Nucleic acids for detecting Aspergillus species and other filamentous fungi

Abstract

Nucleic acids for detecting Aspergillus species and other filamentous fungi are provided. Unique internal transcribed space 2 coding regions permit the development of nucleic acid probes specific for five different species of Aspergillus, three species of Fusarium, four species of Mucor, two species of Penecillium, five species of Rhizopus, one species of Rhizomucor, as well as probes for Absidia corymbifer, Cunninghamella elagans, Pseudallescheria boydii, and Sporothrix schenkii. Methods are disclosed for the species-specific detection and diagnosis of infection by Aspergillus, Fusarium, Mucor, Penecillium, Rhizomucor, absidia, Cunninghaemella, Pseudallescheria or Sporthrix in a subject. Furthermore, genus-specific probes are also provided for Aspergillus, Fusarium and Mucor, in addition to an all-fungus nucleic acid probe.

Description

TECHNICAL FIELD

This application relates in general to the field of diagnostic microbiology. In particular, the invention relates to the species-specific detection of Aspergillus, Fusarium, Mucor, Penicillium, Rhizopus, Rhizomucor, Absidia, Cunninghamella, Pseudallescheria boydii ( Scedosporium apiospermum ), and Sporothrix species.

BACKGROUND OF THE INVENTION

In recent years, chemotherapy for hematological malignancies, and high-dose corticosteroid treatment for organ transplant recipients, along with the spread of AIDS, have greatly increased the number of immunocompromised patients (1, 12, 14, 43). Saprophytic filamentous fungi, such as Aspergillus, Rhizopus, and Mucor species, found in the environment and considered to be of low virulence, are now responsible for an increasing number of infections in the immunocompromised host (17, 20, 43). In addition, these infections are often fulminant and rapidly fatal in immunocompromised patients (7, 11, 12, 20, 44). Morbidity and mortality is extremely high; for example, aspergillosis has a mortality rate of approximately 90% (8, 11).

To complicate matters, diagnosis is difficult and symptoms are often non-specific (18, 27, 29, 42, 44). Antibody-based tests can be unreliable due to the depressed or variable immune responses of immunocompromised patents (2, 9, 18, 46). Antigen detection tests developed to date have fallen short of the desired sensitivity (2, 9, 38). Radiographic evidence can be non-specific and inconclusive (5, 29, 36), although some progress in diagnosis has been made with the advent of computerized tomography (40). However, definitive diagnosis still requires either a positive blood or tissue culture or histopathological confirmation (3, 21). An added complication is that the invasive procedures necessary to obtain biopsy materials are often not recommended in thrombocytopenic patient populations (37, 41).

Even when cultures of blood, lung or rhinocerebral tissues are positive, morphological and biochemical identification of filamentous fungi can require several days for adequate growth and sporulation to occur, delaying targeted drug therapy. Some atypical isolates may never sporulate, making identification even more difficult (23). When histopathology is performed on tissue biopsy sections, the morphological similarities of the various filamentous fungi in tissue make differentiation difficult (16). Fluorescent antibody staining of histopathological tissue sections is not specific unless cross-reactive epitopes are absorbed out which can make the resultant antibody reactions weak (14, 19). Therapeutic choices vary (7, 41, 44) making a test to rapidly and specifically identify filamentous fungi urgently needed for the implementation of appropriately targeted therapy. Early and accurate diagnosis and treatment can decrease morbidity and increase the chances for patient survival (6, 27, 39). Furthermore, identification of filamentous fungi to at least the species level would be epidemiologically useful (24, 31, 43, 47).

PCR-based methods of detection, which show promise as rapid, sensitive means to diagnose infections, have been used in the identification of DNA from Candida species (13, 15, 30) and some other fungi, particularly Aspergillus species (31, 33, 45). However, most of these tests are only genus-specific (28, 38) or are directed to detect only single-copy genes (4, 35). Others have designed probes to detect multi-copy genes so as to increase test sensitivity (31, 33) but in doing so have lost test specificity because they have used highly conserved genes, which detect one or a few species but which are also plagued with cross-reactivities to human, fungal or even viral DNA (25, 31, 33).

Therefore, it is an object of the invention to provide improved materials and methods for detecting and differentiating Aspergillus and other filamentous fungal species in the clinical and laboratory settings.

SUMMARY OF THE INVENTION

The present invention relates to nucleic acids for detecting Aspergillus, Fusarium, Mucor, Penicillium, Rhizopus, Rhizomucor, Absidia, Cunninghamella, Pseudallescheria (Scedosporium), and Sporothrix species. Unique internal transcribed spacer 2 coding regions permit the development of probes specific for five different Aspergillus species, A. flavus, A. fumigatus, A. niger, A. terreus , and A. nidulans . The invention thereby provides methods for the species-specific detection and diagnosis of Aspergillus infection in a subject. In addition, species probes have been developed for three Fusarium, four Mucor, two Penicillium, five Rhizopus and one Rhizomucor species, as well as probes for Absidia corymbifera, Cunninghamella elegans, Pseudallescheria boydii ( Scedosporium apiospermum ), and Sporothrix schenckii . Generic probes for Aspergillus, Fusarium, and Mucor species have also been developed.

These and other objects, features and advantages of the present invention will become apparent after a review of the following detailed description of the disclosed embodiments and the appended claims.

DETAILED DESCRIPTION OF THE INVENTION

This invention provides a simple, rapid, and useful method for differentiating filamentous fungal species from each other and from other medically important fungi. This invention enables a rapid, simple and useful method to isolate fungal DNA from host samples, and to apply the species- and genus-specific probes for the diagnosis of a disease. Ultimately, these probes can be used for in situ hybridization or in situ PCR diagnostics so that the morphology of host tissue, and microorganisms, remain intact.

The invention provides nucleic acids containing regions of specificity for five Aspergillus, three Fusarium, four Mucor, two Penicillium, five Rhizopus and one Rhizomucor species as well as probes for Absidia corymbifera, Cunninghamella elegans, Pseudallescheria boydii ( Scedosporium apiospremum ), and Sporothrix schenckii . These nucleic acids are from the internal transcribed spacer 2 (“ITS2”) region of ribosomal deoxyribonucleic acid (rDNA) of the genome of the aforementioned filamentous fungi. The ITS2 region is located between the 5.8S rDNA region and the 28S rDNA region.

In particular, the invention provides nucleic acids from Aspergillus flavus (SEQ ID NO:1), Aspergillus fumigatus (SEQ ID NO:2), Aspergillus niger (SEQ ID NO:3), Aspergillus terreus (SEQ ID NO:4), Aspergillus nidulans (SEQ ID NO:5), Fusarium solani (SEQ ID NO:6), Fusarium moniliforme (SEQ ID NO:7), Mucor rouxii (SEQ ID NO:8), Mucor racemosus (SEQ ID NO:9), Mucor plumbeus (SEQ ID NO: 10), Mucor indicus (SEQ ID NO:11), Mucor circinilloides f. circinelloides (SEQ ID NO:12), Rhizopus oryzae (SEQ ID NO:13 and NO:14), Rhizopus microsportis (SEQ ID NO:15 and 16), Rhizopus circinans (SEQ ID NO:17 and 18). Rhizopus stolonifer (SEQ ID NO:19), Rhizomucor pusillus (SEQ ID NO:20), Absidia corymbifera (SEQ ID NO:21 and 22), Cunninghamella elegans (SEQ ID NO:23), Pseudallescheria boydii (teleomorph of Scedosporium apiospermum ) (SEQ ID NO:24, 25, 26, and 27), Penicillium notatum (SEQ ID NO:28), and Sporothrix schenkii (SEQ ID NO:29). These sequences can be used to identify and distinguish the respective species of Aspergillus, Fusariunm, Mucor, Rhizopus, and Penicillium, and identify and distinguish these species from each other and from Absidia corymbifera, Cunninghamella elegans, Pseudallescheria boydii ( Scedosporium apiospermum ), and Sporothrix schenkii.

Furthermore, the invention provides isolated nucleic acid probes derived from GenBank nucleic acid sequences (for Penicillium marneffei and Fusarium oxysporum only) or from the above nucleic acid sequences which may be used as species-specific identifiers of Aspergillus flavus (SEQ ID NO:30 and 31), Aspergillus fumigatus (SEQ ID NO:32), Aspergillus niger (SEQ ID NO:33), Aspergillus terreus (SEQ ID NO:34), Aspergillus nidulans (SEQ ID NO:35), Mucor rouxii (SEQ ID NO:36), Mucor plumbeus (SEQ ID NO:37), Mucor indicus (SEQ ID NO:38), Mucor circinilloides f. circinelloides (SEQ ID NO:39), Mucor racemosus (SEQ ID NO:40), Rhizopus oryzae (SEQ ID NO:41), Rhizopus circinans (SEQ ID NO:42), Rhizomucor pusillus (SEQ ID NO:43), Rhizopus stolonifer (SEQ ID NO:44), Pseudallescheria boydii ( Scedosporium apiospermumn )(SEQ ID NO:45), Penicillium notatum (SEQ ID NO:46), Penicillium marneffei (SEQ ID NO:47 and 48), Fusarium moniliforme (SEQ ID NO:49), Fusarium oxysporum (SEQ ID NO:50), Fusarium solani (SEQ ID NO:51), Cunninghamella elegans (SEQ ID NO:52, 53, and 54), Absidia corymbifera (SEQ ID NO:55), Sporothrix schenkii (SEQ ID NO:56), and Rhizopus microsporus (SEQ ID NO:57). Such probes can be used to selectively hybridize with samples containing nucleic acids from species of Aspergillus, Fusarium, Mucor, Rhizopus (or Rhizomucor), Penicillium, or from Absidia corymbifera, Cunninghamella elegans, Pseudallescheria boydii ( Scedosporium apiospermum ), and Sporothrix schenkii . These fungi can be detected after polymerase chain reaction or ligase chain reaction amplification of fungal DNA and specific probing of amplified DNA with DNA probes labeled with digoxigenin, reacted with anti-digoxigenin antibodies labeled with horseradish peroxidase and a colorimetric substrate, for example. Additional probes can routinely be derived from the sequences given in SEQ ID NOs: 1-29, which are specific for the respective species. Therefore, the probes shown in SEQ ID NOs:30-57 are only provided as examples of the species-specific probes that can be derived from SEQ ID NOs: 1-29.

Generic probes for Aspergillus (SEQ ID NO:58), Fusarium, (SEQ ID NO:59) and Mucor (SEQ ID NO:60) species have also been developed to identify all members of their respective species which are listed above as well as an all-fungus biotinylated probe (SEQ ID NO:61) to capture all species-specific and generic probes listed above for their detection.

By “isolated” is meant nucleic acid free from at least some of the components with which it naturally occurs. By “selective” or “selectively” is meant a sequence which does not hybridize with other nucleic acids to prevent adequate determination of an Aspergillus, Fusarium, Mucor, Penicillium, Rhizopus or Rhizomucor genus or species or of Absidia corymbifera, Cunninghamella elegans, Pseudallescheria boydii ( Scedosporium apiospermum ), or Sporothrix schenckii species.

The hybridizing nucleic acid should have at least 70% complementarity with the segment of the nucleic acid to which it hybridizes. As used herein to describe nucleic acids, the term “selectively hybridizes” excludes the occasional randomly hybridizing nucleic acids and thus has the same meaning as “specifically hybridizing”. The selectively hybridizing nucleic acids of the invention can have at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, and 99% complementarity with the segment of the sequence to which it hybridizes.

The invention contemplates sequences, probes and primers which selectively hybridize to the complementary, or opposite, strand of DNA as those specifically provided herein. Specific hybridization with nucleic acid can occur with minor modifications or substitutions in the nucleic acid, so long as functional species-specific or genus-specific hybridization capability is maintained. By “probe” is meant nucleic acid sequences that can be used as probes or primers for selective hybridization with complementary nucleic acid sequences for their detection or amplification, which probes can vary in length from about 5 to 100 nucleotides, or preferably from about 10 to 50 nucleotides, or most preferably about 18 nucleotides. The invention provides isolated nucleic acids that selectively hybridize with the species-specific nucleic acids under stringent conditions and should have at least 5 nucleotides complementary to the sequence of interest. See generally, Maniatis (26).

If used as primers, the invention provides compositions including at least two nucleic acids which hybridize with different regions so as to amplify a desired region. Depending on the length of the probe or primer, target region can range between 70% complementary bases and full complementarity and still hybridize under stringent conditions. For example, for the purpose of diagnosing the presence of the Aspergillus, the degree of complementarity between the hybridizing nucleic acid (probe or primer) and the sequence to which it hybridizes (e.g., Aspergillus DNA from a sample) is at least enough to distinguish hybridization with a nucleic acid from other yeasts and filamentous fungi. The invention provides examples of nucleic acids unique to each filamentous fungus in the listed sequences so that the degree of complementarity required to distinguish selectively hybridizing from nonselectively hybridizing nucleic acids under stringent conditions can be clearly determined for each nucleic acid.

Alternatively, the nucleic acid probes can be designed to have homology with nucleotide sequences present in more than one species of the fungi listed above. Such a nucleic acid probe can be used to selectively identify a group of species such as the generic probes listed for Aspergillus (SEQ ID NO:58), Fusarium (SEQ ID NO:59), and Mucor (SEQ ID NO:60) as well as all fungi listed (SEQ ID NO:61). Additionally, the invention provides that the nucleic acids can be used to differentiate the filamentous fungi listed in general from other filamentous fungi and yeasts, such as Candida species. Such a determination is clinically significant, since therapies for these infections differ.

The invention further provides methods of using the nucleic acids to detect and identify the presence of the filamentous fungi listed, or particular species thereof. The method involves the steps of obtaining a sample suspected of containing filamentous fungi. The sample may be taken from an individual, such as blood, saliva, lung lavage fluids, vaginal mucosa, tissues, etc., or taken from the environment. The filamentous fungal cells can then be lysed, and the DNA extracted and precipitated. The DNA is preferably amplified using universal primers derived from the internal transcribed spacer regions, 18S, 5.8S and 28S regions of the filamentous fungal rDNA. Examples of such universal primers are shown below as ITS1 (SEQ ID NO:62), ITS3 (SEQ ID NO:63), ITS4 (SEQ ID NO:64). Detection of filamentous fungal DNA is achieved by hybridizing the amplified DNA with a species-specific probe that selectively hybridizes with the DNA. Detection of hybridization is indicative of the presence of the particular genus (for generic probes) or species (for species probes) of filamentous fungus.

Preferably, detection of nucleic acid (e.g. probes or primers) hybridization can be facilitated by the use of detectable moieties. For example, the species-specific or generic probes can be labeled with digoxigenin, and an all-fungus probe, such as described in SEQ ID NO:61, can be labeled with biotin and used in a streptavidin-coated microtiter plate assay. Other detectable moieties include radioactive labeling, enzyme labeling, and fluorescent labeling, for example.

The invention further contemplates a kit containing one or more species-specific probes, which can be used for the detection of particular filamentous fungal species and genera in a sample. Such a kit can also contain the appropriate reagents for hybridizing the probe to the sample and detecting bound probe. The invention may be further demonstrated by the following non-limiting examples.

EXAMPLES

In this example, PCR assay employing universal, fungus-specific primers and a simple, rapid EIA-based format for amplicon detection were used.

Extraction of Filamentous Fungal DNA

A mechanical disruption method was used to obtain DNA from filamentous fungal species and an enzymatic disruption method described previously (13) was used to obtain DNA from yeasts. Filamentous fungi were grown for 4 to 5 days on Sabouraud dextrose agar slants (BBL, division of Becton Dickinson, Cockeysville, Md.) at 35° C. Two slants were then washed by vigorously pipeting 5 mls of 0.01 M potassium phosphate buffered saline (PBS) onto the surface of each slant and the washes were transferred to 500 ml Erlenmeyer flasks containing 250 ml of Sabouraud dextrose broth (BBL). Flasks were then incubated for 4 to 5 days on a rotary shaker (140 rpm) at ambient temperature. Growth was then harvested by vacuum filtration through a sterile Whatman #1 filter paper which had been placed into a sterile Buchner funnel attached to a 2 L side-arm flask. The resultant cellular mat was washed on the filtration apparatus three times with sterile distilled water, removed from the filter paper by gentle scraping with a rubber policeman, and placed into a sterile Petri plate which was then sealed with parafilm and frozen at −20° C. until used.

Just prior to use, a portion of the frozen cellular mat, equal in size to a quarter, was removed and placed into a cold mortar (6″ diameter). Liquid nitrogen was added to cover the mat which was then ground into a powder with a pestle. Additional liquid nitrogen was added as needed to keep the mat frozen during grinding.

DNA was then purified using proteinase K and RNase treatment, multiple phenol extractions, and ethanol precipitation by conventional means (26).

PCR amplification

The fungus-specific, universal primer pair ITS3 (5′-GCA TCG ATG AAG AAC GCA GC-3′) (SEQ ID NO:63) and ITS4 (5′-TCC TCC GCT TAT TGA TAT GC-3′) (SEQ ID NO:64) was used to amplify a portion of the 5.8S rDNA region, the entire ITS2 region, and a portion of the 28S rDNA region for each species as previously described (13, 34). DNA sequencing used this primer pair and also the fungus-specific, universal primer pair ITS1 (5′-TCC GTA GGT GAA CCT GCG G-3′) (SEQ ID NO: 62) and ITS4 to amplify a portion of the 18S rDNA region, the entire 5.8S region, the entire ITS1 and ITS2 regions, and a portion of the 28S rDNA region.

A DNA reagent kit (TaKaRa Biomedicals, Shiga, Japan) was used for PCR amplification of genomic DNA. PCR was performed using 2 μl of test sample in a total PCR reaction volume of 100 μl consisting of 10 μl of 10×Ex Tag buffer, 2.5 mM each of dATP, dGTP, dCTP, and dTTP, in 8 μl 0.2 μM of each primer, and 0.5 U of TaKaRa Ex Tag DNA polymerase. Thirty cycles of amplification were performed in a Perkin-Elmer 9600 thermal cycler (Emeryville, Calif.) after initial denaturation of DNA at 95° C. for 5 minutes. Each cycle consisted of a denaturation step at 95° C. for 30 seconds, an annealing step at 58° C. for 30 seconds, and an extension step at 72° C. for 1 minute. A final extension at 72° C. for 5 minutes followed the last cycle. After amplification, samples were stored at −20° C. until used.

TABLE 1
Synthetic Universal Oligonucleotides Used in PCR
and Hybridization Analyses
Primers	Nucleotide Sequence	Chemistry
or Probes	(5′ to 3′)	and Location
ITS3	GCA TCG ATG AAG	5.85 rDNA universal 5′
	AAC GCA GC	primer
	(SEQ ID NO:63)
ITS4	TCC TCC GCT TAT	28S rDNA universal 3′
	TGA TAT GC	primer
	(SEQ ID NO:64)
ITSI	TCC GTA GGT GAA	185 rDNA universal 5′
	CCT GCG G	primer
	(SEQ ID NO:62)

DNA Sequencing

Primary DNA amplifications were conducted as described above. The aqueous phase of the primary PCR reaction was purified using QIAquick Spin Columns (Quiagen, Chatsworth, Calif.). DNA was eluted from each column with 50 μl of heat-sterilized Tris-EDTA buffer (10 mM Tris, 1 mM EDTA, pH 8.0).

Purified DNA was labeled using a dye terminator cycle sequencing kit (ABI PRISM, Perkin Elmer, Foster City, Calif.). One mix was made for each of the primers so that sequencing could be performed in both the forward and reverse directions. The reaction volume (20 μl) contained 9.5 μl Terminator Premix, 2 μl (1 ng) DNA template, 1 μl primer (3.2 pmol) and 7.5 μl heat-sterilized distilled H 2 O. The mixture was then placed into a pre-heated (96° C.) Perkin Elmer 9600 thermal cycler for 25 cycles of 96° C. for 10 seconds, 50° C. for 5 seconds, 60° C. for 4 minutes. The PCR product was then purified before sequencing using CentriSep spin columns (Princeton Separations, Adelphia, N.J.). DNA was then vacuum dried, resuspended in 6 μl of formamide-EDTA (5 μl deionized formamide plus 1 μl 50 mM EDTA, pH 8.0), and denatured for 2 min at 90° C. prior to sequencing using an automated capillary DNA sequencer (ABI Systems, Model 373, Bethesda, Md.).

The sequencing results were as follows:

Aspergillus flavus 5.8S ribosomal RNA gene, partial sequence, internal transcribed spacer 2, complete sequence, and 28S ribosomal RNA gene, partial sequence.

(SEQ ID NO:1)
GCTGCCCATC AAGCACGGC  TTGTGTGTTG GGTCGTCGTC
CCCTCTCCGG GGGGGACGGG CCCCAAAGGC AGCGGCGGCA
CCGCGTCCGA TCCTCGAGCG TATGGGGCTT TGTCACCCGC
TCTGTAGGCC CGGCCGGCGC TTGCCGAACG CAAATCAATC
TTTTTCCAGG TTGACCTCGG ATCAGGTAGG GATACCCGCT
GAACTTCAA

Aspergillus fumigatus 5.8S ribosomal RNA gene, partial sequence, internal transcribed spacer 2, complete sequence, and 28S ribosomal RNA gene, partial sequence.

(SEQ ID NO:2)
AAACTTTCAA CAATGGATCT CTTGGTTCCG GCATCGATGA
AGAACGCAGC GAAATGCGAT AACTAATGTG AATTGCAGAA
TTCAGTGAAT CATCGAGTCT TTGAACGCAC ATTGCGCCCC
CTGGTATTCC GGGGGGCATG CCTGTCCGAG CGTCATTGCT
GCCCATCAAG CACGGCTTGT GTGTTGGGCC CCCGTCCCCC
TCTCCCGGGG GACGGGCCCG AAAGGCAGCG GCGGCACCGC
GTCCGGTCCT CGAGCGTATG GGGCTTGTCA CCTGCTCTGT
AGGCCCGGCC GGCGCCAGCC GACACCCAAC TTTATTTTTC
TAAGGTTGAC CTCGGATCAG GTAGGGATAC CCGCTGAACT TAAA

Aspergillus niger 5.8S ribosomal RNA gene, partial sequence, internal transcribed spacer 2, complete sequence, and 28S ribosomal RNA gene, partial sequence.

(SEQ ID NO:3)
AAACTTTCAA CAATGGATCT CTTGGTTCCG GCATCGATGA
AGAACGCAGC GAAATGCGAT AACTAATGTG AATTGCAGAA
TTCAGTGAAT CATCGAGTCT TTGAACGCAC ATTGCGCCCC
CTGGTATTCC GGGGGGCATG CCTGTCCGAG CGTCATTGCT
GCCCTCAAGC ACGGCTTGTG TGTTGGGTCG CCGTCCCCCT
CTCCCGGGGG ACGGGCCCGA AAGGCAGCGG CGGCACCGCG
TCCGATCCTC GAGCGTATGG GGCTTTGTCA CCTGCTCTGT
AGGCCCGGCC GGCGCCTGCC GACGTTATCC AACCATTTTT
TTCCAGGTTG ACCTCGGATC AGGTAGGGAT ACCCGCTGAA CTTAA

Aspergillus terreus 5.8S ribosomal RNA gene, partial sequence, internal transcribed spacer 2, complete sequence, and 28S ribosomal RNA gene, partial sequence.

(SEQ ID NO:4)
AAACTTTCAA CAATGGATCT CTTGGTTCCG GCATCGATGA
AGAACGCAGC GAAATGCGAT AACTAATGTG AATTGCAGAA
TTCAGTGAAT CATCGAGTCT TTGAACGCAC ATTGCGCCCC
CTGGTATTCC GGGGGGGCAT GCCTGTCCGA GCGTCATTGC
TGCCCTCAAG CCCGGCTTGT GTGTTGGGCC CTCGTCCCCC
GGCTCCCGGG GGACGGGCCC GAAAGGCAGC GGCGGCACCG
CGTCCGGTCC TCGAGCGTAT GGGGCTTCGT CTTCCGCTCC
GTAGGCCCGG CCGGCGCCCG CCGAACGCAT TTATTTGCAA
CTTGTTTTTT TTTCCAGGTT GACCTCGGAT CAGGT

Aspergillus nidulans 5.8S ribosomal RNA gene, partial sequence, internal transcribed spacer 2, complete sequence, and 28S ribosomal RNA gene, partial sequence.

(SEQ ID NO:5)
AAACTTTCAA CAATGGATCT CTTGGTTCCG GCATCGATGA
AGAACGCAGC GAACTGCGAT AAGTAATGTG AATTGCAGAA
TTCAGTGAAT CATCGAGTCT TTGAACGCAC ATTGCGCCCC
CTGGCATTCC GGGGGGCATG CCTGTCCGAG CGTCATTGCT
GCCCTCAAGC CCGGCTTGTG TGTTGGGTCG TCGTCCCCCC
CCCCGGGGGA CGGGCCCGAA AGGCAGCGGC GGCACCGGTC
CGGTCCTCGA GCGTATGGGG CTTGGTCACC CGCTCGATTA
GGGCCGGCCG GGCGCCAGCC GGCGTCTCCA ACCTTATCTT
TCTCAGGTTG ACCTCGGATC AGGTAGGGAT ACCCGCTGAA CTTAA

Fusarium solani (strain ATCC62877) internal transcribed spacer 2 and adjacent regions.

(SEQ ID NO:6)
GAAAATGCGA TAAGTAATGT GAATTGCAGA ATTCAGTGAA
TCATCGAATC TTTGAACGCA CATTGCGCCC GCCAGTATTC
TGGCGGGCAT GCCTGTTCGA GCGTCATTAC AACCCTCAGG
CCCCCGGGCC TGGCGTTGGG GATCGGCGGA AGCCCCCTGC
GGGCACAACG CCGTCCCCCA AATACAGTGG CGGTCCCGCC
GCAGCTTCCA TTGCGTAGTA GCTAACACCT CGCAACTGGA
GAGCGGCGCG GCCACGCCGT AAAACACCCA ACTTCTGAAT
GTTGACCTCG AATCAGGTAG GAATACCCGC TGAACTTAA

Fusarium moniliforme (strain ATCC38519) internal transcribed spacer 2 and adjacent regions.

(SEQ ID NO:7)
AAATGCGATA AGTAATGTGA ATTGCAAAAT TCAGTGAATC
ATCGAATCTT TGAACGCACA TTGCGCCCGC CAGTATTCTG
GCGGGCATGC CTGTTCGAGC GTCATTTCAA CCCTCAAGCC
CCCGGGTTTG GTGTTGGGGA TCGGCAAGCC CTTGCGGCAA
GCCGGCCCCG AAATCTAGTG GCGGTCTCGC TGCAGCTTCC
ATTGCGTAGT AGTAAAACCC TCGCAACTGG TACGCGGCGC
GGCCAAGCCG TTAAACCCCC AACTTCTGAA TGTTGACCTC
GGATCAGGTA GGAATACCCG CTGAACTTAA

Mucor rouxii (strain ATCC24905) internal transcribed spacer 2 and adjacent regions.

(SEQ ID NO:8)
AAAGTGCGAT AACTAGTGTG AATTGCATAT TCAGTGAATC
ATCGAGTCTT TGAACGCAAC TTGCGCTCAT TGGTATTCCA
ATGAGCACGC CTGTTTCAGT ATCAAAACAA ACCCTCTATC
CAGCATTTTG TTGAATAGGA ATACTGAGAG TCTCTTGATC
TATTCTGATC TCGAACCTCT TGAAATGTAC AAAGGCCTGA
TCTTGTTTAA ATGCCTGAAC TTTTTTTTAA TATAAAGAGA
AGCTCTTGCG GTAAACTGTG CTGGGGCCTC CCAAATAATA
CTCTTTTTAA ATTTGATCTG AAATCAGGCG GGATTACCCG
CTGAACTTAA

Mucor racemosus (strain ATCC22365) internal transcribed spacer 2 and adjacent regions.

(SEQ ID NO:9)
AAAGTGCGAT AACTAGTGTG AATTGCATAT TCAGTGAATC
ATCGAGTCTT TGAACGCAAC TTGCGCTCAT TGGTATTCCA
ATGAGCACGC CTGTTTCAGT ATCAAAACAA ACCCTCTATC
CAACTTTTGT TGTATAGGAT TATTGGGGGC CTCTCGATCT
GTATAGATCT TGAAATCCCT GAAATTTACT AAGGCCTGAA
CTTGTTTAAA TGCCTGAACT TTTTTTTAAT ATAAAGGAAA
GCTCTTGTAA TTGACTTTGA TGGGGCCTCC CAAATAAATC
TCTTTTAAAT TTGATCTGAA ATCAGGCGGG ATTACCCGCT
GAACTTAA

Mucor plumbeus (strain ATCC4740) internal transcribed spacer 2 and adjacent regions.

(SEQ ID NO:10)
AAAGTGCGAT AACTAGTGTG AATTGCATAT TCAGTGAATC
ATCGAGTCTT TGAACGCAAC TTGCGCTCAT TGGTATTCCA
ATGAGCACGC CTGTTTCAGT ATCAAAACAA ACCCTCTATC
CAACTTTTGT TGTATAGGAT TATTGGGGGC CTCTCGATCT
GTATAGATCT TGAAACCCTT GAAATTTACT AAGGCCTGAA
CTTGTTTAAT GCCTGAACTT TTTTTTAATA TAAAGGAAAG
CTCTTGTAAT TGACTTTGAT GGGGCCTCCC AAATAAATCT
TTTTTAAATT TGATCTGAAA TCAGGTGGGA TTACCCGCTG
AACTTAA

Mucor indicus (strain ATCC4857) internal transcribed spacer 2 and adjacent regions.

(SEQ ID NO:11)
AAAGTGCGAT AACTAGTGTG AATTGCATAT TCAGTGAATC
ATCGAGTCTT TGAACGCATC TTGCACTCAA TGGTATTCCA
TTGAGTACGC CTGTTTCAGT ATCAAAAAC  AACCCTTATT
CAAAATTCTT TTTTTGAATA GATATGAGTG TAGCAACCTT
ACAAGTTGAG ACATTTTAAA TAAAGTCAGG CCATATCGTG
GATTGAGTGC CGATACTTTT TTAATTTTGA AAAGGTAAAG
CATGTTGATG TCCGCTTTTT GGGCCTCCCA AATAACTTTT
TAAACTTGAT CTGAAATCAG GTGGGATTAC CCGCTGAACT
TAA

Mucor circinelloides f. circinelloides (strain ATCC1209B) internal transcribed spacer 2 and adjacent regions.

AAAGTGCGAT AACTAGTGTG AATTGCATAT TCAGTGAATC
ATCGAGTCTT TGAACGCAAC TTGCGCTCAT TGGTATTCCA
ATGAGCACGC CTGTTTCAGT ATCAAAACAA ACCCTCTATC
CAACATTTTT GTTGAATAGG ATGACTGAGA GTCTCTTGAT
CTATTCTGAT CTCGAAGCTC TTGAAATGTA CAAAGGCCTG
ATCTTGTTTG AATGCCTGAA CTTTTTTTTA ATATAAAGAG
AAGCTCTTGC GGTAAACTGT GCTGGGGCCT CCCAAATAAC
ACATCTTTAA ATTTGATCTG AAATCAGGT  GGGACTACCC
GCTGAACTT  AA (SEQ ID NO:12)

Rhizopus oryzae (strain ATCC34965) internal transcribed spacer 2 and adjacent regions.

AGTGCGATAA CTAGTGTGAA TTGCATATTC AGTGAATCAT
CGAGTCTTTG AACGCAGCTT GCACTCTATG GTTTTTCTAT
AGAGTACGCC TGCTTCAGTA TCATCACAAA CCCACACATA
ACATTTGTTT ATGTGGTGAT GGGTCGCATC GCTGTTTTAT
TACAGTGAGC ACCTAAAATG TGTGTGATTT TCTGTCTGGC
TTGCTAGGCA GGAATATTAC GCTGGTCTCA GGATCTTTTT
TTTTGGTTCG CCCAGGAAGT AAAGTACAAG AGTATAATCC
AGTAACTTTC AAACTATGAT CTGAAGTCAG GTGGGATTAC
CCGCTGAACT TAA (SEQ ID NO:13)

Rhizopus oryzae (strain ATCC11886) internal transcribed spacer 2 and adjacent regions.

AGTGCGATAA CTAGTGTGAA TTGCATATTC AGTGAATCAT
CGAGTCTTTG AACGCAGCTT GCACTCTATG GTTTTTCTAT
AGAGTACGCC TGCTTCAGTA TCATCACAAA CCCACACATA
ACATTTGTTT ATGTGGTAAT GGGTCGCATC GCTGTTTTAT
TACAGTGAGC ACCTAAAATG TGTGTGATTT TCTGTCTGGC
TTGCTAGGCA GGAATATTAC GCTGGTCTCA GGATCTTTTT
CTTTGGTTCG CCCAGGAAGT AAAGTACAAG AGTATAATCC
AGCAACTTTC AAACTATGAT CTGAAGTCAG GTGGGATTAC
CCGCTGAACT TAA (SEQ ID NO:14)

Rhizopus microsporus (strain ATCC14056) internal transcribed spacer 2 and adjacent regions.

AAAGTGCGAT AACTAGTGTG AATTGCATAT TCGTGAATCA
TCGAGTCTTT GAACGCAGCT TGCACTCTAT GGATCTTCTA
TAGAGTACGC TTGCTTCAGT ATCATAACCA ACCCACACAT
AAAATTTATT TTATGTGGTG ATGGACAAGC TCGGTTAAAT
TTAATTATTA TACCGATTGT CTAAAATACA GCCTCTTTGT
AATTTTCATT AAATTACGAA CTACCTAGCC ATCGTGCTTT
TTTGGTCCAA CCAAAAAACA TATAATCTAG GGGTTCTGCT
AGCCAGCAGA TATTTTAATG ATCTTTAACT ATGATCTGAA
GTCAAGTGGG ACTACCCGCT GAACTTAA (SEQ ID NO:15)

Rhizopus microsporus (strain ATCC12276) internal transcribed spacer 2 and adjacent regions.

AAAGTGCGAT AACTAGTGTG AATTGCATAT TCGTGAATCA
TCGAGTCTTT GAACGCAGCT TGCACTCTAT GGATCTTCTA
TAGAGTACGC TTGCTTCAGT ATCATAACCA ACCCACACAT
AAAATTTATT TTATGTGGTG ATGGACAAGC TCGGTTAAAT
TTAATTATTA TACCGATTGT CTAAAATACA GCCTCTTTGT
AATTTTCATT AAATTACGAA CTACCTAGCC ATCGTGCTTT
TTTGGTCCAA CCAAAAAACA TATAATCTAG GGGTTCTGCT
AGCCAGCAAA TATTTTAATG ATCTTTAACC TATGATCTGA
AGTCAAGTGG GACTACCCGC TGAACTTAA (SEQ ID NO:16)

Rhizopus circinans (strain ATCC34106) internal transcribed spacer 2 and adjacent regions.

AAATTGCGAT AACTAGTGTG AATTGCATTT TCAGTGAATC
ATCGAGTCTT TGAACGCAT  CTTGCGCTCT TGGGATTCTT
CCCTAGAGCA CACTTGCTTC AGTATCATAA CAAAACCCTC
ACCTAATATT TTTTTTTTTT AAAAAAAAAA TATTAGAGTG
GTATTGGGGT CTCTTTGGTA ATTCTTTGTA ATTATAAAAG
TACCCTTAAA TGTCATAAAC AGGTTAGCTT TAGCTTGCCT
TTAAAGATCT TCTTAGGGTA TCATTACTTT TCGTAAATCT
TTAATAGGCC TGTCACATAA TTCTACCCTT AAATTTCTTA
AACCTTGATC TGAAGTCAAG TGGGAGTACC CGCTGAACTT AA
(SEQ ID NO:17)

Rhizopus circinans (strain ATCC34101) internal transcribed spacer 2 and adjacent regions.

AAATTGCGAT AACTAGTGTG AATTGCATTT TCAGTGAATC
ATCGAGTCTT TGAACGCATC TTGCGCTCTT GGGATTCTTC
CCTAGAGCAC ACTTGCTTCA GTATCATAAC AAAACCCTCA
CCTAATATTT TTTTTTAAAA AAAAAAAATA TTAGAGTGGT
ATTGGGGTCT CTTTGGTAAT TCTTTGTAAT TATAAAAGTA
CCCTTAAATG TCATAAACAG GTTAGCTTTA GCTTGCCTTT
AAAGATCTTC TTAGGGTATC ATTACTTTTC GTAAATCTTT
AATAGGCCTG TCACATAATT CTACCCTTAA ATTTCTTAAA
CCTTGATCTG AAGTCAAGTG GGAGTACCCG CTGAACTTAA
(SEQ ID NO:18)

Rhizous stolonifer (strains ATCC14037 and 6227A) internal transcribed spacer 2 and adjacent regions.

AAAGTGCGAT AACTAGTGTG AATTGCATAT TCAGTGAATC
ATCGAGTCTT TGAACGCAAC TTGCACTCTA TGGTTTTCCG
TAAAGTACGC TTGCTTCAGT ATCATAAAGA CCCCATCCTG
ATTATTATTT TTTTATTAAA ATAATTAATT TTGGAGATAA
TAAAAATGAG GCTCTTTCTT TTCTTTTTTT TTTTTTTAAA
AAAAAGGGGG GGAAAGGGTC TTTTAAAATG GGCAAATTCT
GGGTTTTTTA CTAAACCTGA ACTCCCCCCA AAAATTCAAA
AAAAAAAAAA TGGGTTTTAC CAAATTTTTT TTTTTTTTCT
CCTTTTTGTG TAGTTAATAC TCTATTAAAT TTATTTACTT
GGTATTATAA CGATTATGCA AGAAGGGAGA GAACAAAGAA
TAATGAAAGA GAGTTTTTAA ATAAATTCTT TTTTCATTTT
TTCAATCAAT GATCTGAAGT CAAGTGGGAT TACCCGCTGA
ACTTAA (SEQ ID NO:19)

Rhizomucor pusillus (strain ATCC36606) internal transcribed spacer 2 and adjacent regions.

AAATTGCGAA AAGTAATGCG ATCTGCAGCC TTTGCGAATC
ATCGAATTCT CGAACGCACC TTGCACCCTT TGGTTCATCC
ATTGGGTACG TCTAGTTCAG TATCTTTATT AACCCCTAAA
GGTTTATTTT TTGATAAATC TTTGGATTTG CGGTGCTGAT
GGATTTTCAT CCGTTCAAGC TACCCGAACA ATTTGTATGT
TGTTGACCCT TGATATTTCC TTGAGGGCTT GCATTGGTAT
CTAATTTTTT ACCAGTGTGC TTCGAGATGA TCAAGTATAA
AGGTCAATCA ACCACAAATA AATTTCAACT ATGGATCTGA
ACTTAGATGG GATTACCCGC TGAACTTAA (SEQ ID NO:20)

Absidia corymbifera (strain ATCC46774) internal transcribed spacer 2 and adjacent regions.

AAAGTGCGAT AATTATTGCG ACTTGCATTC ATAGCGAATC
ATCGAGTTCT CGAACGCATC TTGCGCCTAG TAGTCAATCT
ACTAGGCACA GTTGTTTCAG TATCTGCAAC TACCAATCAG
TTCAACTTGG TTCTTTGAAC CTAAGCGAGC TGGAAATGGG
CTTGTGTTGA TGGCATTCAG TTGCTGTCAT GGCCTTAAAT
ACATTTAGTC CTAGGCAATT GGCTTTAGTC ATTTGCCGGA
TGTAGACTCT AGAGTGCCTG AGGAGCAACG ACTTGGTTAG
TGAGTTCATA ATTCCAAGTC AATCAGTCTC TTCTTGAACT
AGGTCTTAAT CTTTATGGAC TAGTGAGAGG ATCTAACTTG
GGTCTTCTCT TAAAACAAAC TCACATCTAG ATCTGAAATC
AACTGAGATC ACCCGCTGAA CTTAA (SEQ ID NO:21)

Absidia corymbifera (strain ATCC46773) internal transcribed spacer 2 and adjacent regions.

AAAGTGCGAT AATTATTGCG ACTTGCATTC ATAGTGAATC
ATCGAGTTCT TGAACGCATC TTGCGCCTAG TAGTCAATCT
ACTAGGCACA GTTGTTTCAG TATCTGCATC CACCAATCAA
CTTAACCTTT TGTGTTGAGT TGGAACTGGG CTTCTAGTTG
ATGGCATTTA GTTGCTGTCA TGGCCTTAAA TCAATGTCCT
AGGTGTTAGA ACATCTAACA CCGGATGGAA ACTTTAGAGC
GCTTTAAGAG CAGCTTGGTT AGTGAGTTCA ATAATTCCAA
GCATTAAGTC TTTTAATGAA CTAGCTTTTC TATCTATGGG
ACACTACTTG GAGAAATCCA AGTAACCTTT AAACTCCCAT
TTAGATCTGA AATCAACTGA GACCACCCGC TGAACTTAA
(SEQ ID NO:22)

Cunninghamella elegans (strain ATCC42113) internal transcribed spacer 2 and adjacent regions.

AAATCGCGAT ATGTAATGTG ACTGCCTATA GTGAATCATC
AAATCTTTGA AACGCATCTT GCACCTTATG GTATTCCATA
AGGTACGTCT GTTTCAGTAC CACTAATAAA TCTCTCTCTA
TCCTTGATGA TAGAAAAAAA AAAAATAATT TTTACTGGGC
CCGGGGAATC CTTTTTTTTT TTTAATAAAA AGGACCAATT
TTGGCCCAAA AAAAAGGGTT GAACTTTTTT TACCAGATCT
TGCATCTAGT AAAAACCTAG TCGGCTTTAA TAGATTTTTA
TTTTCTATTA AGTTTATAGC CATTCTTATA TTTTTTAAAA
TCTTGGCCTG AAATCAGATG GGATACCCGC TGAACTTAA
(SEQ ID NO:23)

Pseudallescheria boydii (strain ATCC44328) internal transcribed spacer 2 and adjacent regions (teleomorph of Scedosporium apiospennum ).

AAATGCGATA AGTAATGTAA ATTGCAAAAT TCAGTGAATC
ATCGAATCTT TGAAACGCAC ATTGCGCCCG GCAGTAATCT
GCCGGGCATG CCTGTCCGAG CGTCATTTCA ACCCTCGAAC
CTCCGTTTC  CTTAGGGAAG CCTAGGGTCG GTGTTGGGGC
GCTACGGCAA GTCCTCGCAA CCCCCGTAGG CCCTGAAATA
CAGTGGCGGT CCCGCCGCGG TTGCCTTCTG CGTAGTAAGT
CTCTTTTGCA AGCTCGCATT GGGTCCCGGC GGAGGCCTGC
CGTCAAACCA CCTAACAACT CCAGATGGTT TGACCTCGGA
TCAGGTAGGG TTACCCGCTG AACTTAA (SEQ ID NO:24)

Pseudallescheria boydii (strain ATCC36282) internal transcribed spacer 2 and adjacent regions (teleomorph of Scedosporium apiospermum ).

GAAATGCGAT AAGTAATGTG AATTGCAGAA TTCAGTGAAT
CATCGAATCT TTGAAACGCA CATTGCGCCC GGCAGTAATC
TGCCGGGCAT GCCTGTCCGA GCGTCATTTC AACCCTCGAA
CCTCCGTTTC CTCAGGGAAG CTCAGGGTCG GTGTTGGGGC
GCTACGGCAA GTCTTCGCAA CCCTCCGTAG GCCCTGAAAT
ACAGTGGCGG TCCCGCCGCG GTTGCCTTCT GCGTAGAAGT
CTCTTTTGCA AGCTCGCATT GGGTCCCGGC GGAGGCCTGC
CGTCAAACCA CCTATAACTC CAAATGGTTT GACCTCGGAT
CAGGTAGGGT TACCCGCTGA ACTTAA (SEQ ID NO:25)

Scedosporium apiospermum (strain ATCC64215) internal transcribed spacer 2 and adjacent regions.

GAAATGCGAT AAGTAATGTG AATTGCAGAA TTCAGTGAATC
ATCGAATCTT TGAACGCACA TTGCGCCCGG CAGTAATCTG
CCGGGCATGC CTGTCCGAGC GTCATTTCAA CCCTCGAACC
TCCGTTTCCT CAGGGAAGCT CAGGGTCGGT GTTGGGGCGC
TACGGCGAGT CTTCGCGACC CTCCGTAGGC CCTGAAATAC
AGTGGCGGTC CCGCCGCGGT TGCCTTCTGC GTAGTAAGTC
TCTTTTGCAA GCTCGCATTG GGTCCCGGCG GAGGCCTGCC
GTCAAACCAC CTATAACTCC AGATGGTTTG ACCTCGGATC
AGGTAGGTAC CCGCTGAACT TAA (SEQ ID NO:26)

Scedosporium apiospermum (strain ATCC46173) internal transcribed spacer 2 and adjacent regions.

AAATGCGATA AGTAATGTGA ATTGCAGAAT TCAGTGAATC
ATCGAATCTT TGAACGCACA TTGCGCCCGG CAGTAATCTG
CCGGGCATGC CTGTCCGAGC GTCATTTCAA CCCTCGAACC
TCCGTTTCCT CAGGGAAGCT CAGGGTCGGT GTTGGGGCGC
TACGGCGAGT CTTCGCGACC CTCCGTAGGC CCTGAAATAC
AGTGGCGGTC CCGCCGCGGT TGCCTTCTGC GTAGTAAGTC
TCTTTTGCAA GCTCGCATTG GGTCCCGGCG GAGGCCTGCC
GTCAAACCAC CTATAACTCC AGATGGTTTG ACCTCGGATC
AGGTAGGTAC CCGCTGAACT TAA (SEQ ID NO:27)

Penicillium notatum (strain ATCC10108) internal transcribed spacer 2 and adjacent regions.

AAATGCGATA CGTAATGTGA ATTGCAAATT CAGTGAATCA
TCGAGTCTT  TGAACGCACA TTGCGCCCCC TGGTATTCCG
GGGGGCATGC CTGTCCGAGC GTCATTGCTG CCCTCAAGCA
CGGCTTGTGT GTTGGGCCCC GTCCTCCGAT CCCGGGGGAC
GGGCCCGAAA GGCAGCGGCG GCACCGCGTC CGGTCCTCGA
GCGTATGGGG CTTTGTCACC CGCTCTGTAG GCCCGGCCGG
CGCTTGCCGA TCAACCCAAA TTTTTATCCA GGTTGACCTC
GGATCAGGTA GGGATACCCG CTGAACTTAA (SEQ ID NO:28)

Sporothrix schenckii (strain ATCC14284) internal transcribed spacer 2 and adjacent regions.

GAAATGCGAT ACTAATGTGA ATTGCAGAAT TCAGCGAACC
ATCGAATCTT TGAACGCACA TTGCGCCCGC CAGCATTCTG
GCGGGCATGC CTGTCCGAGC GTCATTTCCC CCCTCACGCG
CCCCGTTGCG CGCTGGTGTT GGGGCGCCCT CCGCCTGGCG
GGGGGCCCCC GAAAGCGAGT GGCGGGCCCT GTGGAAGGCT
CCGAGCGCAG TACCGAACGC ATGTTCTCCC CTCGCTCCGG
AGGCCCCCCA GGCGCCCTGC CGGTGAAAAC GCGCATGACG
CGCAGCTCTT TTTACAAGGT TGACCTCGGA TCAGGTGAGG 2
ATACCCGCTG ACTTAA (SEQ ID NO:29)

Contamination Precautions

Precautions were taken to avoid possible contamination of PCR samples by following the guidelines of Fujita and Kwok (13, 22). All buffers and distilled water used for PCR assays were autoclaved and fresh PCR reagents were aliquoted prior to use. Physical separation of laboratory areas used to prepare PCR assays and to analyze PCR products, and the use of aerosol-resistant pipette tips, reduced possible cross-contamination of samples by aerosols. Appropriate negative controls were included in each test run, including controls omitting either the primer or the DNA template during PCR assays.

Agarose gel Electrophoresis

Gel electrophoresis was conducted in TBE buffer (0.1 M Tris, 0.09 M boric acid, 1 mM EDTA, pH 8.4) at 80 V for 1 to 2 hours using gels composed of 1% (w/vol) agarose (International Technologies, New Haven, Conn.) and 1% (w/vol) NuSieve agar (FMC Bioproducts, Rockland, Me.). Gels were stained with 0.5 μg of ethidium bromide (EtBr) per ml of distilled H 2 O for 10 minutes followed by three serial washes for 10 minutes each with distilled H 2 O.

Microtitration Plate Enzyme Immunoassay for the Detection of PCR Products

Amplicons were detected using species-specific and genus probes labeled with digoxigenin and an all-filamentous fungal probe labeled with biotin in a streptavidin-coated microtiter plate format (13, 34). Ten μl of PCR product was added to each 1.5 ml Eppendorf tube. Single-stranded DNA was then prepared by heating the tubes at 95° C. for 5 minutes and cooling immediately on ice. Two-tenths of a ml of hybridization solution [4×SSC (saline sodium citrate buffer, 0.6 M NaCl, 0.06 M trisodium citrate, pH 7.0) containing 20 mM Hepes, 2 mM EDTA, and 0.15% (vol/vol) Tween 20] supplemented with 50 ng/ml each of the all-Aspergillus biotinylated probe and a species-specific digoxigenin-labeled probe was added to each tube containing denatured PCR product. Tubes were mixed by inversion and placed in a water bath at 37° C. to allow probes to anneal to PCR product DNA. After 1 hour, 100 μl of each sample was added to duplicate wells of a commercially prepared streptavidin-coated microtitration plate (Boehringer Mannheim, Indianapolis, Ind.). The plate was incubated at ambient temperature for 1 hour with shaking, using a microtitration plate shaker (manufactured for Dynatech by CLTI, Middletown, N.Y.). Plates were washed 6 times with 0.01 M potassium phosphate buffered saline, pH 7.2, containing 0.05% Tween 20 (PBST). Each well then received 100 μl of horseradish peroxidase-conjugated, anti-digoxigenin Fab fragment (Boehringer Mannheim) diluted 1:1000 in hybridization buffer. After incubation at ambient temperature for 30 minutes with shaking, the plate was washed 6 times with PBST. One hundred μl of a mixture of one volume of 3, 3′, 5, 5′-tetramethyl benzidine peroxidase substrate (Kirkegaard and Perry Laboratories, Inc., Gaithersberg, Md.) and one volume of peroxidase solution (Kirkegaard and Perry Laboratories) was added to each well and the plate was placed at ambient temperature for 10 minutes for color development. The A 650 nm of each well was determined with a microtitration plate reader (UV Max, Molecular Devices, Inc., Menlo Park, Calif.). The absorbance value for the reagent blank, where DNA was absent but replaced with distilled H 2 O, was subtracted from each test sample.

Statistical Analysis

The Student's t test was used to determine differences between sample means. Means are expressed as the mean plus or minus the standard error from the mean. Differences were considered significant when P<0.05.

The following probes were used to detect and distinguish each species.

TABLE 2
Probe Sequences
	5′ to 3′
	OLIGONUCLEOTIDE
PROBES	SEQUENCE
Generic Biotin Probe	5′ end-labeled biontinylated
	probe
	5.8S region of rDNA
B-58	GAA TCA TCG A(AG)T CTT	SEQ ID NO 61
	TGA ACG
Digoxigenin-probe	5′ end-labeled digoxigenin probe
	ITS2 region of rDNA
Aspergillus species
A. flavus 22	GCA AAT CAA TCT TTT TCC	SEQ ID NO 30
A. flavus 23	GAA CGC AAA TCA ATC TTT	SEQ ID NO 31
A. fumigatus	CCG ACA CCC ATC TTT ATT	SEQ ID NO 32
A. niger	GAC GTT ATC CAA CCA TTT	SEQ ID NO 33
A. nidulans	GGC GTC TCC AAC CTT ATC	SEQ ID NO 35
A. terreus	GCA TTT ATT TGC AAC TTG	SEQ ID NO 34
Fusarium species
F. moniliforme	TCT AGT GAC GGT CTC GCT	SEQ ID NO 49
F. oxysporum	CGT TAA TTC GCG TTC CTC	SEQ ID NO 50
F. solani	CTA ACA CCT CGC AAC TGG	SEQ ID NO 51
	AGA
Mucor species
M. circinelloides	AAC ATT TTT GTG AAT AGG	SEQ ID NO 39
	ATG
M. indicus	CGT GGA TTG AGT GCC GAT	SEQ ID NO 38
M. plumbeus	GAA ACC CTT GAA ATT	SEQ ID NO 37
M. rouxii	GAA TAG GAA TAC TGA GAG	SEQ ID NO 36
M. racemosus	GAA ATC CCT GAA ATT	SEQ ID NO 40
Penicillium species
Penicillium marneffei 1	GGG TTG GTC ACC ACC ATA	SEQ ID NO 47
Penicillium marneffei 2	TGG TCA CCA CCA TAT TTA	SEQ ID NO 48
Penicillium notatum	GAT CAA CCC AAA TTT TTA	SEQ ID NO 46
Rhizopus species
R. circinans	CTT AGG GTA TCA TTA CTT	SEQ ID NO 42
R. microsporus	CAT ATA ATC TAG GGG TTC	SEQ ID NO 57
R. oryzae	GAG TAT AAT CCA G(CT)A	SEQ ID NO 41
	ACT
R. stolonifer	CTT GGT ATT ATA ACG ATT	SEQ ID NO 44
Rhizomucor pusillus	TCC TTG AGG GCT TGC ATT	SEQ ID NO 43
Other Genera
Absidia corymbifera	GTT GCT GTC ATG GCC TTA	SEQ ID NO 55
Cunninghamella elegans 4	TAG TCG GCT TTA ATA GAT	SEQ ID NO 52
Cunninghamella elegans 5	TAT TAA GTT TAT AGC CAT	SEQ ID NO 53
Cunninghamella elegans 6	TAA GTt TAT AGC CAT TCT	SEQ ID NO 54
Pseudallescheria boydii	AAG TCT CTT TTG CAA GCT	SEQ ID NO 45
Sporothrix schoenckii	GAC GCG CAG CTC TTT TTA	SEQ ID NO 56
Genus Probes
G-ASPERGILLUS	CCT CGA GCG TAT GGG GCT	SEQ ID NO 58
G-FUSARIUM	CCC AAC TTC TGA ATG TTG	SEQ ID NO 59
G-MUCOR	(AC)TG GGG CCT CCC AAA	SEQ ID NO 60
	TAA

Species-specific probes to the ITS2 region of rDNA for Aspergillus fumigatus (SEQ ID NO:32), A. flavus (SEQ ID NO:31), A. niger (SEQ ID NO:33), A. terreus (SEQ ID NO:34), and A. nidulans (SEQ ID NO:35) correctly identified each of the respective species (P<0.001), and gave no false-positive reactions with Rhizopus, Mucor, Fusarium, Penicillium, or Candida species. The A. flavus probe also recognized A. oryzae , which belongs to the A. flavus group. Identification time was reduced from a mean of 5 days by conventional methods to 8 hours.

TABLE 3
Aspergillus Probes
Fungus	A. fumigatus	A. nidulans	A. niger	A. terreus	A. flavus
A. fumigatus	2.197 ±	0.002	0.000	0.001	0.001
(n = 6)	0.187
A. nidulans	0.001	1.315 ±	0.002	0.000	0.001
(n = 3)		0.464
A. niger	0.000	0.000	1.242 ±	0.001	0.003
(n = 5)			0.471
A. terreus	0.001	0.000	0.001	1.603 ±	0.001
(n = 4)				0.378
A. flavus	0.001	0.001	0.000	0.001	2.043 ±
(n = 6)					0.390
A. oryzae	0.001	0.002	0.001	0.001	2.445 ±
(n = 2)					0.106
A. parasitica	0.001	0.002	0.002	0.002	0.051
(n = 1)
A. clavus	0.005	0.005	0.006	0.005	0.003
(n = 1)
C. albicans	0.002	0.001	0.002	0.000	0.000
(n = 1)
C. parasilosis	0.001	0.002	0.002	0.002	0.001
(n = 1)
C. glabrata	0.001	0.003	0.001	0.001	0.005
(n = 1)
C. krusei	0.002	0.002	0.002	0.001	0.001
(n = 1)
C. tropicalis	0.002	0.002	0.001	0.000	0.001
(n = 1)
F. moniliforme	0.003	0.003	0.001	0.001	0.001
(n = 1)
F. solani	0.006	0.002	0.001	0.000	0.001
(n = I)
R. oryzae	0.001	0.001	0.001	0.001	0.001
(n = 1)
M. racemosus	0.001	0.002	0.005	0.002	0.000
(n = 1)
P. notatum	0.001	0.002	0.002	0.002	0.000
(n = 1)
Avg ± SD	0.001 ±	0.001 ±	0.000 ±	0.000 ±	0.002 ±
negative	0.002	0.001	0.002	0.002	0.010
controls

Species-specific probes to the ITS2 region of rDNA for Fusarium oxysporum, F. solani , and F. moniliforme , correctly identified each of the respective species (P<0.001), and gave no false-positive reactions with Blastomyces, Apophysomyces, Candida, Aspergillus, Mucor, Penecillium, Rhizopus, Rhizomucor, Absidia, Cunninghamella, Pseudallescheria, Sporothrix, or Neosartorya. Empty boxes in Table 4 represent zero probe reactivity.

TABLE 4
Fusarium Probes
				Generic
Fungus	F. oxysporum	F. solani	F. moniliforme	Fusarium
F. oxysporum	1.40 ±			1.76 ±
(n = 3)	0.13			0.27
F. solani		1.57 ±		1.35 ±
(n = 5)		0.07		0.28
F. moniliforme			1.40 ±	1.34 ±
(n = 2)	0.01	0.91
Negative control
A. fumigatus
A. flavus
A. niger
A. nidulans
A. terreus
A. parasiticus
A. clavatus
P. marneffei		0.01	0.01
P. notatum	0.01	0.01	0.01
Rhizopus oryzae		0.03	0.01
Rhizopus microsporus		0.01	0.01
Rhizopus circinans		0.01	0.01
Rhizopus stolonifer	0.01	0.01
Rhizomucor pusillus	0.03	0.02
M. racemosus
M. circinelloides
M. rouxii
M. plumbeus
M. indicus
Absidia corymbifera		0.01	0.01
Cunninghamella elegans		0.01	0.02
P. boydii	0.02
Sporothrix schenckii		0.01	0.01
C. albicans
C. tropicalis
C. krusei
C. parasilosis
C. glabrata
Neosartorya fischeri		0.01
Blastomyces dermatitidis
Apophysomyces elegans
Average of negative controls	0.001 ±	0.005 ±	0.004 ±
	0.002	0.01	0.006

Species-specific probes to various other zygomyces are presented in Table 5, showing correct identification of each species and no false positives. The exceptions are that the M. circinelloides probe hybridized with the M. rouxii DNA and the M. plumbeus probe hybridized with the M. racemosus DNA. However, the M. rouxii probe did not hybridize with M. circinelloides DNA, nor did the M. racemosus probe hybridize with M. plumbeus DNA. Therefore, by a process of elimination, each species can be correctly identified. Empty boxes in Table 5 represent zero probe reactivity.

TABLE 5

Zygomyces Probes

D-probes

FUNGUS

RORY

RMIC

RCIR

RSTOL

RPUS

MRACE

MCIR

MRX

MPLUM

MIND

ABS

CUN

R. oryzae

1.50 ±

0.01

(n = 5)

0.48

R. microsporus

0.96 ±

(n = 5)

0.61

R. circinans

1.56 ±

(n = 3)

0.19

R. stolonifer

2.53 ±

0.01

(n = 5)

0.07

Rhizomucor pusillus

1.10 ±

(n = 2)

0.68

M. racemosus

0.01

2.02 ±

0.29 ±

(n = 6)

0.34

0.52

M. circinelloides

1.63 ±

0.01

0.02

(n = 3)

0.37

M. rouxii

1.77

0.76

(n = 1)

M. plumbeus

2.14 ±

(n = 2)

0.25

M. indicus

0.01

1.70 ±

(n = 1)

0.04

Absidia corymbifera

0.01

0.01

1.61 ±

(n = 2)

0.08

Cunninhamella

0.01

2.26 ±

elegans

0.03

(n = 2)

Negative control

A. fumigatus

0.01

0.02

A. flavus

0.01

0.05

A. niger

0.01

A. nidulans

0.01

0.01

A. terreus

0.01

A. parasiticus

0.01

0.03

A. clavatus

0.02

P. marneffei

0.01

P. notatum

0.03

F. oxysporum

0.01

F. solani

F. moniliforme

0.01

0.01

0.01

0.01

P. boydii

0.02

Sporothrix schenckii

C. albicans

C. tropicalis

C. krusei

C. parasilosis

C. glabrata

Neosartorya fischeri

0.01

Blastomyces

dermatifidis

Apophysomyces

elegans

Average

0.001 ±

0.001 ±

0.000 ±

0.000 ±

0.001 ±

0.001 ±

0.001 ±

0.001 ±

0.003 ±

0.005 ±

0.001 ±

.004

0.02

0.002

0.003

0.003

0.002

0.002

0.003

0.005

0.01

0.001

Species-specific probes to various other fungi are presented in Table 6, showing correct identification of each species and no false positives. Empty boxes in Table 6 represent zero probe reactivity.

TABLE 6
Pseudallescheria and Sporothrix Probes
				Sporothrix
Fungus	P. boydii	P. marneffei	P. notatum	schenckii
P. boydii	1.65 ±
(n = 4)	0.48
P. marneffei	0.01	1.24 ±
(n = 3)		0.12
P. notatum			1.93 ±
(n = 3)			0.25
Sporothrix schenckii	0.01			1.94 ±
(n = 3)				0.25
Negative control
A. fumigatus	0.01
A. flavus
A. niger
A. nidulans
A. terreus
A. parasiticus
A. clavatus			0.11
F. oxysporum		0.10
F. solani		0.14
F. moniliforme		0.08
R. oryzae	0.01
R. microsporus	0.01
R. circinans	0.01
R. stolonifer	0.01
Rhizomucor pusilus
M. racemosus		0.04
M. circinelloides	0.01	0.09
M. rouxii	0.01
M. plumbeus		0.05
M. indicus
Absidia corymbifera	0.01
Cunninghamela bertholietiae	0.01
C. albicans
C. tropicalis		0.02
C. krusei
C. parasilosis
C. glabrata
Neosatorya pseudofischeri		0.03
Blastomyces dermatitidis	0.01
Apophysomyces elegans	0.01
Average Negative Controls	0.004 ±	0.013 ±	0.002 ±	0.001 ±
	0.002	0.03	0.019	0.002

All of the references mentioned in this Specification are hereby incorporated by reference in their entirety.

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61 1 208 DNA Aspergillus flavus 1gctgcccatc aagcacggct tgtgtgttgg gtcgtcgtcc cctctccggg ggggacgggc 60cccaaaggca gcggcggcac cgcgtccgat cctcgagcgt atggggcttt gtcacccgct 120ctgtaggccc ggccggcgct tgccgaacgc aaatcaatct ttttccaggt tgacctcgga 180tcaggtaggg atacccgctg aacttcaa 208 2 364 DNA Aspergillus fumigatus 2aaactttcaa caatggatct cttggttccg gcatcgatga agaacgcagc gaaatgcgat 60aactaatgtg aattgcagaa ttcagtgaat catcgagtct ttgaacgcac attgcgcccc 120ctggtattcc ggggggcatg cctgtccgag cgtcattgct gcccatcaag cacggcttgt 180gtgttgggcc cccgtccccc tctcccgggg gacgggcccg aaaggcagcg gcggcaccgc 240gtccggtcct cgagcgtatg gggcttgtca cctgctctgt aggcccggcc ggcgccagcc 300gacacccaac tttatttttc taaggttgac ctcggatcag gtagggatac ccgctgaact 360taaa 364 3 365 DNA Aspergillus niger 3aaactttcaa caatggatct cttggttccg gcatcgatga agaacgcagc gaaatgcgat 60aactaatgtg aattgcagaa ttcagtgaat catcgagtct ttgaacgcac attgcgcccc 120ctggtattcc ggggggcatg cctgtccgag cgtcattgct gccctcaagc acggcttgtg 180tgttgggtcg ccgtccccct ctcccggggg acgggcccga aaggcagcgg cggcaccgcg 240tccgatcctc gagcgtatgg ggctttgtca cctgctctgt aggcccggcc ggcgcctgcc 300gacgttatcc aaccattttt ttccaggttg acctcggatc aggtagggat acccgctgaa 360cttaa 365 4 355 DNA Aspergillus terreus 4aaactttcaa caatggatct cttggttccg gcatcgatga agaacgcagc gaaatgcgat 60aactaatgtg aattgcagaa ttcagtgaat catcgagtct ttgaacgcac attgcgcccc 120ctggtattcc gggggggcat gcctgtccga gcgtcattgc tgccctcaag cccggcttgt 180gtgttgggcc ctcgtccccc ggctcccggg ggacgggccc gaaaggcagc ggcggcaccg 240cgtccggtcc tcgagcgtat ggggcttcgt cttccgctcc gtaggcccgg ccggcgcccg 300ccgaacgcat ttatttgcaa cttgtttttt tttccaggtt gacctcggat caggt 355 5 365 DNA Aspergillus nidulans 5aaactttcaa caatggatct cttggttccg gcatcgatga agaacgcagc gaactgcgat 60aagtaatgtg aattgcagaa ttcagtgaat catcgagtct ttgaacgcac attgcgcccc 120ctggcattcc ggggggcatg cctgtccgag cgtcattgct gccctcaagc ccggcttgtg 180tgttgggtcg tcgtcccccc ccccggggga cgggcccgaa aggcagcggc ggcaccggtc 240cggtcctcga gcgtatgggg cttggtcacc cgctcgatta gggccggccg ggcgccagcc 300ggcgtctcca accttatctt tctcaggttg acctcggatc aggtagggat acccgctgaa 360cttaa 365 6 319 DNA Fusarium solani 6gaaaatgcga taagtaatgt gaattgcaga attcagtgaa tcatcgaatc tttgaacgca 60cattgcgccc gccagtattc tggcgggcat gcctgttcga gcgtcattac aaccctcagg 120cccccgggcc tggcgttggg gatcggcgga agccccctgc gggcacaacg ccgtccccca 180aatacagtgg cggtcccgcc gcagcttcca ttgcgtagta gctaacacct cgcaactgga 240gagcggcgcg gccacgccgt aaaacaccca acttctgaat gttgacctcg aatcaggtag 300gaatacccgc tgaacttaa 319 7 310 DNA Fusarium moniliforme 7aaatgcgata agtaatgtga attgcaaaat tcagtgaatc atcgaatctt tgaacgcaca 60ttgcgcccgc cagtattctg gcgggcatgc ctgttcgagc gtcatttcaa ccctcaagcc 120cccgggtttg gtgttgggga tcggcaagcc cttgcggcaa gccggccccg aaatctagtg 180gcggtctcgc tgcagcttcc attgcgtagt agtaaaaccc tcgcaactgg tacgcggcgc 240ggccaagccg ttaaaccccc aacttctgaa tgttgacctc ggatcaggta ggaatacccg 300ctgaacttaa 310 8 330 DNA Mucor rouxii 8aaagtgcgat aactagtgtg aattgcatat tcagtgaatc atcgagtctt tgaacgcaac 60ttgcgctcat tggtattcca atgagcacgc ctgtttcagt atcaaaacaa accctctatc 120cagcattttg ttgaatagga atactgagag tctcttgatc tattctgatc tcgaacctct 180tgaaatgtac aaaggcctga tcttgtttaa atgcctgaac ttttttttaa tataaagaga 240agctcttgcg gtaaactgtg ctggggcctc ccaaataata ctctttttaa atttgatctg 300aaatcaggcg ggattacccg ctgaacttaa 330 9 328 DNA Mucor racemosus 9aaagtgcgat aactagtgtg aattgcatat tcagtgaatc atcgagtctt tgaacgcaac 60ttgcgctcat tggtattcca atgagcacgc ctgtttcagt atcaaaacaa accctctatc 120caacttttgt tgtataggat tattgggggc ctctcgatct gtatagatct tgaaatccct 180gaaatttact aaggcctgaa cttgtttaaa tgcctgaact tttttttaat ataaaggaaa 240gctcttgtaa ttgactttga tggggcctcc caaataaatc tcttttaaat ttgatctgaa 300atcaggcggg attacccgct gaacttaa 328 10 327 DNA Mucor plumbeus 10aaagtgcgat aactagtgtg aattgcatat tcagtgaatc atcgagtctt tgaacgcaac 60ttgcgctcat tggtattcca atgagcacgc ctgtttcagt atcaaaacaa accctctatc 120caacttttgt tgtataggat tattgggggc ctctcgatct gtatagatct tgaaaccctt 180gaaatttact aaggcctgaa cttgtttaat gcctgaactt ttttttaata taaaggaaag 240ctcttgtaat tgactttgat ggggcctccc aaataaatct tttttaaatt tgatctgaaa 300tcaggtggga ttacccgctg aacttaa 327 11 322 DNA Mucor indicus 11aaagtgcgat aactagtgtg aattgcatat tcagtgaatc atcgagtctt tgaacgcatc 60ttgcactcaa tggtattcca ttgagtacgc ctgtttcagt atcaaaaaca acccttattc 120aaaattcttt ttttgaatag atatgagtgt agcaacctta caagttgaga cattttaaat 180aaagtcaggc catatcgtgg attgagtgcc gatacttttt taattttgaa aaggtaaagc 240atgttgatgt ccgctttttg ggcctcccaa ataacttttt aaacttgatc tgaaatcagg 300tgggattacc cgctgaactt aa 322 12 330 DNA Mucor circinelloides f. 12aaagtgcgat aactagtgtg aattgcatat tcagtgaatc atcgagtctt tgaacgcaac 60ttgcgctcat tggtattcca atgagcacgc ctgtttcagt atcaaaacaa accctctatc 120caacattttt gttgaatagg atgactgaga gtctcttgat ctattctgat ctcgaagctc 180ttgaaatgta caaaggcctg atcttgtttg aatgcctgaa ctttttttta atataaagag 240aagctcttgc ggtaaactgt gctggggcct cccaaataac acatctttaa atttgatctg 300aaatcaggtg ggactacccg ctgaacttaa 330 13 333 DNA Rhizopus oryzae 13agtgcgataa ctagtgtgaa ttgcatattc agtgaatcat cgagtctttg aacgcagctt 60gcactctatg gtttttctat agagtacgcc tgcttcagta tcatcacaaa cccacacata 120acatttgttt atgtggtgat gggtcgcatc gctgttttat tacagtgagc acctaaaatg 180tgtgtgattt tctgtctggc ttgctaggca ggaatattac gctggtctca ggatcttttt 240ttttggttcg cccaggaagt aaagtacaag agtataatcc agtaactttc aaactatgat 300ctgaagtcag gtgggattac ccgctgaact taa 333 14 333 DNA Rhizopus oryzae 14agtgcgataa ctagtgtgaa ttgcatattc agtgaatcat cgagtctttg aacgcagctt 60gcactctatg gtttttctat agagtacgcc tgcttcagta tcatcacaaa cccacacata 120acatttgttt atgtggtaat gggtcgcatc gctgttttat tacagtgagc acctaaaatg 180tgtgtgattt tctgtctggc ttgctaggca ggaatattac gctggtctca ggatcttttt 240ctttggttcg cccaggaagt aaagtacaag agtataatcc agcaactttc aaactatgat 300ctgaagtcag gtgggattac ccgctgaact taa 333 15 348 DNA Rhizopus microsporus 15aaagtgcgat aactagtgtg aattgcatat tcgtgaatca tcgagtcttt gaacgcagct 60tgcactctat ggatcttcta tagagtacgc ttgcttcagt atcataacca acccacacat 120aaaatttatt ttatgtggtg atggacaagc tcggttaaat ttaattatta taccgattgt 180ctaaaataca gcctctttgt aattttcatt aaattacgaa ctacctagcc atcgtgcttt 240tttggtccaa ccaaaaaaca tataatctag gggttctgct agccagcaga tattttaatg 300atctttaact atgatctgaa gtcaagtggg actacccgct gaacttaa 348 16 349 DNA Rhizopus microsporus 16aaagtgcgat aactagtgtg aattgcatat tcgtgaatca tcgagtcttt gaacgcagct 60tgcactctat ggatcttcta tagagtacgc ttgcttcagt atcataacca acccacacat 120aaaatttatt ttatgtggtg atggacaagc tcggttaaat ttaattatta taccgattgt 180ctaaaataca gcctctttgt aattttcatt aaattacgaa ctacctagcc atcgtgcttt 240tttggtccaa ccaaaaaaca tataatctag gggttctgct agccagcaaa tattttaatg 300atctttaacc tatgatctga agtcaagtgg gactacccgc tgaacttaa 349 17 361 DNA Rhizopus circinans 17aaattgcgat aactagtgtg aattgcattt tcagtgaatc atcgagtctt tgaacgcatc 60ttgcgctctt gggattcttc cctagagcac acttgcttca gtatcataac aaaaccctca 120cctaatattt ttttttttta aaaaaaaaat attagagtgg tattggggtc tctttggtaa 180ttctttgtaa ttataaaagt acccttaaat gtcataaaca ggttagcttt agcttgcctt 240taaagatctt cttagggtat cattactttt cgtaaatctt taataggcct gtcacataat 300tctaccctta aatttcttaa accttgatct gaagtcaagt gggagtaccc gctgaactta 360a 361 18 360 DNA Rhizopus circinans 18aaattgcgat aactagtgtg aattgcattt tcagtgaatc atcgagtctt tgaacgcatc 60ttgcgctctt gggattcttc cctagagcac acttgcttca gtatcataac aaaaccctca 120cctaatattt ttttttaaaa aaaaaaaata ttagagtggt attggggtct ctttggtaat 180tctttgtaat tataaaagta cccttaaatg tcataaacag gttagcttta gcttgccttt 240aaagatcttc ttagggtatc attacttttc gtaaatcttt aataggcctg tcacataatt 300ctacccttaa atttcttaaa ccttgatctg aagtcaagtg ggagtacccg ctgaacttaa 360 19 486 DNA Rhizopus stolonifer 19aaagtgcgat aactagtgtg aattgcatat tcagtgaatc atcgagtctt tgaacgcaac 60ttgcactcta tggttttccg taaagtacgc ttgcttcagt atcataaaga ccccatcctg 120attattattt ttttattaaa ataattaatt ttggagataa taaaaatgag gctctttctt 180ttcttttttt tttttttaaa aaaaaggggg ggaaagggtc ttttaaaatg ggcaaattct 240gggtttttta ctaaacctga actcccccca aaaattcaaa aaaaaaaaaa tgggttttac 300caaatttttt ttttttttct cctttttgtg tagttaatac tctattaaat ttatttactt 360ggtattataa cgattatgca agaagggaga gaacaaagaa taatgaaaga gagtttttaa 420ataaattctt ttttcatttt ttcaatcaat gatctgaagt caagtgggat tacccgctga 480acttaa 486 20 349 DNA Rhizomucor pusillus 20aaattgcgaa aagtaatgcg atctgcagcc tttgcgaatc atcgaattct cgaacgcacc 60ttgcaccctt tggttcatcc attgggtacg tctagttcag tatctttatt aacccctaaa 120ggtttatttt ttgataaatc tttggatttg cggtgctgat ggattttcat ccgttcaagc 180tacccgaaca atttgtatgt tgttgaccct tgatatttcc ttgagggctt gcattggtat 240ctaatttttt accagtgtgc ttcgagatga tcaagtataa aggtcaatca accacaaata 300aatttcaact atggatctga acttagatgg gattacccgc tgaacttaa 349 21 425 DNA Absidia corymbifera 21aaagtgcgat aattattgcg acttgcattc atagcgaatc atcgagttct cgaacgcatc 60ttgcgcctag tagtcaatct actaggcaca gttgtttcag tatctgcaac taccaatcag 120ttcaacttgg ttctttgaac ctaagcgagc tggaaatggg cttgtgttga tggcattcag 180ttgctgtcat ggccttaaat acatttagtc ctaggcaatt ggctttagtc atttgccgga 240tgtagactct agagtgcctg aggagcaacg acttggttag tgagttcata attccaagtc 300aatcagtctc ttcttgaact aggtcttaat ctttatggac tagtgagagg atctaacttg 360ggtcttctct taaaacaaac tcacatctag atctgaaatc aactgagatc acccgctgaa 420cttaa 425 22 399 DNA Absidia corymbifera 22aaagtgcgat aattattgcg acttgcattc atagtgaatc atcgagttct tgaacgcatc 60ttgcgcctag tagtcaatct actaggcaca gttgtttcag tatctgcatc caccaatcaa 120cttaaccttt tgtgttgagt tggaactggg cttctagttg atggcattta gttgctgtca 180tggccttaaa tcaatgtcct aggtgttaga acatctaaca ccggatggaa actttagagc 240gctttaagag cagcttggtt agtgagttca ataattccaa gcattaagtc ttttaatgaa 300ctagcttttc tatctatggg acactacttg gagaaatcca agtaaccttt aaactcccat 360ttagatctga aatcaactga gaccacccgc tgaacttaa 399 23 359 DNA Cunninghamella elegans 23aaatcgcgat atgtaatgtg actgcctata gtgaatcatc aaatctttga aacgcatctt 60gcaccttatg gtattccata aggtacgtct gtttcagtac cactaataaa tctctctcta 120tccttgatga tagaaaaaaa aaaaataatt tttactgggc ccggggaatc cttttttttt 180tttaataaaa aggaccaatt ttggcccaaa aaaaagggtt gaactttttt taccagatct 240tgcatctagt aaaaacctag tcggctttaa tagattttta ttttctatta agtttatagc 300cattcttata ttttttaaaa tcttggcctg aaatcagatg ggatacccgc tgaacttaa 359 24 346 DNA Pseudallescheria boydii 24aaatgcgata agtaatgtaa attgcaaaat tcagtgaatc atcgaatctt tgaaacgcac 60attgcgcccg gcagtaatct gccgggcatg cctgtccgag cgtcatttca accctcgaac 120ctccgtttcc ttagggaagc ctagggtcgg tgttggggcg ctacggcaag tcctcgcaac 180ccccgtaggc cctgaaatac agtggcggtc ccgccgcggt tgccttctgc gtagtaagtc 240tcttttgcaa gctcgcattg ggtcccggcg gaggcctgcc gtcaaaccac ctaacaactc 300cagatggttt gacctcggat caggtagggt tacccgctga acttaa 346 25 346 DNA Pseudallescheria boydii 25gaaatgcgat aagtaatgtg aattgcagaa ttcagtgaat catcgaatct ttgaaacgca 60cattgcgccc ggcagtaatc tgccgggcat gcctgtccga gcgtcatttc aaccctcgaa 120cctccgtttc ctcagggaag ctcagggtcg gtgttggggc gctacggcaa gtcttcgcaa 180ccctccgtag gccctgaaat acagtggcgg tcccgccgcg gttgccttct gcgtagaagt 240ctcttttgca agctcgcatt gggtcccggc ggaggcctgc cgtcaaacca cctataactc 300caaatggttt gacctcggat caggtagggt tacccgctga acttaa 346 26 344 DNA Scedosporium apiospermum 26gaaatgcgat aagtaatgtg aattgcagaa ttcagtgaat catcgaatct ttgaacgcac 60attgcgcccg gcagtaatct gccgggcatg cctgtccgag cgtcatttca accctcgaac 120ctccgtttcc tcagggaagc tcagggtcgg tgttggggcg ctacggcgag tcttcgcgac 180cctccgtagg ccctgaaata cagtggcggt cccgccgcgg ttgccttctg cgtagtaagt 240ctcttttgca agctcgcatt gggtcccggc ggaggcctgc cgtcaaacca cctataactc 300cagatggttt gacctcggat caggtaggta cccgctgaac ttaa 344 27 343 DNA Scedosporium apiospermum 27aaatgcgata agtaatgtga attgcagaat tcagtgaatc atcgaatctt tgaacgcaca 60ttgcgcccgg cagtaatctg ccgggcatgc ctgtccgagc gtcatttcaa ccctcgaacc 120tccgtttcct cagggaagct cagggtcggt gttggggcgc tacggcgagt cttcgcgacc 180ctccgtaggc cctgaaatac agtggcggtc ccgccgcggt tgccttctgc gtagtaagtc 240tcttttgcaa gctcgcattg ggtcccggcg gaggcctgcc gtcaaaccac ctataactcc 300agatggtttg acctcggatc aggtaggtac ccgctgaact taa 343 28 309 DNA Penicillium notatum 28aaatgcgata cgtaatgtga attgcaaatt cagtgaatca tcgagtcttt gaacgcacat 60tgcgccccct ggtattccgg ggggcatgcc tgtccgagcg tcattgctgc cctcaagcac 120ggcttgtgtg ttgggccccg tcctccgatc ccgggggacg ggcccgaaag gcagcggcgg 180caccgcgtcc ggtcctcgag cgtatggggc tttgtcaccc gctctgtagg cccggccggc 240gcttgccgat caacccaaat ttttatccag gttgacctcg gatcaggtag ggatacccgc 300tgaacttaa 309 29 336 DNA Sporothrix schenckii 29gaaatgcgat actaatgtga attgcagaat tcagcgaacc atcgaatctt tgaacgcaca 60ttgcgcccgc cagcattctg gcgggcatgc ctgtccgagc gtcatttccc ccctcacgcg 120ccccgttgcg cgctggtgtt ggggcgccct ccgcctggcg gggggccccc gaaagcgagt 180ggcgggccct gtggaaggct ccgagcgcag taccgaacgc atgttctccc ctcgctccgg 240aggcccccca ggcgccctgc cggtgaaaac gcgcatgacg cgcagctctt tttacaaggt 300tgacctcgga tcaggtgagg atacccgctg acttaa 336 30 18 DNA Aspergillus flavus 30gcaaatcaat ctttttcc 18 31 18 DNA Aspergillus fumigatus 31gaacgcaaat caatcttt 18 32 18 DNA Aspergillus fumigatus 32ccgacaccca tctttatt 18 33 18 DNA Aspergillus niger 33gacgttatcc aaccattt 18 34 18 DNA Aspergillus terreus 34gcatttattt gcaacttg 18 35 18 DNA Aspergillus nidulans 35ggcgtctcca accttatc 18 36 18 DNA Mucor rouxii 36gaataggaat actgagag 18 37 15 DNA Mucor indicus 37gaaacccttg aaatt 15 38 18 DNA Mucor indicus 38cgtggattga gtgccgat 18 39 21 DNA Mucor circinelloides f. 39aacatttttg tgaataggat g 21 40 15 DNA Mucor racemosus 40gaaatccctg aaatt 15 41 18 DNA Rhizopus oryzae 41gagtataatc cagyaact 18 42 18 DNA Rhizopus circinans 42cttagggtat cattactt 18 43 18 DNA Rhizomucor pusillus 43tccttgaggg cttgcatt 18 44 18 DNA Rhizopus stolonifer 44cttggtatta taacgatt 18 45 18 DNA Pseudallescheria boydii 45aagtctcttt tgcaagct 18 46 18 DNA Penicillium notatum 46gatcaaccca aattttta 18 47 18 DNA Penicillium marneffei 47gggttggtca ccaccata 18 48 18 DNA Penicillium marneffei 48tggtcaccac catattta 18 49 18 DNA Fusarium moniliforme 49tctagtgacg gtctcgct 18 50 18 DNA Fusarium oxysporum 50cgttaattcg cgttcctc 18 51 21 DNA Fusarium solani 51ctaacacctc gcaactggag a 21 52 18 DNA Cunninghamella elegans 52tagtcggctt taatagat 18 53 18 DNA Cunninghamella elegans 53tattaagttt atagccat 18 54 18 DNA Cunninghamella elegans 54taagtttata gccattct 18 55 18 DNA Absidia corymbifera 55gttgctgtca tggcctta 18 56 18 DNA Sporothrix schenckii 56gacgcgcagc tcttttta 18 57 18 DNA Rhizopus microsporus 57catataatct aggggttc 18 58 18 DNA Aspergillus sp. 58cctcgagcgt atggggct 18 59 18 DNA Fusarium sp. 59cccaacttct gaatgttg 18 60 18 DNA Mucor sp. 60mtggggcctc ccaaataa 18 61 21 DNA Artificial Sequence Description of Artificial Sequence B-58 biotin probe 61gaatcatcga rtctttgaac g 21

Claims

1. An isolated nucleic acid probe that consists essentially of 10 to 50 consecutive nucleotides for species-specific identification of Aspergillus, wherein the probe selectively hybridizes under stringent conditions to the internal transcribed spacer 2 nucleic acid sequence of one of Aspergillus flavus (SEQ ID NO:1), Aspergillus fumigatus (SEQ ID NO:2), Aspergillus niger (SEQ ID NO:3), Aspergillus terreus (SEQ ID NO:4), or Aspergillus nidulans (SEQ ID NO:5), but does not selectively hybridize under stringent conditions to the internal transcribed spacer 2 region of any other Aspergillus species, nor does it hybridize to the internal transcribed spacer 2 nucleic acid sequence of Fusarium solani (SEQ ID NO:6), Fusarium moniliforme (SEQ ID NO:7), Mucor rouxii (SEQ ID NO:8), Mucor racemosus (SEQ ID NO:9), Mucor plumbeus (SEQ ID NO:10), Mucor indicus (SEQ ID NO:11), Mucor circinilloides f. circinelloides (SEQ ID NO:12), Rhizopus oryzae (SEQ ID NO:13 and NO:14), Rhizopus microsporus (SEQ ID NO:15 and 16), Rhizopus circinans (SEQ ID NO:17 and 18), Rhizopus stolonifer (SEQ ID NO:19), Rhizomucor pusillus (SEQ ID NO:20), Absidia corymbifera (SEQ ID NO:21 and 22), Cunninghamella elegans (SEQ ID NO:23), Pseudallescheria boydii (teleomorph of Scedosporium apiospermum) (SEQ ID NO:24, 25, 26, and 27), Penicillium notatum (SEQ ID NO:28), or Sporothrix schenkii (SEQ ID NO:29).

2. The isolated nucleic acid probe of claim 1 wherein the probe selectively hybridizes with an Aspergillus flavus nucleic acid of SEQ ID NO:1, or a complementary sequence thereof.

3. The isolated nucleic acid probe of claim 1 wherein the probe selectively hybridizes with an Aspergillus fumigatus nucleic acid of SEQ ID NO:2, or a complementary sequence thereof.

4. The isolated nucleic acid probe of claim 1 wherein the probe selectively hybridizes with an Aspergillus niger nucleic acid of SEQ ID NO:3, or a complementary sequence thereof.

5. The isolated nucleic acid probe of claim 1 wherein the probe selectively hybridizes with an Aspergillus terreus nucleic acid of SEQ ID NO:4, or a complementary sequence thereof.

6. The isolated nucleic acid probe of claim 1 wherein the probe selectively hybridizes with an Aspergillus nidulans nucleic acid of SEQ ID NO:5, or a complementary sequence thereof.

7. A method of detecting a species of Aspergillus flavus (SEQ ID NO:1), Aspergillus fumigatus (SEQ ID NO:2), Aspergillus niger SEQ ID NO:3), Aspergillus terreus (SEQ ID NO:4), or Aspergillus nidulans (SEQ ID NO:5) in a sample comprisingcontacting the sample with a nucleic acid probe consisting essentially of 10 to 50 consecutive nucleotides that selectively hybridizes with a nucleic acid having a sequence as set forth as SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, or SEQ ID NO:5, or a complementary sequence thereof; wherein hybridization of the nucleic acid probe with the sample indicates the detection of the Aspergillus species in the sample.

8. The method of claim 7, wherein the probe selectively hybridizes with an Aspergillus flavus nucleic acid of SEQ ID NO:1, or a complementary sequence thereof.

9. The method of claim 7, wherein the probe selectively hybridizes with an Aspergillus fumigatus nucleic acid of SEQ ID NO:2, or a complementary sequence thereof.

10. The method of claim 7, wherein the probe selectively hybridizes with an Aspergillus niger nucleic acid of SEQ ID NO:3, or a complementary sequence thereof.

11. The method of claim 7, wherein the probe selectively hybridizes with an Aspergillus terreus nucleic acid of SEQ ID NO:4, or a complementary sequence thereof.

12. The method of claim 7, wherein the probe selectively hybridizes with an Aspergillus nidulans nucleic acid of SEQ ID NO:5, or a complementary sequence thereof.

13. An isolated nucleic acid probe for identifying a filamentous fungus wherein the probe consists essentially of a nucleic acid having a sequence as set forth as SEQ ID NO:61, or a complementary sequence thereof, respectively.

14. The isolated nucleic acid probe of claim 1, wherein the probe consists essentially of a nucleotide sequence having a sequence as set forth as SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, or SEQ ID NO:35.

15. The isolated nucleic acid probe of claim 1, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:30.

16. The isolated nucleic acid probe of claim 1, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:31.

17. The isolated nucleic acid probe of claim 1, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:32.

18. The isolated nucleic acid probe of claim 1, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:33.

19. The isolated nucleic acid probe of claim 1, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:34.

20. The isolated nucleic acid probe of claim 1, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:35.

21. The method of claim 7, wherein the probe consists essentially of a nucleotide sequence as set forth as SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, and SEQ ID NO:34.

22. The method of claim 7, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:30.

23. The method of claim 7, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:31.

24. The method of claim 7, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:32.

25. The method of claim 7, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:33.

26. The method of claim 7, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:34.

27. The isolated nucleic acid probe of claim 1, wherein the probe consists essentially of the nucleotide sequence set forth as SEQ ID NO:35.

28. An isolated nucleic acid comprising a sequence as set forth as SEQ ID NO:1 or SEQ ID NO:2.

29. An isolated nucleic acid consisting essentially of a sequence as set forth as SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:5.