Electrochemical detection of bacterial and/or fungal infections

Abstract

The present disclosure relates to methods and devices for amplifying a plurality of targets in a single PCR run while distinguishing between clinically relevant amplification and amplification from other sources such as from background contamination. The methods and devices further enable discrimination between gram-positive, gram-negative and fungal infections as wells as identify antimicrobial resistance genes. When applying the methods and devices of the invention, the species or genus of an infection(s), and genus of a fungal co-infection(s) or category of bacterial (gram-positive or negative) co-infection(s) are identified. Species identification of co-infections can also be achieved. Further, when applying the methods and devices of the invention, organisms which are likely to be contaminating organisms from a blood draw are identified.

What is claimed is: 
     
         1 . A method for validating a target analyte detection system comprising:
 a) processing a first quality control to produce a quality control record;   b) storing the first quality control record by a target analyte detection instrument in a base station; and   c) either i) releasing the quality control record to a hospital LIS by the target analyte detection instrument; or
 ii) preventing the processing of a patient sample by the target analyte detection instrument if a first quality control has not been processed. 
   
     
     
         2 . The method of  claim 1 , further comprising sending an alert if the first quality control is due. 
     
     
         3 . The method of  claim 1 , further comprising after the releasing step c):
 d) processing a first patient sample by the target analyte detection instrument and generating run data; and   e) removing patient data from the run data by the target analyte detection instrument prior to releasing the run data.   
     
     
         4 . The method of  claim 2 , wherein the alert is sent 24 or 48 hours before the first quality control is due. 
     
     
         5 . The method of  claim 1 , further comprising after the releasing step c):
 d) processing a plurality of patient samples by the target analyte detection instrument; and   e) generating an epidemiology report by converting nano-Amp signal from detected targets from the patient samples to an excel format.   
     
     
         6 . The method of  claim 1 , further comprising after the releasing step c):
 d) processing a plurality of patient samples by the target analyte detection system; and   e) generating an epidemiology report through the LIS interchange.   
     
     
         7 . The method of  claim 1 , further comprising after the releasing step c):
 d) processing a first patient sample by the target analyte detection instrument, wherein the first patient sample is in a cartridge, the cartridge comprising a first and a second machine readable identification tag, wherein the target analyte detection instrument discontinues processing the first patient sample if the first machine readable identification tag does not match the second machine readable identification tag.   
     
     
         8 . The method of  claim 1 , further comprising after the releasing step c):
 d) processing a first patient sample by the target analyte detection instrument, wherein at least one pathogen in the first patient sample is a blood stream pathogen that causes or is suspected of causing sepsis.   
     
     
         9 . The method of  claim 1 , further comprising after the releasing step c):
 d) processing a first patient sample by the target analyte detection instrument; and   e) sending an alert by the target analyte detection instrument when the sample turnaround time for the first patient sample is violated.   
     
     
         10 . The method of  claim 1 , further comprising after the releasing step c):
 d) processing a first patient sample by the target analyte detection instrument; and   e) sending an alert by the target analyte detection instrument when a sample stability time for the first patient sample is violated.   
     
     
         11 . The method of  claim 1 , further comprising after the releasing step c):
 d) processing a first patient sample; and   e) sending an alert by the target analyte detection instrument when the target analyte detection instrument has detected 4 or more pathogens in the first patient sample.   
     
     
         12 . The method of  claim 1 , further comprising after the releasing step c,
 d) processing a first patient sample by the target analyte detection instrument, wherein the first patient sample is processed according to an assay ordered to detect a target, and   e) sending an alert by the target analyte detection instrument when the target detected does not match the assay ordered.   
     
     
         13 . The method of  claim 1 , further comprising after the releasing step c),
 d) processing a first patient sample by the target analyte detection instrument, wherein processing a first patient sample by the target analyte detection instrument, comprises performing a single detuned multiplex end-point polymerase chain reaction (PCR) on the first patient sample, the PCR comprising about 30 to about 35 cycles.   
     
     
         14 . A method for validating a target analyte detection system, comprising:
 a) processing a first quality control to produce a quality control record;   b) storing the quality control record by a target analyte detection instrument in a base station; and   c) preventing the processing of a patient sample by the target analyte detection instrument if a second quality control has not been processed by the target analyte detection instrument.   
     
     
         15 . The method of  claim 14 , wherein the preventing step c) occurs when the patient sample is loaded into a first test cartridge and the first test cartridge is from a new lot. 
     
     
         16 . The method of  claim 14 , further comprising:
 d) releasing the quality control record to a hospital LIS by the target analyte detection instrument.   
     
     
         17 . The method of  claim 14 , further comprising:
 d) tracking preventative maintenance for the target analyte detection instrument by the target analyte detection instrument.   
     
     
         18 . A method for validating a target analyte detection system in order to process a first patient sample and a second patient sample comprising:
 a) processing a first quality control to produce a first quality control record;   b) storing the quality control record by a target analyte detection instrument in a base station;   c) releasing the first quality control record to a hospital LIS by the target analyte detection instrument;   d) receiving a first test order for the first patient sample in a first file format for the first patient sample, and a second test order for the second patient sample in a first file format for the second patient sample, by a bi-directional LIS interchange, wherein the bidirectional LIS interchange is on a target analyte detection instrument, and the bi-directional LIS interchange converts the first file format for the first patient sample to a second file format for the first patient sample, and converts the first file format for the second patient sample to a second file format for the second patient sample;   e) populating the second file format for the first patient sample with a first accession number and populating the second file format for the second patient sample with a second accession number; and   f) processing the first patient sample and the second patent sample, when the first accession number and the second accession number are different.   
     
     
         19 . The method of  claim 18 , wherein the first patient sample is in a cartridge for the target analyte detection instrument, the cartridge comprising a first and a second machine readable identification tag, wherein the target analyte detection instrument discontinues processing the first patient sample if the first machine readable identification tag does not match the second machine readable identification tag. 
     
     
         20 . The method of  claim 18 , wherein processing the first patient sample comprises performing a single detuned multiplex end-point polymerase chain reaction (PCR) on the first patient sample, the PCR comprising about 30 to about 35 cycles.