Reagents, methods and kits for classification of fungi and direction of anti-fungal therapy

Abstract

Provided herein are methods, kits and compositions to classify fungi. Methods are provided for classification of fungi according to established phenotypes, for example, antimicrobial susceptibility profiles. More specifically, the invention provides methods for the use of PNA probes in diagnostic applications, which will aid in the direction of appropriate therapy against fungi.

What is claimed is: 
     
         1 . A probe comprising the nucleic acid sequence of SEQ ID NO: 19, 20 or 21. 
     
     
         2 . A reagent for the classification of fungi, comprising the probe of  claim 1 , wherein the reagent is used to determine at least one fungal drug susceptibility-type. 
     
     
         3 . The reagent of  claim 2 , further comprising one or more additional probe sets complementary to nucleic acid sequences of other fungi of other drug susceptibility-types. 
     
     
         4 . The probe of  claim 1 , further comprising one or more of nucleic acid probes, locked nucleic acid probes, peptide nucleic acid probes, or other nucleic acid probe mimics or analogues. 
     
     
         5 . The reagent of  claim 2 , wherein a fungal drug-susceptibility type comprises a full spectrum of response to a compound, wherein the full spectrum of response comprises one or more of susceptible; susceptible/intermediate; intermediate; susceptible/susceptible, dose-dependent; susceptible, dose-dependent; susceptible, dose-dependent/resistant; susceptible-dose/delivery dependent; intermediately resistant; or resistant. 
     
     
         6 . The reagent of  claim 2 , wherein the fungal drug susceptibility-type comprises resistance to an anti-fungal compound, or combination of compounds. 
     
     
         7 . The reagent of  claim 6 , wherein the anti-fungal compound comprises fluconazole. 
     
     
         8 . The reagent of  claim 2 , wherein at least one fungal drug susceptibility type is a fluconazole-resistant drug susceptibility-type. 
     
     
         9 . The reagent of  claim 8 , wherein the fluconazole-resistant drug susceptibility-type comprises one or more of  Candida glabrata.    
     
     
         10 . The reagent of  claim 2 , wherein at least a portion of the probe is at least about 86% identical to the nucleic acid sequence of SEQ. ID NO: 19, 20 or 21, or complement thereof. 
     
     
         11 . The reagent of  claim 2 , wherein the probe comprises at least one detectable moiety. 
     
     
         12 . The reagent of  claim 11 , wherein the detectable moiety or moieties comprise one or more of a conjugate, a branched detection system, a chromophore, a fluorophore, a spin label, a radioisotope, an enzyme, a hapten, an acridinium ester or a luminescent compound. 
     
     
         13 . The reagent of  claim 11 , wherein coincidental fluorescence is used to detect a fungal susceptibility-type. 
     
     
         14 . A method for determining the susceptibility-type of fungi, comprising:
 contacting a sample with the probe of  claim 1 , and correlating hybridization of a probe to an established susceptibility-type.   
     
     
         15 . The method of  claim 14 , wherein the hybridization is indicative of presence, identity and/or amount of microorganisms in the sample. 
     
     
         16 . A method for selecting antifungal therapy, comprising:
 a) contacting a sample with the probe of  claim 1 ;   b) hybridizing the probe set to a nucleic acid sample; and   c) detecting hybridization; and   d) selecting antifungal therapy based on hybridization, if any.   
     
     
         17 . A kit for selecting antifungal therapy, comprising: the probe of  claim 1 , and instructions for use.