Molecular predictors of fungal infection

Abstract

Methods for identifying fungal infection, assays for identifying genomic and protein markers of fungal infection, and methods for diagnosing the fungal infection. In one aspect, the method of identifying fungal infection by proteomic assay involves measuring the protein levels of proteins listed in Table 2A in a peripheral blood cell sample and comparing the determined protein levels to standard protein levels. In another aspect, subjects identified as being infected with fungal infection are treated with anti-fungals.

1 .- 62 . (canceled) 
     
     
         63 . A method of identifying and treating a subject having candidiasis comprising:
 a) determining gene expression levels of candidemia versus control (“CavC”) genes in a peripheral blood cell sample of the subject wherein the CavC genes consist of Adam19, Adam8, Anxa2, Bcl6, Bst1, Ccr1, Cd14, Cd177, Cd300Lf, Cd33, Cd52, Cklf, Crlf2, Csf2Rb, Csf3R, Ebi3, Fcer1G, Fcgr2A, Glipr1, Gpr97, Icoslg, Ifitm1, Ifitm2, Ifitm6, Ikbkap, Il10Rb, Il13Ra1, Il1B, Il1F9, Il1R2, II1Rap, Il1Rn, Il8Rb, Irg1, Klra1, Lcp1, Lgals3, Lilra6, Lilrb4, Lsp1, Ly6C1, Lyst, Mboat7, Nfam1, Nfil3, Ngp, Nlrp3, Pbx1, Pxn, Rtp4, S100A11, Sell, Slpi, Socs3, Steap4, Tacstd2, Tirap, Tlr1, Tlr4, and Tnfsf14;   b) comparing the gene expression levels of the CavC genes to standard gene expression levels wherein the standard gene expression levels corresponds to the gene expression levels for the CavC genes in a subject that does not have candidiasis, wherein the gene expression levels of mRNA is measured,   c) using the expression levels of each of the CavC genes in the peripheral blood cell sample as features for a logistic regression model to generate a factor score;   d) identifying the subject as having candidiasis if the factor score is higher than a factor score for a control, wherein the candidiasis is candidemia; and   e) administering an effective amount of an antifungal therapy to treat the subject identified as having candidiasis;   wherein the subject is human or mice.   
     
     
         64 . The method of  claim 63 , wherein step (a) comprises a method selected from the group consisting of assaying the sample with an array comprising a plurality of nucleic acid oligomers, Northern blot hybridization analysis, RT-PCR, and quantitative RT-PCR.