Electrochemical detection of bacterial and/or fungal infections
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.
1. A method for processing at least a first patient sample comprising:
a) receiving a first patient sample;
b) receiving a first test order by a bi-directional LIS interchange in a first file format from a hospital laboratory information system (LIS) for the first patient sample, wherein the bidirectional LIS interchange is on a target analyte detection instrument, and the bi-directional LIS interchange converts the first file format to a second file format; and
c) processing the first patient sample in the target analyte detection instrument using the second file format, wherein the target analyte detection instrument generates;
a first result identifying at least one pathogen in the first patient sample processed by the target analyte detection instrument; and wherein the first result is automatically reported from the bi-directional LIS interchange.
2. The method of claim 1 , wherein the LIS interchange automatically reports the first result to the hospital LIS.
3. The method of claim 1 , wherein the first test order is in an HL7 or ASTM format and the LIS interchange converts the test order from the HL7 or ASTM format to a CSV format.
4. The method of claim 1 , wherein the bi-directional LIS interchange connects to more than one hospital LIS.
5. The method of claim 1 , wherein the at least one pathogen in the first patient sample processed is a viable gram-positive bacteria and the first patient sample comprises viable gram-positive bacteria and non-viable gram-positive bacteria.
6. The method of claim 5 , wherein the target analyte detection instrument performs a single detuned multiplex end-point polymerase chain reaction (PCR) on the first patient sample, the PCR comprising about 30 to about 35 cycles.
7. The method of claim 1 , wherein the target analyte detection instrument sends an alert when preventative maintenance for the target analyte detection instrument is needed.
8. The method of claim 1 , wherein the target analyte detection instrument sends an alert notifying a target analyte detection instrument operator that the first patient sample has an accession number that is the same as the accession number for a second patient sample.
9. A method for processing at least a first and second patient sample comprising:
a) receiving a first and second patient sample;
b) receiving a first and second test order by a bi-directional LIS interchange in a first file format from a hospital LIS for the first and second test order, respectively, wherein the bidirectional LIS interchange is on a target analyte detection instrument, and the bi-directional LIS interchange converts the first file format to a second file format; and
c) processing the first patient sample according to the first test order and processing the second patient sample according to the second test order, in the target analyte detection instrument using the second file format, wherein the target analyte detection instrument generates;
a first result that identifies at least one pathogen in the first patient sample and generates a second result that identifies at least one value for the second patient sample; and wherein the first result and the second result are
automatically reported to the bi-directional LIS interchange.
10. The method of claim 9 , wherein the LIS interchange automatically reports the first result to the hospital LIS.
11. The method of claim 9 , wherein automatically reporting the first result to the bi-directional LIS interchange comprises generating a first detection report, and wherein the method further comprises manually applying comments to the first detection report.
12. The method of claim 9 , wherein the first test order and the second test order are in a flat file format.
13. A method for processing at least a first patient sample comprising:
a) receiving a first patient sample;
b) receiving a first test order by a bi-directional LIS interchange in a first file format from a hospital LIS for the first patient sample, wherein the bidirectional LIS interchange is on a sample processing instrument, and the bi-directional LIS interchange converts the first file format to a second file format;
c) loading the first patient sample into a cartridge, the cartridge comprising a machine readable information tag;
d) loading the cartridge into the sample processing instrument comprising a first device that scans machine readable identification tags;
e) scanning the machine readable identification tag by the first device; and
f) processing the first patient sample in the sample processing instrument using the second file format, wherein the sample processing instrument generates;
a first result identifying at least one pathogen in the first patient sample processed by the sample processing instrument; and wherein the first result is automatically reported from the bi-directional LIS interchange.
14. The method of claim 13 , wherein the at least one pathogen in the first patient sample is a blood stream pathogen that causes or is suspected of causing sepsis.
15. The method of claim 13 , wherein the cartridge comprises a second machine readable identification tag and the second machine readable identification tag is scanned by a second device that scans machine readable identification tags prior to loading the cartridge into the sample processing instrument.
16. The method of claim 15 , wherein the sample processing instrument discontinues processing the cartridge if the first machine readable identification tag does not match the second machine readable identification tag.
17. The method of claim 13 , wherein the first result further identifies the presence of a resistance gene present in the at least one pathogen in the first patient sample.
18. The method of claim 13 , wherein the at least one pathogen is a human pathogen, and wherein the first patient sample further comprises a contaminating pathogen.
19. The method of claim 13 , wherein the sample processing instrument sends an alert if a threshold for stability is violated for the first patient sample.
20. The method of claim 13 , wherein the sample processing instrument performs a single detuned multiplex end-point polymerase chain reaction (PCR) on the first patient sample, the PCR comprising about 30 to about 35 cycles.