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 - 26 . (canceled) 
     
     
         27 . A method of identifying a target nucleic acid in a test sample, the method comprising:
 providing a test sample suspected of comprising a target nucleic acid, wherein the test sample is a crude sample;   exposing the test sample to one or more nucleic acid probes designed to bind specifically to one or more target nucleic acid sequences, wherein the exposure occurs for a time and under conditions in which binding between the probe and the target nucleic acid can occur wherein the exposure occurs for less than one hour; and   detecting the one or more target nucleic acid sequences and thereby identifying the target nucleic acid in the test sample.   
     
     
         28 . The method of  claim 27 , wherein the one or more target nucleic acid sequences uniquely identifies a pathogen. 
     
     
         29 . The method of  claim 27 , wherein the pathogen is a virus or an infectious disease pathogen. 
     
     
         30 . The method of  claim 27 , wherein the test sample is obtained from a subject, optionally wherein the subject is human. 
     
     
         31 . The method of  claim 27 , further comprising treating the test sample under conditions that release nucleic acid from cells of the test sample. 
     
     
         32 . The method of  claim 27 , wherein the probes are designed to bind to two or more different target nucleic acid sequences. 
     
     
         33 . The method of  claim 28 , wherein the target nucleic acid is highly conserved across all strains of the identified pathogen. 
     
     
         34 . The method of  claim 31 , wherein the cells are lysed mechanically, optionally wherein the cells are lysed via sonication, French press, electroporation or a microfluidic device comprising fabricated structures. 
     
     
         35 . The method of  claim 27 , wherein the method comprises use of a microfluidic device or a microarray. 
     
     
         36 . The method of  claim 28 , wherein two or more probes are used that bind specifically to a target nucleic acid that uniquely identifies the pathogen. 
     
     
         37 . The method of  claim 27 , wherein the method further comprises exposing the test sample to a reporter nucleic acid probe that is conjugated to a fluorescent tag, optionally wherein the tag is a bar code. 
     
     
         38 . The method of  claim 27 , wherein one or more of the nucleic acid probes is conjugated to a label, optionally wherein the label is selected from the group consisting of a fluorophore, biotin, digoxygenin, and a radioactive isotope. 
     
     
         39 . The method of  claim 27 , wherein the method is used to monitor a pathogen infection. 
     
     
         40 . The method of  claim 27 , wherein the method further comprises determining or selecting a treatment for the subject, and optionally administering the treatment to the subject. 
     
     
         41 . The method of  claim 28 , wherein the method further comprises selecting a fluoroquinolone as a treatment for the subject, optionally further comprising administering the fluoroquinolone to the subject. 
     
     
         42 . A method of identifying a target nucleic acid in a test sample, the method comprising:
 providing a test sample suspected of comprising a target nucleic acid, wherein the test sample is a crude sample;   exposing the test sample to one or more nucleic acid probes that are designed to bind specifically to one or more target nucleic acid sequences, wherein the exposure occurs for a time and under conditions in which binding between the probe and the target nucleic acid can occur wherein the exposure occurs for less than one hour; and   determining the target nucleic acid sequences by imaging or counting reporter tags to indicate the target nucleic acid in the test sample.   
     
     
         43 . The method of  claim 42 , wherein the reporter tag is a fluorescent tag. 
     
     
         44 . The method of  claim 42 , further comprising treating the test sample under conditions that release nucleic acid from cells of the test sample. 
     
     
         45 . The method of  claim 42 , wherein the probes are designed to bind to two or more different target nucleic acid sequences. 
     
     
         46 . The method of  claim 42 , wherein the one or more target nucleic acid sequences uniquely identifies a pathogen, optionally wherein the target nucleic acid is highly conserved across all strains of the identified pathogen. 
     
     
         47 . A kit comprising a plurality of nucleic acid probes for use in the method of  claim 27 , and instructions for its use. 
     
     
         48 . A kit comprising a plurality of nucleic acid probes for use in the method of  claim 42 , wherein the reporter probes have a fluorescent tag, and instructions for its use. 
     
     
         49 . A method for performing public health surveillance of an outbreak of a pathogen, the method comprising identifying the pathogen in one or more test samples by the method of  claim 28 . 
     
     
         50 . The method of  claim 49 , wherein a sudden rise in numbers of the pathogen within a particular area is identified. 
     
     
         51 . The method of  claim 49 , wherein the pathogen is a virus.