Nucleic acid probes for the detection and identification of fungi

A species specific reference oligonucleotide having a nucleotide residue sequence selected from the group consisting of SEQ ID NO:

• 24 (Acremonium species), SEQ ID NO:
• 25 (Aspergillus clavatus), SEQ ID NO:
• 26 (Aspergillis flavus), SEQ ID NO:
• 28 (Aspergillus glaucus), SEQ ID NO:
• 29 (Aspergillus nidulans), SEQ ID NO:
• 30 (Aspergillus niger), SEQ ID NO:
• 31 (Aspergillus ochraceus), SEQ ID NO:
• 32 (Aspergillus terreus), SEQ ID NO:
• 33 (Aspergillus unguis), SEQ ID NO:
• 34 (Aspergillus ustus) and the complements thereof.

A species specific reference oligonucleotide having a nucleotide residue sequence selected from the group consisting of SEQ ID NO:

• 35 (Beauveria species), SEQ ID NO:
• 36 (Bipolaris species), SEQ ID NO:
• 37 (Blastochizomyces species), SEQ ID NO:
• 38 (Blastomyces dermatitidis), SEQ ID NO:
• 39 (Chrysoporium species), SEQ ID NO:
• 40 (Cladosporium species), SEQ ID NO:
• 41 (Curvularia species), SEQ ID NO:
• 42 (Candida albicans), SEQ ID NO:
• 43 (Candida glabrata), SEQ ID NO:
• 44 (Candida guilliermondii) and the complements thereof.

A species specific reference oligonucleotide having a nucleotide residue sequence selected from the group consisting of SEQ ID NO:

• 45 (Coccidioides immitis), SEQ ID NO:
• 46 (Candida kefyr), SEQ ID NO:
• 48 (Cryptoccus laurentii) , SEQ ID NO:
• 49 (Candida lusitaniae) , SEQ ID NO:
• 50 (Cryptococcus neoformans var gattii), SEQ ID NO:
• 51 (Cryptococcus neoformans), SEQ ID NO:
• 52 (Candida parapsilosis), SEQ ID NO:
• 53 (Cryptococcus terreus), SEQ ID NO:
• 54 (Candida tropicalis) and the complements thereof.

A species specific reference oligonucleotide having a nucleotide residue sequence selected from the group consisting of SEQ ID NO:

• 55 (Fusarium species), SEQ ID NO:
• 56 (Filobasidium capsuligenum), SEQ ID NO:
• 57 (Filobasidiella neoformans var bacillispora), SEQ ID NO:
• 58 (Filobasidiella neoformans), SEQ ID NO:
• 59 (Filobasidium uniguttulam) , SEQ ID NO:
• 60 (Geotrichum species), SEQ ID NO:
• 61 (Histoplasma capsulatum), SEQ ID NO:
• 62 (Malbranchea species), SEQ ID NO:
• 63 (Mucor species), SEQ ID NO:
• 64 (Paecilomyces species) and the complements thereof.

A species specific reference oligonucleotide having a nucleotide residue sequence selected from the group consisting of SEQ ID NO:

• 65 (Penicillium species), SEQ ID NO:
• 66 (Pseudallescheria boydii), SEQ ID NO:
• 67 (Rhizopus species), SEQ ID NO:
• 68 (Rhizopus species), SEQ ID NO:
• 69 (Rhizopus species), SEQ ID NO:
• 70 (Sporothrix species), SEQ ID NO:
• 71 (Scopulariopsis brevicaulis), SEQ ID NO:
• 72 (Scopulariopsis brumptii), SEQ ID NO:
• 73 (Saccharomyces cerevisiae), SEQ ID NO:
• 74 (Trichosporon beigelii) and the complements thereof.

A method of determining whether one or more fungal species selected from the group of fungal species consisting of Acremonium species, Aspergillus clavatus, Aspergillis flavus, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus terreus, Aspergillus unguis, Aspergillus ustus, Beauveria species, Bipolaris species, Blastochizomyces species, Blastomyces dermatitidis, Chrysoporium species, Cladosporium species, Curvularia species, Candida albicans, Candida glabrata, Candida guilliermondii, Coccidioides immitis, Candida kefyr, Candida brusei, Cryptoccus laurentii, Candida lusitaniae, Cryptococcus neoformans var gattii, Cryptococcus neoformans, Candida parapsilosis, Cryptococcus terreus, Candida tropicalis, Fusarium species, Filobasidium capsuligenum, Filobasidiella neoformans var bacillispora, Filobasidiella neoformans var neoformans, Filobasidium uniguttulam, Geotrichum species, Histoplasma capsulatum, Malbranchea species, Mucor species, Paecilomyces species, Penicillium species, Pseudallescheria boydii, Rhizopus species (NO:

• 1), Rhizopus species (NO:
• 2), Rhizopus species (NO:
• 3), Sporothrix species, Scopulariopsis brevicaulis, Scopulariopsis brumptii, Saccharomyces cerevisiae and Trichosporon beigelii is present in a sample of fungi, said method comprising the following steps:
• a) extracting the nucleic acid material from the fungi contained in said sample;
• b) adding a universal fungal probe selected from the group consisting of (SEQ ID NO:
• 1), (SEQ ID NO:
• 2) and the complements thereof;
• c) using one or more second probes, each said second probe being specific for one of said fungal species from said group, wherein each said one or more second probes is fully complementary to a species-unique nucleotide sequence in said hypervariable region and wherein, further, said one or more second probes each has a nucleotide residue sequence consisting of from 10 to 50 consecutive nucleotide residues from a sequence selected from the group consisting of (SEQ ID NO:
• 24) through (SEQ ID NO:
• 74) and the complements thereof;
• and
• d) determining whether said fungal species identified by each said second probe is present in said sample,
• wherein at least one of said probes is connected to a signal moiety and at least one of said probes is connected to a moiety that allows separation of said probes.