||
US08/435,684 | 1995-05-05 | ||
US08/435,684 US5707802A (en) | 1995-01-13 | 1995-05-05 | Nucleic acid probes for the detection and identification of fungi |
Publications (1)
Publication Number | Publication Date |
---|---|
WO1996021741A1 true WO1996021741A1 (en) | 1996-07-18 |
Family
ID=23471085
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/IB1996/000026 WO1996021741A1 (en) | 1995-01-13 | 1996-01-12 | Nucleic acid probes for the detection and identification of fungi |
Country Status (9)
Country | Link |
---|---|
US (2) | US5763169A (en) |
EP (1) | EP0804619A1 (en) |
JP (1) | JPH11500305A (en) |
KR (1) | KR19987001336A (en) |
AU (1) | AU693625B2 (en) |
BR (1) | BR9607497A (en) |
CA (1) | CA2209247A1 (en) |
PL (1) | PL321139A1 (en) |
WO (1) | WO1996021741A1 (en) |
Cited By (21)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
DE19635347C1 (en) * | 1996-08-31 | 1997-12-18 | Univ Eberhard Karls | Oligo:nucleotide probes specific for fungal species |
WO1998011257A1 (en) * | 1996-09-16 | 1998-03-19 | THE GOVERNMENT OF THE UNITED STATES OF AMERICA, represented by THE SECRETARY, DEPARTMENT OF HEALTH AND HUMAN SERVICES, Centers for Disease Control and Prevention, Technology Transfer Office | Methods and compositions for the detection of candida spp. |
WO1998050584A2 (en) * | 1997-05-02 | 1998-11-12 | THE GOVERNMENT OF THE UNITED STATES OF AMERICA as represented by THE SECRETARY OF THE DEPARTMENT OF HEALTH AND HUMAN SERVICES, c/o Centers for Disease Control and Prevention, Technology Transfer Offic | Nucleic acids for detecting aspergillus species and other filamentous fungi |
WO1998055649A1 (en) * | 1997-06-06 | 1998-12-10 | Bayer Corporation | Nucleic acid probes for the detection and identification of fungi |
WO1999006596A1 (en) * | 1997-07-30 | 1999-02-11 | The Government Of The United States Of America, Represented By The Secretary Of The Department Of Health And Human Services, Centers For Disease Control And Prevention, Office Of Technology Transfer, Building 4, Suite 1103, Executive Park | Nucleic acid probes for detecting candida species |
WO1999054508A1 (en) * | 1998-04-21 | 1999-10-28 | The Government Of The United States Of America, Represented By The Secretary Of The Department Of Health And Human Services | RAPID AND SENSITIVE METHOD FOR DETECTING $i(HISTOPLASMA CAPSULATUM) |
EP1036196A1 (en) * | 1997-12-08 | 2000-09-20 | E. & J. Gallo Winery | Detection of fungal pathogens |
WO2000073499A2 (en) * | 1999-05-28 | 2000-12-07 | Innogenetics N.V. | Nucleic acid probes and methods for detecting clinically important fungal pathogens |
US6469156B1 (en) | 1999-04-20 | 2002-10-22 | The United States Of America As Represented By The Department Of Health And Human Services | Rapid and sensitive method for detecting histoplasma capsulatum |
WO2004079333A2 (en) * | 2003-01-15 | 2004-09-16 | Ic & G Co., Ltd. | Method and kit for extracting rna from sputum |
US7052837B2 (en) | 2001-03-13 | 2006-05-30 | The Board Of Trustees Of The University Of Arkansas | Histoplasma capsulatum catalase sequences and their use in the detection of Histoplamsa capsulatum and histoplasmosis |
US7217519B1 (en) | 2002-11-21 | 2007-05-15 | The Board Of Trustees Of The University Of Arkansas | Histoplasma capsulatum chitin synthase sequences and their use for detection of Histoplasma capsulatum and histoplasmosis |
WO2007132589A1 (en) * | 2006-05-16 | 2007-11-22 | Kirin Beer Kabushiki Kaisha | Primer set for detection of dekkera yeast or brettanomyces yeast |
US7449328B2 (en) | 1999-05-03 | 2008-11-11 | Gen-Probe Incorporated | Probe matrix-based device for identifying microorganisms |
US20100068718A1 (en) * | 2008-08-22 | 2010-03-18 | Hooper Dennis G | Methods and Compositions for Identifying Yeast |
WO2011098907A2 (en) | 2010-02-15 | 2011-08-18 | Council Of Scientific & Industrial Research | Method for detecting fungal pathogens |
EP2765204A1 (en) * | 2013-02-06 | 2014-08-13 | Medical Service Consultation International LLC | Methods and compositions for detecting aspergillus terreus, aspergillus niger, and mycotoxins |
US8962251B2 (en) | 2009-10-08 | 2015-02-24 | Medical Service Consultation International, Llc | Methods and compositions for identifying sulfur and iron modifying bacteria |
US9103829B2 (en) | 2006-04-01 | 2015-08-11 | Medical Service Consultation International, Llc | Methods and compositions for detecting fungi and mycotoxins |
CN112680541A (en) * | 2021-01-20 | 2021-04-20 | 中迅优检生物科技(江苏)有限公司 | LNA-Taqman-multiplex fluorescence PCR technology and application thereof in rapid detection of candida |
CN113106167A (en) * | 2021-04-26 | 2021-07-13 | 北京大学第一医院 | Primer and probe for invasive aspergillosis pathogenic bacteria, implementation method and detection system thereof |
Families Citing this family (78)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20110166040A1 (en) * | 1997-09-05 | 2011-07-07 | Ibis Biosciences, Inc. | Compositions for use in identification of strains of e. coli o157:h7 |
WO2001014592A2 (en) * | 1999-08-25 | 2001-03-01 | Clarity Biosciences, Inc. | Identifying organisms by detecting intronic nucleic acid or encoded proteins |
US6248535B1 (en) * | 1999-12-20 | 2001-06-19 | University Of Southern California | Method for isolation of RNA from formalin-fixed paraffin-embedded tissue specimens |
ATE527373T1 (en) * | 2001-03-01 | 2011-10-15 | Clarity Biosciences Inc | PRODUCTION METHODS AND USES FOR COMPOSITIONS MODULATING PROTEIN FUNCTION ENCODED IN THE INTRON AREA |
US20040121313A1 (en) * | 2002-12-06 | 2004-06-24 | Ecker David J. | Methods for rapid detection and identification of bioagents in organs for transplantation |
US7718354B2 (en) | 2001-03-02 | 2010-05-18 | Ibis Biosciences, Inc. | Methods for rapid identification of pathogens in humans and animals |
US7666588B2 (en) | 2001-03-02 | 2010-02-23 | Ibis Biosciences, Inc. | Methods for rapid forensic analysis of mitochondrial DNA and characterization of mitochondrial DNA heteroplasmy |
WO2004060278A2 (en) | 2002-12-06 | 2004-07-22 | Isis Pharmaceuticals, Inc. | Methods for rapid identification of pathogens in humans and animals |
US20030027135A1 (en) | 2001-03-02 | 2003-02-06 | Ecker David J. | Method for rapid detection and identification of bioagents |
US7226739B2 (en) | 2001-03-02 | 2007-06-05 | Isis Pharmaceuticals, Inc | Methods for rapid detection and identification of bioagents in epidemiological and forensic investigations |
WO2002079512A2 (en) * | 2001-03-29 | 2002-10-10 | University Of Nevada - Las Vegas | Method for detection and quantification of the fungus aspergillus fumigatus using quantitative pcr |
US7217510B2 (en) | 2001-06-26 | 2007-05-15 | Isis Pharmaceuticals, Inc. | Methods for providing bacterial bioagent characterizing information |
US8073627B2 (en) * | 2001-06-26 | 2011-12-06 | Ibis Biosciences, Inc. | System for indentification of pathogens |
US20050065330A1 (en) * | 2002-04-24 | 2005-03-24 | The Cleveland Clinic Foundation | Identification of Histoplasma capsulatum using a PCR assay |
AU2004206246B2 (en) * | 2003-01-17 | 2009-10-01 | Luminex Corporation | Nucleic acid amplification using non-standard bases |
US8046171B2 (en) | 2003-04-18 | 2011-10-25 | Ibis Biosciences, Inc. | Methods and apparatus for genetic evaluation |
US8057993B2 (en) | 2003-04-26 | 2011-11-15 | Ibis Biosciences, Inc. | Methods for identification of coronaviruses |
US7964343B2 (en) | 2003-05-13 | 2011-06-21 | Ibis Biosciences, Inc. | Method for rapid purification of nucleic acids for subsequent analysis by mass spectrometry by solution capture |
US8158354B2 (en) | 2003-05-13 | 2012-04-17 | Ibis Biosciences, Inc. | Methods for rapid purification of nucleic acids for subsequent analysis by mass spectrometry by solution capture |
US8546082B2 (en) | 2003-09-11 | 2013-10-01 | Ibis Biosciences, Inc. | Methods for identification of sepsis-causing bacteria |
US20100129811A1 (en) * | 2003-09-11 | 2010-05-27 | Ibis Biosciences, Inc. | Compositions for use in identification of pseudomonas aeruginosa |
US8097416B2 (en) | 2003-09-11 | 2012-01-17 | Ibis Biosciences, Inc. | Methods for identification of sepsis-causing bacteria |
US20120122103A1 (en) | 2003-09-11 | 2012-05-17 | Rangarajan Sampath | Compositions for use in identification of bacteria |
US8163895B2 (en) | 2003-12-05 | 2012-04-24 | Ibis Biosciences, Inc. | Compositions for use in identification of orthopoxviruses |
US7666592B2 (en) * | 2004-02-18 | 2010-02-23 | Ibis Biosciences, Inc. | Methods for concurrent identification and quantification of an unknown bioagent |
US8119336B2 (en) | 2004-03-03 | 2012-02-21 | Ibis Biosciences, Inc. | Compositions for use in identification of alphaviruses |
EP2458619B1 (en) | 2004-05-24 | 2017-08-02 | Ibis Biosciences, Inc. | Mass spectrometry with selective ion filtration by digital thresholding |
US20050266411A1 (en) | 2004-05-25 | 2005-12-01 | Hofstadler Steven A | Methods for rapid forensic analysis of mitochondrial DNA |
US7811753B2 (en) | 2004-07-14 | 2010-10-12 | Ibis Biosciences, Inc. | Methods for repairing degraded DNA |
US7309589B2 (en) | 2004-08-20 | 2007-12-18 | Vironix Llc | Sensitive detection of bacteria by improved nested polymerase chain reaction targeting the 16S ribosomal RNA gene and identification of bacterial species by amplicon sequencing |
CA2600184A1 (en) | 2005-03-03 | 2006-09-08 | Isis Pharmaceuticals, Inc. | Compositions for use in identification of adventitious viruses |
US8084207B2 (en) | 2005-03-03 | 2011-12-27 | Ibis Bioscience, Inc. | Compositions for use in identification of papillomavirus |
US8026084B2 (en) | 2005-07-21 | 2011-09-27 | Ibis Biosciences, Inc. | Methods for rapid identification and quantitation of nucleic acid variants |
EP1945810B1 (en) * | 2005-09-20 | 2015-07-01 | AdvanDx, Inc. | Reagents, methods and kits for classification of fungi and direction of anti-fungal therapy |
JP4886784B2 (en) * | 2005-09-27 | 2012-02-29 | ザ ガバメント オブ ザ ユナイテッド ステイツ オブ アメリカ アズ リプレゼンティド バイ ザ セクレタリー オブ ザ ディパートメント オブ ヘルス アンド ヒューマン サービシズ, センターズ | Compositions and methods for detection of Candida species |
EP1960536B1 (en) * | 2005-11-30 | 2013-06-26 | St. Anna Kinderkrebsforschung | Detection of fungi |
JP2007159411A (en) * | 2005-12-09 | 2007-06-28 | Canon Inc | Probe set, probe-fixing carrier and method for examining gene |
WO2007118222A2 (en) | 2006-04-06 | 2007-10-18 | Ibis Biosciences, INC | Compositions for the use in identification of fungi |
US9149473B2 (en) | 2006-09-14 | 2015-10-06 | Ibis Biosciences, Inc. | Targeted whole genome amplification method for identification of pathogens |
IE20060925A1 (en) * | 2006-12-15 | 2008-06-25 | Nat University Of Ireland Galway | Nucleic acids probes for detection of yeast and fungal species |
WO2008104002A2 (en) | 2007-02-23 | 2008-08-28 | Ibis Biosciences, Inc. | Methods for rapid forensic dna analysis |
WO2009023358A2 (en) * | 2007-05-25 | 2009-02-19 | Ibis Biosciences, Inc. | Compositions for use in identification of strains of hepatitis c virus |
WO2008151023A2 (en) | 2007-06-01 | 2008-12-11 | Ibis Biosciences, Inc. | Methods and compositions for multiple displacement amplification of nucleic acids |
US20110045456A1 (en) * | 2007-06-14 | 2011-02-24 | Ibis Biosciences, Inc. | Compositions for use in identification of adventitious contaminant viruses |
US7989186B2 (en) * | 2007-06-20 | 2011-08-02 | Medical Diagnostic Laboratories, Llc | Compositions and methods for detecting cryptococcus neoformans |
CA2715991A1 (en) * | 2007-12-26 | 2009-07-09 | Gen-Probe Incorporated | Amplification oligomers and methods to detect candida albicans 26s rrna or encoding dna |
US20110097704A1 (en) * | 2008-01-29 | 2011-04-28 | Ibis Biosciences, Inc. | Compositions for use in identification of picornaviruses |
US20110245094A1 (en) * | 2008-05-02 | 2011-10-06 | Immunetics, Inc. | Detection of microbial nucleic acids |
WO2009155103A2 (en) * | 2008-05-30 | 2009-12-23 | Ibis Biosciences, Inc. | Compositions for use in identification of tick-borne pathogens |
WO2009151982A1 (en) * | 2008-05-30 | 2009-12-17 | Ibis Biosciences, Inc. | Compositions for use in identification of francisella |
US20110151437A1 (en) * | 2008-06-02 | 2011-06-23 | Ibis Biosciences, Inc. | Compositions for use in identification of adventitious viruses |
EP2349549B1 (en) | 2008-09-16 | 2012-07-18 | Ibis Biosciences, Inc. | Mixing cartridges, mixing stations, and related kits, and system |
US8534447B2 (en) | 2008-09-16 | 2013-09-17 | Ibis Biosciences, Inc. | Microplate handling systems and related computer program products and methods |
US8148163B2 (en) | 2008-09-16 | 2012-04-03 | Ibis Biosciences, Inc. | Sample processing units, systems, and related methods |
US20110189687A1 (en) * | 2008-10-02 | 2011-08-04 | Ibis Bioscience, Inc. | Compositions for use in identification of members of the bacterial genus mycoplasma |
US20110200985A1 (en) * | 2008-10-02 | 2011-08-18 | Rangarajan Sampath | Compositions for use in identification of herpesviruses |
WO2010039787A1 (en) * | 2008-10-03 | 2010-04-08 | Ibis Biosciences, Inc. | Compositions for use in identification of clostridium difficile |
WO2010039870A1 (en) * | 2008-10-03 | 2010-04-08 | Ibis Biosciences, Inc. | Compositions for use in identification of neisseria, chlamydia, and/or chlamydophila bacteria |
WO2010039848A2 (en) * | 2008-10-03 | 2010-04-08 | Ibis Biosciences, Inc. | Compositions for use in identification of streptococcus pneumoniae |
US20110190170A1 (en) * | 2008-10-03 | 2011-08-04 | Ibis Biosciences, Inc. | Compositions for use in identification of antibiotic-resistant bacteria |
US20110183343A1 (en) * | 2008-10-03 | 2011-07-28 | Rangarajan Sampath | Compositions for use in identification of members of the bacterial class alphaproteobacter |
HUP0800722A2 (en) * | 2008-11-26 | 2010-05-28 | Debreceni Egyetem | Oligonucleotides for the identification of fungi belonging to the aspergillus genus |
WO2010093943A1 (en) | 2009-02-12 | 2010-08-19 | Ibis Biosciences, Inc. | Ionization probe assemblies |
WO2010104798A1 (en) | 2009-03-08 | 2010-09-16 | Ibis Biosciences, Inc. | Bioagent detection methods |
MX352246B (en) | 2009-03-18 | 2017-10-25 | Instituto Potosino De Investig Cientifica Y Tecnologica A C | In vitro method for detecting candida glabrata, diagnosis kit and use thereof. |
US9393564B2 (en) | 2009-03-30 | 2016-07-19 | Ibis Biosciences, Inc. | Bioagent detection systems, devices, and methods |
US8950604B2 (en) | 2009-07-17 | 2015-02-10 | Ibis Biosciences, Inc. | Lift and mount apparatus |
EP2454000A4 (en) | 2009-07-17 | 2016-08-10 | Ibis Biosciences Inc | Systems for bioagent identification |
WO2011014811A1 (en) | 2009-07-31 | 2011-02-03 | Ibis Biosciences, Inc. | Capture primers and capture sequence linked solid supports for molecular diagnostic tests |
WO2011017656A2 (en) | 2009-08-06 | 2011-02-10 | Ibis Biosciences, Inc. | Non-mass determined base compositions for nucleic acid detection |
US20110065111A1 (en) * | 2009-08-31 | 2011-03-17 | Ibis Biosciences, Inc. | Compositions For Use In Genotyping Of Klebsiella Pneumoniae |
ES2628739T3 (en) | 2009-10-15 | 2017-08-03 | Ibis Biosciences, Inc. | Multiple displacement amplification |
CA2803401C (en) * | 2010-01-26 | 2019-02-19 | The Translational Genomics Research Institute | Methods and kits used in the detection of fungus |
WO2011115840A2 (en) * | 2010-03-14 | 2011-09-22 | Ibis Biosciences, Inc. | Parasite detection via endosymbiont detection |
JP5680989B2 (en) * | 2011-02-25 | 2015-03-04 | ハウス食品グループ本社株式会社 | Primer / probe set for detecting non-human animals |
CN107130015B (en) * | 2016-02-29 | 2023-07-11 | 上海翔琼生物技术有限公司 | Fluorescent quantitative PCR kit for detecting aspergillus fumigatus |
CN108034745B (en) * | 2017-12-21 | 2020-04-17 | 杭州缔蓝生物技术有限公司 | Primer probe combination and kit for simultaneously detecting four candida |
CN109536634A (en) * | 2019-01-25 | 2019-03-29 | 武汉睿健医药科技有限公司 | Universal primer, kit and the detection method that fungal contamination detects in cell product |
Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP0422872A2 (en) * | 1989-10-12 | 1991-04-17 | Gene-Trak Systems | Nucleic acid probes and methods for detecting fungi |
US5352579A (en) * | 1991-06-28 | 1994-10-04 | Gen Probe, Inc. | Nucleic acid probes to histoplasma capsulatum |
Family Cites Families (14)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5288611A (en) * | 1983-01-10 | 1994-02-22 | Gen-Probe Incorporated | Method for detecting, identifying, and quantitating organisms and viruses |
EP0531798B2 (en) * | 1983-01-10 | 2003-12-17 | Gen-Probe Incorporated | Method for detecting, identifying, and quantitating organisms and viruses |
US5541308A (en) * | 1986-11-24 | 1996-07-30 | Gen-Probe Incorporated | Nucleic acid probes for detection and/or quantitation of non-viral organisms |
DE3752172T3 (en) * | 1986-11-24 | 2008-04-10 | Gen-Probe Inc., San Diego | Nucleic acid probes for the detection and / or quantitation of non-viral organisms |
US5525464A (en) * | 1987-04-01 | 1996-06-11 | Hyseq, Inc. | Method of sequencing by hybridization of oligonucleotide probes |
GB8802667D0 (en) * | 1988-02-05 | 1988-03-02 | Chancellor Masters & Scholars | Probe for pneumoxystis carinii |
PT94001A (en) * | 1989-05-11 | 1991-02-08 | Xytronyx Inc | PROCESS OF DETECTION OF THE PRESENCE OF AN INFECTION BY PNEUMOCYSTIS CARINII |
AU6356390A (en) * | 1989-08-11 | 1991-03-11 | Gene-Trak Systems | Nucleic acid probes for the detection of (pneumocystis carinii) |
US5364759B2 (en) * | 1991-01-31 | 1999-07-20 | Baylor College Medicine | Dna typing with short tandem repeat polymorphisms and identification of polymorphic short tandem repeats |
US5292874A (en) * | 1991-09-04 | 1994-03-08 | Gen-Probe Incorporated | Nucleic acid probes to Staphylococcus aureus |
US5284747A (en) * | 1991-12-18 | 1994-02-08 | Gen-Probe Incorporated | Nucleic acid probes to Coccidioides immitis |
US5407814A (en) * | 1992-03-20 | 1995-04-18 | The Secretary Of State For The Minister Of Agriculture, Fisheries & Food In Her Britannic Majesty's Government Of The United Kingdom Of Great Britain And Northern Ireland | Genetic fingerprinting of yeasts |
US5580971A (en) * | 1992-07-28 | 1996-12-03 | Hitachi Chemical Company, Ltd. | Fungal detection system based on rRNA probes |
US5503980A (en) * | 1992-11-06 | 1996-04-02 | Trustees Of Boston University | Positional sequencing by hybridization |
-
1995
- 1995-01-13 US US08/373,127 patent/US5763169A/en not_active Expired - Fee Related
-
1996
- 1996-01-12 EP EP96900051A patent/EP0804619A1/en not_active Withdrawn
- 1996-01-12 WO PCT/IB1996/000026 patent/WO1996021741A1/en not_active Application Discontinuation
- 1996-01-12 PL PL96321139A patent/PL321139A1/en unknown
- 1996-01-12 BR BR9607497A patent/BR9607497A/en not_active Application Discontinuation
- 1996-01-12 AU AU43138/96A patent/AU693625B2/en not_active Ceased
- 1996-01-12 JP JP8521540A patent/JPH11500305A/en active Pending
- 1996-01-12 CA CA002209247A patent/CA2209247A1/en not_active Abandoned
-
1997
- 1997-07-10 KR KR19977004725A patent/KR19987001336A/ko unknown
- 1997-09-22 US US08/934,877 patent/US5958693A/en not_active Expired - Fee Related
Patent Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP0422872A2 (en) * | 1989-10-12 | 1991-04-17 | Gene-Trak Systems | Nucleic acid probes and methods for detecting fungi |
US5352579A (en) * | 1991-06-28 | 1994-10-04 | Gen Probe, Inc. | Nucleic acid probes to histoplasma capsulatum |
Non-Patent Citations (6)
Title |
---|
CARR L G ET AL: "ORGANIZATION OF THE 5.8S 16-18S AND 23-28S RIBOSOMAL RNA GENES OF CEPHALOSPORIUM-ACREMONIUM", CURR GENET, 12 (3). 1987. 209-214., XP002002932 * |
LECLERC M C ET AL: "Phylogeny of dermatophytes and dimorphic fungi based on large subunit ribosomal RNA sequence comparisons", JOURNAL OF MEDICAL AND VETERINARY MYCOLOGY, 32 (5). 1994. 331-341., XP002002929 * |
MOUKHAMEDOV R ET AL: "Use of polymerase chain reaction-amplified ribosomal intergenic sequences for the diagnosis of Verticillium tricorpus", PHYTOPATHOLOGY, 84 (3). 1994. 256-259., XP002002931 * |
NEUVEGLISE C ET AL: "Identification of group-I introns in the 28s rDNA of the entomopathogenic fungus Beauveria brongniartii", CURRENT GENETICS, 27 (1). 1994. 38-45., XP002002930 * |
SANDHU G S ET AL: "Molecular probes for diagnosis of fungal infections", JOURNAL OF CLINICAL MICROBIOLOGY, 33 (11). 1995. 2913-2919., XP002002934 * |
VILGALYS R. ET AL.: "Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species", JOURNAL OF BACTERIOLOGY, vol. 172, no. 8, 1990, pages 4238 - 4246, XP002002933 * |
Cited By (45)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US6180339B1 (en) | 1995-01-13 | 2001-01-30 | Bayer Corporation | Nucleic acid probes for the detection and identification of fungi |
WO1998008972A1 (en) * | 1996-08-31 | 1998-03-05 | Eberhard-Karls-Universität Tübingen | Sequential hybridization of fungal cell dna and method for the detection of fungal cells in clinical material |
DE19635347C1 (en) * | 1996-08-31 | 1997-12-18 | Univ Eberhard Karls | Oligo:nucleotide probes specific for fungal species |
US6046006A (en) * | 1996-08-31 | 2000-04-04 | Eberhard-Karls-Universitat | Sequential hybridization of fungal cell DNA and method for the detection of fungal cells in clinical material |
WO1998011257A1 (en) * | 1996-09-16 | 1998-03-19 | THE GOVERNMENT OF THE UNITED STATES OF AMERICA, represented by THE SECRETARY, DEPARTMENT OF HEALTH AND HUMAN SERVICES, Centers for Disease Control and Prevention, Technology Transfer Office | Methods and compositions for the detection of candida spp. |
US6235890B1 (en) | 1996-09-16 | 2001-05-22 | The United States Of America As Represented By The Department Of Health And Human Services | Methods and compositions for the detection of Candida spp. |
WO1998050584A2 (en) * | 1997-05-02 | 1998-11-12 | THE GOVERNMENT OF THE UNITED STATES OF AMERICA as represented by THE SECRETARY OF THE DEPARTMENT OF HEALTH AND HUMAN SERVICES, c/o Centers for Disease Control and Prevention, Technology Transfer Offic | Nucleic acids for detecting aspergillus species and other filamentous fungi |
WO1998050584A3 (en) * | 1997-05-02 | 1999-02-18 | Us Health | Nucleic acids for detecting aspergillus species and other filamentous fungi |
US7052836B2 (en) | 1997-05-02 | 2006-05-30 | The Government Of The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services | Nucleic acids for detecting fusarium species |
US6372430B1 (en) | 1997-05-02 | 2002-04-16 | The United States Of America As Represented By The Department Of Health And Human Services | Nucleic acids for detecting Aspergillus species and other filamentous fungi |
WO1998055649A1 (en) * | 1997-06-06 | 1998-12-10 | Bayer Corporation | Nucleic acid probes for the detection and identification of fungi |
WO1999006596A1 (en) * | 1997-07-30 | 1999-02-11 | The Government Of The United States Of America, Represented By The Secretary Of The Department Of Health And Human Services, Centers For Disease Control And Prevention, Office Of Technology Transfer, Building 4, Suite 1103, Executive Park | Nucleic acid probes for detecting candida species |
US6242178B1 (en) | 1997-07-30 | 2001-06-05 | Centers For Disease Control And Prevention | Nucleic acid probes for detecting Candida species |
EP1036196A1 (en) * | 1997-12-08 | 2000-09-20 | E. & J. Gallo Winery | Detection of fungal pathogens |
EP1036196A4 (en) * | 1997-12-08 | 2004-08-04 | Gallo Winery E & J | Detection of fungal pathogens |
WO1999054508A1 (en) * | 1998-04-21 | 1999-10-28 | The Government Of The United States Of America, Represented By The Secretary Of The Department Of Health And Human Services | RAPID AND SENSITIVE METHOD FOR DETECTING $i(HISTOPLASMA CAPSULATUM) |
US6469156B1 (en) | 1999-04-20 | 2002-10-22 | The United States Of America As Represented By The Department Of Health And Human Services | Rapid and sensitive method for detecting histoplasma capsulatum |
US7449328B2 (en) | 1999-05-03 | 2008-11-11 | Gen-Probe Incorporated | Probe matrix-based device for identifying microorganisms |
WO2000073499A2 (en) * | 1999-05-28 | 2000-12-07 | Innogenetics N.V. | Nucleic acid probes and methods for detecting clinically important fungal pathogens |
WO2000073499A3 (en) * | 1999-05-28 | 2001-08-09 | Innogenetics Nv | Nucleic acid probes and methods for detecting clinically important fungal pathogens |
US7741461B2 (en) | 1999-05-28 | 2010-06-22 | Innogenetics N.V. | Nucleic acid probes and methods for detecting clinically important fungal pathogens |
US6858387B1 (en) | 1999-05-28 | 2005-02-22 | Innogenetics, N.V. | Nucleic acid probes and methods for detecting clinically important fungal pathogens |
US7052837B2 (en) | 2001-03-13 | 2006-05-30 | The Board Of Trustees Of The University Of Arkansas | Histoplasma capsulatum catalase sequences and their use in the detection of Histoplamsa capsulatum and histoplasmosis |
US7217519B1 (en) | 2002-11-21 | 2007-05-15 | The Board Of Trustees Of The University Of Arkansas | Histoplasma capsulatum chitin synthase sequences and their use for detection of Histoplasma capsulatum and histoplasmosis |
WO2004079333A2 (en) * | 2003-01-15 | 2004-09-16 | Ic & G Co., Ltd. | Method and kit for extracting rna from sputum |
WO2004079333A3 (en) * | 2003-01-15 | 2005-03-24 | Ic & G Co Ltd | Method and kit for extracting rna from sputum |
US9103829B2 (en) | 2006-04-01 | 2015-08-11 | Medical Service Consultation International, Llc | Methods and compositions for detecting fungi and mycotoxins |
US10274493B2 (en) | 2006-04-01 | 2019-04-30 | Advatect Diagnostics, Llc | Methods and compositions for detecting fungi and mycotoxins |
US10036748B2 (en) | 2006-04-01 | 2018-07-31 | Advatect Diagnostics, Llc | Methods and compositions for detecting fungi and mycotoxins |
US9182398B2 (en) | 2006-04-01 | 2015-11-10 | Medical Service Consultation International, Llc | Methods and compositions for detecting fungi and mycotoxins |
WO2007132589A1 (en) * | 2006-05-16 | 2007-11-22 | Kirin Beer Kabushiki Kaisha | Primer set for detection of dekkera yeast or brettanomyces yeast |
JPWO2007132589A1 (en) * | 2006-05-16 | 2009-09-24 | 麒麟麦酒株式会社 | Primer set for detection of Deckella yeast and Brettanomyces yeast |
US9487836B2 (en) | 2008-08-22 | 2016-11-08 | Medical Service Consultation International, Llc | Methods and compositions for identifying yeast |
US10030278B2 (en) | 2008-08-22 | 2018-07-24 | Advatect Diagnostics, Llc | Methods and compositions for identifying yeast |
US20100068718A1 (en) * | 2008-08-22 | 2010-03-18 | Hooper Dennis G | Methods and Compositions for Identifying Yeast |
US10793920B2 (en) | 2008-08-22 | 2020-10-06 | Mycodart, Inc. | Methods and compositions for identifying yeast |
US8962251B2 (en) | 2009-10-08 | 2015-02-24 | Medical Service Consultation International, Llc | Methods and compositions for identifying sulfur and iron modifying bacteria |
US10443106B2 (en) | 2009-10-08 | 2019-10-15 | Advatect Diagnostics, Llc | Methods and compositions for identifying sulfur and iron modifying bacteria |
WO2011098907A2 (en) | 2010-02-15 | 2011-08-18 | Council Of Scientific & Industrial Research | Method for detecting fungal pathogens |
US9150934B2 (en) | 2013-02-06 | 2015-10-06 | Medical Service Consultation International, Llc | Methods and compositions for detecting Aspergillus terreus, Aspergillus niger, and mycotoxins |
EP2765204A1 (en) * | 2013-02-06 | 2014-08-13 | Medical Service Consultation International LLC | Methods and compositions for detecting aspergillus terreus, aspergillus niger, and mycotoxins |
US8956821B2 (en) | 2013-02-06 | 2015-02-17 | Medical Service Consultation International, Llc | Methods and compositions for detecting Aspergillus terreus, Aspergillus niger, and mycotoxins |
CN112680541A (en) * | 2021-01-20 | 2021-04-20 | 中迅优检生物科技(江苏)有限公司 | LNA-Taqman-multiplex fluorescence PCR technology and application thereof in rapid detection of candida |
CN113106167A (en) * | 2021-04-26 | 2021-07-13 | 北京大学第一医院 | Primer and probe for invasive aspergillosis pathogenic bacteria, implementation method and detection system thereof |
CN113106167B (en) * | 2021-04-26 | 2022-09-20 | 北京大学第一医院 | Primer and probe for invasive aspergillosis pathogenic bacteria, implementation method and detection system thereof |
Also Published As
Publication number | Publication date |
---|---|
AU4313896A (en) | 1996-07-31 |
PL321139A1 (en) | 1997-11-24 |
MX9705292A (en) | 1997-10-31 |
BR9607497A (en) | 1997-12-23 |
JPH11500305A (en) | 1999-01-12 |
US5763169A (en) | 1998-06-09 |
CA2209247A1 (en) | 1996-07-18 |
KR19987001336A (en) | 1998-05-15 |
US5958693A (en) | 1999-09-28 |
AU693625B2 (en) | 1998-07-02 |
EP0804619A1 (en) | 1997-11-05 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
AU693625B2 (en) | Nucleic acid probes for the detection and identification of fungi | |
US5707802A (en) | Nucleic acid probes for the detection and identification of fungi | |
US6180339B1 (en) | Nucleic acid probes for the detection and identification of fungi | |
Sandhu et al. | Molecular probes for diagnosis of fungal infections | |
Oliveira et al. | Differentiation of Candida albicans and Candida dubliniensis by fluorescent in situ hybridization with peptide nucleic acid probes | |
JP4997277B2 (en) | Candidasppp. Methods and compositions for detection of | |
US5688644A (en) | Nucleic acid probes for candida parapsilosis and methods for detecting candidiasis in blood | |
US5403710A (en) | Nucleic acid probes and methods for detecting pathogenic candida yeasts | |
JP3155992B2 (en) | Nucleic acid probes and methods for fungal detection | |
JP4425354B2 (en) | Nucleic acids for detecting Aspergillus species and other filamentous fungi | |
US5658726A (en) | Detecting eukaryotic microorganisms | |
US6080543A (en) | Detection of fungal pathogens | |
US5916744A (en) | Testing for infestation of rapeseed and other cruciferae by the fungus Leptosphaeria maculans (blackleg infestation) | |
WO1994006937A1 (en) | Improved strand displacement assay and complex useful therefor | |
EP0996745B1 (en) | Nucleic acid probes for detecting candida species | |
US7427472B2 (en) | Methods for the differentiation and identification of medically important endemic fungi | |
US5693501A (en) | Compounds and methods to determine presence of Histoplasma capsulatum | |
US5464743A (en) | Nucleic acid probes and methods for detecting cryptococcus neoformans | |
MXPA97005292A (en) | Nucleic acid ps for the detection and identification of hon | |
AU769095B2 (en) | Rapid and sensitive method for detecting (Histoplasma capsulatum) | |
KR19980701336A (en) | NUCLEIC ACID PROBES FOR THE DETECTION AND IDENTIFICATION OF FUNGI | |
US5776680A (en) | Diagnostic probes for pneumocystis carini | |
EP0645460A2 (en) | Detection of Yersinia intermedia |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
AK | Designated states |
Kind code of ref document: A1 Designated state(s): AL AM AT AU AZ BB BG BR BY CA CH CN CZ DE DK EE ES FI GB GE HU IS JP KE KG KP KR KZ LK LR LS LT LU LV MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK TJ TM TR TT UA UG US UZ VN AZ BY KZ RU TJ TM |
|
AL | Designated countries for regional patents |
Kind code of ref document: A1 Designated state(s): KE LS MW SD SZ UG AT BE CH DE DK ES FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN ML MR NE SN |
|
DFPE | Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101) | ||
121 | Ep: the epo has been informed by wipo that ep was designated in this application | ||
WWE | Wipo information: entry into national phase |
Ref document number: 1996900051 Country of ref document: EP |
|
ENP | Entry into the national phase |
Ref document number: 2209247 Country of ref document: CA Ref country code: CA Ref document number: 2209247 Kind code of ref document: A Format of ref document f/p: F |
|
WWE | Wipo information: entry into national phase |
Ref document number: 1019970704725 Country of ref document: KR |
|
WWE | Wipo information: entry into national phase |
Ref document number: PA/a/1997/005292 Country of ref document: MX |
|
ENP | Entry into the national phase |
Ref country code: JP Ref document number: 1996 521540 Kind code of ref document: A Format of ref document f/p: F |
|
WWP | Wipo information: published in national office |
Ref document number: 1996900051 Country of ref document: EP |
|
REG | Reference to national code |
Ref country code: DE Ref legal event code: 8642 |
|
WWP | Wipo information: published in national office |
Ref document number: 1019970704725 Country of ref document: KR |
|
WWW | Wipo information: withdrawn in national office |
Ref document number: 1019970704725 Country of ref document: KR |
|
WWW | Wipo information: withdrawn in national office |
Ref document number: 1996900051 Country of ref document: EP |