Methods for diagnosis of bacterial and viral infections

Abstract

Methods for diagnosis of bacterial and viral infections are disclosed. In particular, the invention relates to the use of biomarkers that can determine whether a patient with acute inflammation has a bacterial or viral infection.

What is claimed is: 
     
         1 . A method for diagnosing an infection in a patient, the method comprising:
 a) measuring levels of expression of at least two biomarkers in a biological sample of a patient; the at least two biomarkers selected from either or both of a first set of biomarkers wherein a higher level of expression indicates a bacterial infection, and a second set of biomarkers wherein a higher level of expression indicates a viral infection; wherein the first set of biomarkers comprise at least one of TSPO, EMR1, NINJ2, ACPP, TBXAS1, PGD, S100A12, SORT1, TNIP1, RAB31, SLC12A9, PLP2, IMPA2, GPAA1, LTA4H, RTN3, CETP, TALD01, HK3, ACAA1, CAT, DOK3, SORL1, PYGL, DYSF, TWF2, TKT, CTSB, FLII, PROS1, NRD1, STAT5B, CYBRD1, PTAFR, and LAPTM5; and wherein the second set of biomarkers comprise at least one of OAS1, IFIT1, SAMD9, ISG15, DDX60, HESX1, OASL, LAX1, IFIT5, KCTD14, RTP4, PARP12, LY6E, ADA, IFI44L, IFI27, IFI44, OAS3, IFIH1, SIGLEC1, JUP, STAT1, CUL1, DNMT1, IFIT2, CHST12, ISG20, DHX58, EIF2AK2, XAF1, and GZMB; and   b) analyzing the levels of expression of each biomarker in conjunction with respective reference value ranges for the biomarkers to determine a viral or bacterial infection.   
     
     
         2 . The method of  claim 1 , wherein the at least two biomarkers include SIGLEC1 and SLC12A9. 
     
     
         3 . The method of any prior claim, wherein the levels of expression of the at least two biomarkers provide an area under a receiver operating characteristic curve of at least 0.80. 
     
     
         4 . The method of  claim 1 , wherein the first set of biomarkers comprise at least one of HK3, TNIP1, GPAA1, and CTSB; and wherein the second set of biomarkers comprise at least one of IFI27, JUP, and LAX1 
     
     
         5 . The method of  claim 1 , wherein the biological sample comprises whole blood or peripheral blood mononucleated cells (PBMCS). 
     
     
         6 . The method of  claim 1 , wherein the levels of the biomarkers are compared to time-matched reference values for infected or non-infected subjects. 
     
     
         7 . The method of  claim 1 , further comprising calculating a bacterial/viral metascore for the patient based on the levels of the biomarkers, wherein a positive bacterial/viral metascore for the patient indicates that the patient has a viral infection and a negative bacterial/viral metascore for the patient indicates that the patient has a bacterial infection. 
     
     
         8 . The method of  claim 1 , further comprising normalizing data using COCONUT normalization; COCONUT normalization comprising the steps of:
 a) separating data from multiple cohorts into healthy and diseased components;   b) co-normalizing the healthy components using ComBat co-normalization without covariates;   c) obtaining ComBat estimated parameters for each dataset for the healthy component; and   d) applying the ComBat estimated parameters onto the diseased component.   
     
     
         9 . The method of  claim 1 , wherein the patient is a human being. 
     
     
         10 . The method of  claim 1 , wherein measuring the level of the biomarkers comprises performing one or more methods including microarray analysis via fluorescence, chemiluminesence, or electrical signal detection, polymerase chain reaction (PCR), reverse transcriptase polymerase chain reaction (RT-PCR), digital droplet PCR (ddPCR), solid-state nanopore detection, RNA switch activation, a Northern blot, or a serial analysis of gene expression (SAGE). 
     
     
         11 . A method of diagnosing and treating a patient having inflammation, the method comprising:
 a) measuring levels of expression of IFI27, JUP, LAX1, HK3, TNIP1, GPAA1, CTSB, CEACAM1, ZDHHC19, C9orf95, GNA15, BATF, C3AR1, KIAA1370, TGFBI, MTCH1, RPGRIP1, and HLA-DPB1 biomarkers in a biological sample of the patient; and   b) first analyzing the levels of expression of each biomarker in conjunction with respective reference value ranges for the biomarkers, wherein increased levels of expression of the CEACAM1, ZDHHC19, C9orf95, GNA15, BATF, and C3AR1 biomarkers and decreased levels of expression of the KIAA1370, TGFBI, MTCH1, RPGRIP1, and HLA-DPB1 biomarkers compared to the reference value ranges for the biomarkers for a non-infected control subject indicate that the patient has an infection, and absence of differential expression of the CEACAM1, ZDHHC19, C9orf95, GNA15, BATF, C3AR1, KIAA1370, TGFBI, MTCH1, RPGRIP1, and HLA-DPB1 biomarkers compared the non-infected control subject indicates that the patient does not have an infection; and   c) further analyzing the levels of expression of at least two biomarkers in a biological sample of a patient; the at least two biomarkers selected from either or both of a first set of biomarkers wherein a higher level of expression indicates a bacterial infection, and a second set of biomarkers wherein a higher level of expression indicates a viral infection; wherein the first set of biomarkers comprise at least one of TSPO, EMR1, NINJ2, ACPP, TBXAS1, PGD, S100A12, SORT1, TNIP1, RAB31, SLC12A9, PLP2, IMPA2, GPAA1, LTA4H, RTN3, CETP, TALD01, HK3, ACAA1, CAT, DOK3, SORL1, PYGL, DYSF, TWF2, TKT, CTSB, FLII, PROS1, NRD1, STAT5B, CYBRD1, PTAFR, and LAPTM5; and wherein the second set of biomarkers comprise at least one of OAS1, IFIT1, SAMD9, ISG15, HERC5, DDX60, HESX1, IFI6, MX1, OASL, LAX1, IFIT5, IFIT3, KCTD14, OAS2, RTP4, PARP12, LY6E, ADA, IFI44L, IFI27, RSAD2, IFI44, OAS3, IFIH1, SIGLEC1, JUP, STAT1, CUL1, DNMT1, IFIT2, CHST12, ISG20, DHX58, EIF2AK2, XAF1, and GZMB to determine a bacterial or viral infection.   
     
     
         12 . The method of  claim 11 , further comprising calculating a sepsis metascore for the patient, wherein a sepsis metascore that is higher than the reference value ranges for a non-infected control subject indicates that the patient has an infection, and a sepsis metascore that is within the reference value ranges for a non-infected control subject indicates that the patient has a non-infectious inflammatory condition. 
     
     
         13 . The method of any of  claims 11 - 12 , further comprising calculating a bacterial/viral metascore for the patient if the patient is diagnosed as having an infection, wherein a positive bacterial/viral metascore for the patient indicates that the patient has a viral infection and a negative bacterial/viral metascore for the patient indicates that the patient has a bacterial infection. 
     
     
         14 . The method of  claim 11 , wherein the levels of the biomarkers are compared to time-matched reference values for infected or non-infected subjects. 
     
     
         15 . The method of  claim 11 , wherein the non-infectious inflammatory condition is selected from the group consisting of systemic inflammatory response syndrome (SIRS), an autoimmune disorder, a traumatic injury, and surgery. 
     
     
         16 . The method of  claim 11 , wherein the patient is a human being. 
     
     
         17 . The method of  claim 11 , wherein measuring the levels of the biomarkers comprises performing one or more methods including microarray analysis via fluorescence, chemiluminesence, or electrical signal detection, polymerase chain reaction (PCR), reverse transcriptase polymerase chain reaction (RT-PCR), digital droplet PCR (ddPCR), solid-state nanopore detection, RNA switch activation, a Northern blot, or a serial analysis of gene expression (SAGE). 
     
     
         18 . A kit comprising agents for measuring levels of at least two biomarkers in a biological sample of a patient; the at least two biomarkers selected from either or both of a first set of biomarkers wherein a higher level of expression indicates a bacterial infection, and a second set of biomarkers wherein a higher level of expression indicates a viral infection wherein the first set of biomarkers comprise at least one of TSPO, EMR1, NINJ2, ACPP, TBXAS1, PGD, S100A12, SORT1, TNIP1, RAB31, SLC12A9, PLP2, IMPA2, GPAA1, LTA4H, RTN3, CETP, TALD01, HK3, ACAA1, CAT, DOK3, SORL1, PYGL, DYSF, TWF2, TKT, CTSB, FLII, PROS1, NRD1, STAT5B, CYBRD1, PTAFR, and LAPTM5; and wherein the second set of biomarkers comprise at least one of OAS1, IFIT1, SAMD9, ISG15, DDX60, HESX1, OASL, LAX1, IFIT5, KCTD14, RTP4, PARP12, LY6E, ADA, IFI44L, IFI27, IFI44, OAS3, IFIH1, SIGLEC1, JUP, STAT1, CUL1, DNMT1, IFIT2, CHST12, ISG20, DHX58, EIF2AK2, XAF1, and GZMB. 
     
     
         19 . The kit of  claim 18 , further comprising agents for measuring the levels of CEACAM1, ZDHHC19, C9orf95, GNA15, BATF, C3AR1, KIAA1370, TGFBI, MTCH1, RPGRIP1, and HLA-DPB1 biomarkers. 
     
     
         20 . The kit of any of  claims 18 - 19 , further comprising a microarray. 
     
     
         21 . The kit of  claim 20 , wherein the microarray comprises an oligonucleotide that hybridizes to an IFI27 polynucleotide, an oligonucleotide that hybridizes to a JUP polynucleotide, an oligonucleotide that hybridizes to a LAX1 polynucleotide, an oligonucleotide that hybridizes to a HK3 polynucleotide, an oligonucleotide that hybridizes to a TNIP1 polynucleotide, an oligonucleotide that hybridizes to a GPAA1 polynucleotide, and an oligonucleotide that hybridizes to a CTSB polynucleotide 
     
     
         22 . The kit of  claim 20 , wherein the microarray further comprising an oligonucleotide that hybridizes to a CEACAM1 polynucleotide, an oligonucleotide that hybridizes to a ZDHHC19 polynucleotide, an oligonucleotide that hybridizes to a C9orf95 polynucleotide, an oligonucleotide that hybridizes to a GNA15 polynucleotide, an oligonucleotide that hybridizes to a BATF polynucleotide, an oligonucleotide that hybridizes to a C3AR1 polynucleotide, an oligonucleotide that hybridizes to a KIAA1370 polynucleotide, an oligonucleotide that hybridizes to a TGFBI polynucleotide, an oligonucleotide that hybridizes to a MTCH1 polynucleotide, an oligonucleotide that hybridizes to a RPGRIP1 polynucleotide, and an oligonucleotide that hybridizes to a HLA-DPB1 polynucleotide. 
     
     
         23 . The kit of  claim 18 , further comprising information, in electronic or paper form, comprising instructions to correlate the detected levels of each biomarker with sepsis. 
     
     
         24 . A computer implemented method for diagnosing a patient suspected of having an infection, the computer performing steps comprising:
 a) receiving inputted patient data comprising values for levels of at least two biomarkers in a biological sample of a patient; the at least two biomarkers selected from either or both of a first set of biomarkers wherein a higher level of expression indicates a bacterial infection, and a second set of biomarkers wherein a higher level of expression indicates a viral infection; wherein the first set of biomarkers comprise at least one of TSPO, EMR1, NINJ2, ACPP, TBXAS1, PGD, S100A12, SORT1, TNIP1, RAB31, SLC12A9, PLP2, IMPA2, GPAA1, LTA4H, RTN3, CETP, TALD01, HK3, ACAA1, CAT, DOK3, SORL1, PYGL, DYSF, TWF2, TKT, CTSB, FLII, PROS1, NRD1, STAT5B, CYBRD1, PTAFR, and LAPTM5; and wherein the second set of biomarkers comprise at least one of OAS1, IFIT1, SAMD9, ISG15, DDX60, HESX1, OASL, LAX1, IFIT5, KCTD14, RTP4, PARP12, LY6E, ADA, IFI44L, IFI27, IFI44, OAS3, IFIH1, SIGLEC1, JUP, STAT1, CUL1, DNMT1, IFIT2, CHST12, ISG20, DHX58, EIF2AK2, XAF1, and GZMB biomarkers in the biological sample from the patient;   b) analyzing the level of each of the biomarkers and comparing with respective reference value ranges for the biomarkers;   c) calculating a bacterial/viral metascore for the patient based on the levels of the biomarkers, wherein a positive bacterial/viral metascore for the patient indicates that the patient has a viral infection and a negative bacterial/viral metascore for the patient indicates that the patient has a bacterial infection; and   d) displaying information regarding the diagnosis of the patient.   
     
     
         25 . The method of  claim 24 , wherein the biological sample comprises whole blood or peripheral blood mononucleated cells (PBMCS). 
     
     
         26 . A diagnostic system for performing the method of  claim 24 , comprising:
 a) a storage component for storing data, wherein the storage component has instructions for determining the diagnosis of the patient stored therein;   b) a computer processor for processing data, wherein the computer processor is coupled to the storage component and configured to execute the instructions stored in the storage component in order to receive patient data and analyze patient data according to one or more algorithms; and   c) a display component for displaying information regarding the diagnosis of the patient.   
     
     
         27 . The diagnostic system of  claim 26 , wherein the storage component comprises instructions for calculating the bacterial/viral metascore. 
     
     
         28 . A computer implemented method for diagnosing a patient having inflammation, the computer performing steps comprising:
 a) receiving inputted patient data comprising values for the levels of IFI27, JUP, LAX1, HK3, TNIP1, GPAA1, CTSB, CEACAM1, ZDHHC19, C9orf95, GNA15, BATF, C3AR1, KIAA1370, TGFBI, MTCH1, RPGRIP1, and HLA-DPB1 biomarkers in a biological sample from the patient;   b) analyzing the levels of each of the biomarkers and comparing with respective reference value ranges for the biomarkers;   c) calculating a sepsis metascore for the patient, wherein a sepsis metascore that is higher than the reference value ranges for a non-infected control subject indicates that the patient has an infection, and a sepsis metascore that is within the reference value ranges for a non-infected control subject indicates that the patient has a non-infectious inflammatory condition;   d) calculating a bacterial/viral metascore for the patient if the sepsis metascore indicates that the patient has an infection, wherein a positive bacterial/viral metascore for the patient indicates that the patient has a viral infection and a negative bacterial/viral metascore for the patient indicates that the patient has a bacterial infection; and   e) displaying information regarding the diagnosis of the patient.   
     
     
         29 . The method of  claim 28 , wherein the biological sample comprises whole blood or peripheral blood mononucleated cells (PBMCS). 
     
     
         30 . A diagnostic system for performing the method of  claim 28 , comprising:
 a) a storage component for storing data, wherein the storage component has instructions for determining the diagnosis of the patient stored therein;   b) a computer processor for processing data, wherein the computer processor is coupled to the storage component and configured to execute the instructions stored in the storage component in order to receive patient data and analyze patient data according to one or more algorithms; and   c) a display component for displaying information regarding the diagnosis of the patient.   
     
     
         31 . The diagnostic system of  claim 30 , wherein the storage component comprises instructions for calculating the sepsis metascore and the bacterial/viral metascore. 
     
     
         32 . A method for diagnosing and treating an infection in a patient, the method comprising:
 a) obtaining a biological sample from the patient;   b) measuring the levels of expression of any set of at least two biomarkers in a biological sample of a patient; the at least two biomarkers selected from either or both of a first set of biomarkers wherein a higher level of expression indicates a bacterial infection, and a second set of biomarkers wherein a higher level of expression indicates a viral infection; wherein the first set of biomarkers comprise at least one of TSPO, EMR1, NINJ2, ACPP, TBXAS1, PGD, S100A12, SORT1, TNIP1, RAB31, SLC12A9, PLP2, IMPA2, GPAA1, LTA4H, RTN3, CETP, TALD01, HK3, ACAA1, CAT, DOK3, SORL1, PYGL, DYSF, TWF2, TKT, CTSB, FLII, PROS1, NRD1, STAT5B, CYBRD1, PTAFR, and LAPTM5; and wherein the second set of biomarkers comprise at least one of OAS1, IFIT1, SAMD9, ISG15, DDX60, HESX1, OASL, LAX1, IFIT5, KCTD14, RTP4, PARP12, LY6E, ADA, IFI44L, IFI27, IFI44, OAS3, IFIH1, SIGLEC1, JUP, STAT1, CUL1, DNMT1, IFIT2, CHST12, ISG20, DHX58, EIF2AK2, XAF1, and GZMB; and   c) analyzing the levels of expression of each biomarker in conjunction with respective reference value ranges for a noninfected control subject, wherein differential expression of the viral response genes compared to the reference value ranges for a noninfected control subject indicate that the patient has a viral infection, and differential expression of the bacterial response genes compared to the reference value ranges for a noninfected control subject indicate that the patient has a bacterial infection.   
     
     
         33 . The method of  claim 32 , wherein the set of viral and bacterial response genes are selected from the group consisting of:
 a) a set of viral response genes comprising OAS2 and CUL1 and a set of bacterial response genes comprising SLC12A9, ACPP, STAT5B;   b) a set of viral response genes comprising ISG15 and CHST12 and a set of bacterial response genes comprising EMR1 and FLII;   c) a set of viral response genes comprising IFIT1, SIGLEC1, and ADA and a set of bacterial response genes comprising PTAFR, NRD1, PLP2;   d) a set of viral response genes comprising MX1 and a set of bacterial response genes comprising DYSF, TWF2;   e) a set of viral response genes comprising RSAD2 and a set of bacterial response genes comprising SORT1 and TSPO;   f) a set of viral response genes comprising IFI44L, GZMB, and KCTD14 and a set of bacterial response genes comprising TBXAS1, ACAA1, and S100A12;   g) a set of viral response genes comprising LY6E and a set of bacterial response genes comprising PGD and LAPTM5;   h) a set of viral response genes comprising IFI44, HESX1, and OASL and a set of bacterial response genes comprising NINJ2, DOK3, SORL1, and RAB31;   i) a set of viral response genes comprising OAS1 and a set of bacterial response genes comprising IMPA2 and LTA4H.   
     
     
         34 . The method of any of  claims 32 - 33 , wherein the biological sample comprises whole blood or peripheral blood mononucleated cells (PBMCS). 
     
     
         35 . The method of  claim 32 , wherein the levels of the biomarkers are compared to time-matched reference values for infected or non-infected subjects. 
     
     
         36 . The method of  claim 32 , further comprising calculating a bacterial/viral metascore for the patient t based on the levels of the biomarkers, wherein a positive bacterial/viral metascore for the patient indicates that the patient has a viral infection and a negative bacterial/viral metascore for the patient indicates that the patient has a bacterial infection. 
     
     
         37 . The method of  claim 32 , further comprising measuring levels of expression of IFI27, JUP, LAX1, HK3, TNIP1, GPAA1, CTSB, CEACAM1, ZDHHC19, C9orf95, GNA15, BATF, C3AR1, KIAA1370, TGFBI, MTCH1, RPGRIP1, and HLA-DPB1 biomarkers in the biological sample; and analyzing the levels of expression of each biomarker in conjunction with respective reference value ranges for the biomarkers, wherein increased levels of expression of the CEACAM1, ZDHHC19, C9orf95, GNA15, BATF, and C3AR1 biomarkers and decreased levels of expression of the KIAA1370, TGFBI, MTCH1, RPGRIP1, and HLA-DPB1 biomarkers compared to the reference value ranges for the biomarkers for a non-infected control subject indicate that the patient has an infection, and absence of differential expression of the CEACAM1, ZDHHC19, C9orf95, GNA15, BATF, C3AR1, KIAA1370, TGFBI, MTCH1, RPGRIP1, and HLA-DPB1 biomarkers compared the non-infected control subject indicates that the patient does not have an infection. 
     
     
         38 . A kit comprising agents for measuring the levels of expression of a set of viral response genes and a set of bacterial response genes selected from the group consisting of:
 a) a set of viral response genes comprising OAS2 and CUL1 and a set of bacterial response genes comprising SLC12A9, ACPP, STAT5B;   b) a set of viral response genes comprising ISG15 and CHST12 and a set of bacterial response genes comprising EMR1 and FLII;   c) a set of viral response genes comprising IFIT1, SIGLEC1, and ADA and a set of bacterial response genes comprising PTAFR, NRD1, PLP2;   d) a set of viral response genes comprising MX1 and a set of bacterial response genes comprising DYSF, TWF2;   e) a set of viral response genes comprising RSAD2 and a set of bacterial response genes comprising SORT1 and TSPO;   f) a set of viral response genes comprising IFI44L, GZMB, and KCTD14 and a set of bacterial response genes comprising TBXAS1, ACAA1, and S100A12;   g) a set of viral response genes comprising LY6E and a set of bacterial response genes comprising PGD and LAPTM5;   h) a set of viral response genes comprising IFI44, HESX1, and OASL and a set of bacterial response genes comprising NINJ2, DOK3, SORL1, and RAB31; and   i) a set of viral response genes comprising OAS1 and a set of bacterial response genes comprising IMPA2 and LTA4H.   
     
     
         39 . The kit of  claim 38 , further comprising a microarray. 
     
     
         40 . A computer implemented method for diagnosing a patient suspected of having an infection, the computer performing steps comprising:
 a) receiving inputted patient data comprising values for the levels of expression of at least two biomarkers in a biological sample of a patient; the at least two biomarkers selected from either or both of a first set of biomarkers wherein a higher level of expression indicates a bacterial infection, and a second set of biomarkers wherein a higher level of expression indicates a viral infection, wherein the set of viral response genes comprises one or more genes selected from the group consisting of CUL1, ISG15, CHST12, IFIT1, SIGLEC1, ADA, IFI44L, GZMB, KCTD14, LY6E, IFI44, HESX1, OASL, OAS1, OAS3, EIF2AK2, DDX60, DNMT1, IFIH1, SAMD9, IFIT5, XAF1, ISG20, PARP12, IFIT2, DHX58, STAT1, and the set of bacterial response genes comprises one or more genes selected from the group consisting of SLC12A9, ACPP, STAT5B, EMR1, FLII, PTAFR, NRD1, PLP2, DYSF, TWF2, SORT1, TSPO, TBXAS1, ACAA1, S100A12, PGD, LAPTM5, NINJ2, DOK3, SORL1, RAB31, IMPA2, LTA4H, TALDO1, TKT, PYGL, CETP, PROS1, RTN3, CAT, CYBRD1;   b) analyzing the levels of expression of the set of viral response genes and the set of bacterial response genes and comparing with respective reference value ranges for a noninfected control subject;   c) calculating a bacterial/viral metascore for the patient based on the levels of expression of the set of viral response genes and the set of bacterial response genes; and   d) displaying information regarding the diagnosis of the patient.   
     
     
         41 . A diagnostic system for performing the method of  claim 40 , comprising:
 a) a storage component for storing data, wherein the storage component has instructions for determining the diagnosis of the patient stored therein;   b) a computer processor for processing data, wherein the computer processor is coupled to the storage component and configured to execute the instructions stored in the storage component in order to receive patient data and analyze patient data according to one or more algorithms; and   c) a display component for displaying information regarding the diagnosis of the patient.   
     
     
         42 . The method of  claim 1 , wherein measuring the level of expression of the biomarkers comprises measuring an amount of mRNA, or polynucleotides derived therefrom, present in a biological sample for each of the at least two biomarkers.