Methods of Diagnosing Infectious Disease Pathogens and Their Drug Sensitivity

Abstract

The specification relates generally to methods of detecting, diagnosing, and/or identifying pathogens, e.g., infectious disease pathogens and determining their drug sensitivity and appropriate methods of treatment. This invention also relates generally to methods of monitoring pathogen infection in individual subjects as well as larger populations of subjects.

1 - 4 . (canceled) 
     
     
         5 . A method of identifying an infectious disease pathogen, the method comprising:
 providing a test sample from a subject suspected of being infected with a pathogen;   treating the test sample under conditions that release messenger ribonucleic acid (mRNA);   exposing the test sample to a plurality of nucleic acid probes designed to identify a plurality of pathogens, comprising a plurality of subsets of probes, wherein each subset comprises one or more probes that bind specifically to a target mRNA that uniquely identifies a single pathogen, wherein the exposure occurs for a time and under conditions in which binding between the probe and the target mRNA can occur; and   determining a level of binding between the probe and target mRNA, thereby determining a level of target mRNA;   wherein an increase in the target mRNA of the test sample, relative to a reference sample, indicates the identity of the pathogen in the test sample.   
     
     
         6 . The method of claim  1 , wherein the test sample is selected from the group consisting of sputum, blood, urine, stool, joint fluid, cerebrospinal fluid, and cervical/vaginal swab. 
     
     
         7 . The method of claim  1 , wherein the test sample comprises a plurality of different infectious disease pathogens or non-disease causing organisms. 
     
     
         8 . The method of claim  1 , wherein the one or more nucleic acid probes are selected from Table 2. 
     
     
         9 . The method of claim  1 , wherein the pathogen is a bacterium, fungus, virus, or parasite. 
     
     
         10 . The method of claim  1 , wherein the pathogen is  Mycobacterium tuberculosis.   
     
     
         11 . The method of claim  1 , wherein the mRNA is crude before contact with the probes. 
     
     
         12 . The method of claim  1 , wherein the method does not include amplifying the mRNA. 
     
     
         13 . The method of claim  1 , wherein the method comprises lysing the cells enzymatically, chemically, or mechanically. 
     
     
         14 . The method of claim  1 , wherein the method comprises use of a microfluidic device. 
     
     
         15 . The method of claim  1 , wherein the method is used to monitor a pathogen infection. 
     
     
         16 . (canceled) 
     
     
         17 . The method of  claim 5 , wherein the subject is a human. 
     
     
         18 . The method of  claim 5 , wherein the method further comprises determining or selecting, a treatment for the subject, and optionally administering the treatment to the subject. 
     
     
         19 - 21 . (canceled) 
     
     
         22 . The method of  claim 18 , wherein the method comprises selecting a treatment to which the pathogen is sensitive and administering the selected treatment to the subject, and determining the drug sensitivity of the pathogen in the second sample to the selected treatment using the method of claim  1 , wherein a change in the drug sensitivity of the pathogen indicates whether the pathogen is or is becoming resistant to the treatment. 
     
     
         23 - 24 . (canceled) 
     
     
         25 . A plurality of polynucleotides bound to a solid support, wherein the plurality comprises at least one polynucleotide, each polynucleotide selectively hybridizing to one or more genes selected from Table 2. 
     
     
         26 . The plurality of polynucleotides of  claim 25 , the plurality comprising SEQ ID NOs:1-227, or any combination thereof.