Compositions for the use in identification of fungi

Abstract

The present invention provides compositions, kits and methods for rapid identification and quantification of fungi by molecular mass and base composition analysis.

1 . A method for identification of a fungus in a sample comprising:
 amplifying nucleic acid from said fungus using an isolated oligonucleotide primer pair wherein each of the forward member and reverse member of the primer pair is independently 13 to 35 consecutive nucleobases in length and configured to hybridize with at least 70% complementarity to a region of GenBank Accession Number X70659, said region being from nucleobase 134 to nucleobase 269, to obtain an amplification product that comprises a length from 45-200 consecutive nucleobases.   
     
     
         2 . The method of  claim 1  further comprising the step of determining a molecular mass of said amplification product. 
     
     
         3 . The method of  claim 2  further comprising the step of calculating a base composition from said molecular mass. 
     
     
         4 . The method of  claim 2  further comprising the step of comparing said determined molecular mass with a database of molecular masses indexed to primer pairs and known fungi bioagents, wherein a match between said determined molecular mass and a molecular mass in said database indicates the presence of said fungus in said sample. 
     
     
         5 . The method of  claim 2  further comprising the step of comparing said determined molecular mass with a database of molecular masses indexed to primer pairs and known fungi bioagents, wherein a match between said determined molecular mass and a molecular mass in said database identifies the species or sub-species of said fungus in said sample. 
     
     
         6 . The method of  claim 5  wherein said fungus in said sample is identified as a species of fungus or a sub-species of fungus. 
     
     
         7 . The method of  claim 3  further comprising the step of comparing said calculated base composition with a database of base compositions indexed to primer pairs and known fungi bioagents, wherein a match between said calculated base composition and a base composition in said database indicates the presence of said fungus in said sample. 
     
     
         8 . The method of  claim 3  further comprising the step of comparing said calculated base composition with a database of base compositions indexed to primer pairs and known fungi bioagents, wherein a match between said calculated base composition and a base composition in said database 0 identifies the species or sub-species of said fungus in said sample. 
     
     
         9 . The method of  claim 8  wherein said fungus in said sample is identified as a species of fungus or a sub-species of fungus. 
     
     
         10 . The method of  claim 1  wherein said forward primer member of said primer pair hybridizes with at least 70% complementarity to a region of GenBank Accession Number X70659, said region being from nucleobase 134 to nucleobase 159. 
     
     
         11 . The method of  claim 1  wherein said forward primer member is SEQ ID NO: 10. 
     
     
         12 . The method of  claim 1  wherein said reverse primer member of said primer pair hybridizes with at least 70% complementarity to a region of GenBank Accession Number X70659, said region being from nucleobase 235 to nucleobase 269. 
     
     
         13 . The method of  claim 1  wherein said reverse primer member is SEQ ID NO: 25. 
     
     
         14 . The method of  claim 1  wherein said forward member and said reverse member are each independently configured to hybridize with at least 80% complementarity to a region of GenBank Accession Number X70659. 
     
     
         15 . The method of  claim 1  wherein said forward member and said reverse member are each independently configured to hybridize with at least 90% complementarity to a region of GenBank Accession Number X70659. 
     
     
         16 . The method of  claim 1  wherein said forward member and said reverse member are each independently configured to hybridize with at least 95% complementarity to a region of GenBank Accession Number X70659. 
     
     
         17 . The method of  claim 1  wherein said forward member and said reverse member are each independently configured to hybridize with 100% complementarity to a region of GenBank Accession Number X70659. 
     
     
         18 . The method of  claim 1  wherein at least one of said forward member and said reverse member comprises at least one modified nucleobase. 
     
     
         19 . The method of  claim 18  wherein at least one of said at least one modified nucleobase is a mass modified nucleobase. 
     
     
         20 . The method of  claim 19  wherein said mass modified nucleobase is 5-Iodo-C. 
     
     
         21 - 69 . (canceled)