Compositions for the use in identification of fungi

• US 8,088,582 B2
• Filed: 04/06/2007
• Issued: 01/03/2012
• Est. Priority Date: 04/06/2006
• Status: Expired due to Fees

• Current Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Original Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Inventors: Sampath, Rangarajan, Hall, Thomas A., Ecker, David J.
• Primary Examiner(s): Staples, Mark
• Application Number:
  US12/296,253
• Publication Number:
  US 20090311683A1
• Time in Patent Office: 1,733 Days
• Field of Search: None
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: C12Q 1/6895 for plants, fungi or algae
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

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

Claims

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 the forward member of the primer pair comprises at least 70% sequence identity to SEQ ID NO;

10, and the reverse member of the primer pair is SEQ ID NO;

25 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 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.

5. 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 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 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.

8. 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.

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 9 wherein the fungus in said sample is identified as Candida albicans, Candida dubliniensis, Candida glabrata, Uncinocarpus reesii, Eremothecium gossypii, Saccharomyces cerevisiae, Aspergillus oryzae, Aspergillus fumigatus, Aspergillus terreus, Ajellomyces capsulatus, Neosartorya fischeri, Penicillium verruculosum, Chaetomium globosum, Gibberella moniliformis, Hypocrea jecorina, Verticillium dahliae, Magnaporthe grisea, Symbiotaphrina kochii, Phaeosphaeria nodoru, Lecophagus sp, Botryotinia fuckeliana, Arxula adeninivorans, Saccharomycopsis fibuligera, Schizosaccharomyces japonicus, Schizosaccharomyces pombe, Endogone pisiformis, Tricholoma matsutake, Pneumocystis carinii, Rhizomucor miehei, Mucor racemosus, Rhizopus stolonifer, Endogone lactiflua, Phycomyces blakesleeanus, Cokeromyces recurvatus, Mortierella verticillata, Cryptococcus neoformans, Basidiobolus ranarum, Umbelopsis ramanniana, Mortierella sp., Smittium culisetae, Furculomyces boomerangu, Piptocephalis corymbifera, Kuzuhaea moniliformis, Conidiobolus coronatus, Entomophthora muscae, Dimargaris bacillispora, Orphella haysii, Spiromyces aspiralis, Spiromyces minutus, Coemansia reversa, Rhopalomyces elegans, or Bdelloura candida.

11. The method of claim 1 wherein said forward primer member is SEQ ID NO:

10.

12. The method of claim 1 wherein at least one of said forward member and said reverse member comprises at least one modified nucleobase.

13. The method of claim 12 wherein at least one of said at least one modified nucleobase is a mass modified nucleobase.

14. The method of claim 13 wherein said mass modified nucleobase is 5-Iodo-C.

15. The method of claim 13 wherein said mass modified nucleobase comprises a mass modifying tag.

16. The method of claim 12 wherein at least one of said at least one modified nucleobase is a universal nucleobase.

17. The method of claim 16 wherein said universal nucleobase in inosine.

18. The method of claim 1 wherein at least one of said forward member and said reverse member comprises a non-templated T-residue at its 5′

end.

19. An isolated oligonucleotide primer pair wherein the forward member of the primer pair with comprises at least 70% sequence identity to SEQ ID NO:

10, and the reverse primer of the primer pair is SEQ ID NO;

25 to obtain an amplification product that comprises a length from 45-200 consecutive nucleobases.

20. The isolated oligonucleotide primer pair of claim 19 wherein said forward primer member is SEQ ID NO:

10.

21. The isolated oligonucleotide primer pair of claim 19 wherein at least one of said forward member and said reverse member comprises at least one modified nucleobase.

22. The isolated oligonucleotide primer pair of claim 21 wherein at least one of said at least one modified nucleobase is a mass modified nucleobase.

23. The isolated oligonucleotide primer pair of claim 22 wherein said mass modified nucleobase is 5-Iodo-C.

24. The isolated oligonucleotide primer pair of claim 22 wherein said mass modified nucleobase comprises a mass modifying tag.

25. The isolated oligonucleotide primer pair of claim 21 wherein at least one of said at least one modified nucleobase is a universal nucleobase.

26. The isolated oligonucleotide primer pair of claim 25 wherein said universal nucleobase in inosine.

27. The isolated oligonucleotide primer pair of claim 19 wherein at least one of said forward member and said reverse member comprises a non-templated T-residue at its 5′

end.