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 to diagnose a gram-positive bacterial infection and a gram-negative bacterial and/or fungal co-infection in a patient, the method comprising:
a. assessing, in a sample identified by a gram-stain culture as gram-positive, data that detects:
i. gram-positive bacteria in the sample by its genus,
ii. the gram-positive bacteria in the sample by its species,
iii. gram-negative bacteria,
iv. the gram-negative bacteria by its species, and
v. fungus in the sample by its species,
wherein data that detects gram-negative bacteria by its species and fungus in the sample by its species is co-infection species data;
b. categorizing the data from group (iii) and group (iv) as either positive or negative for gram-negative bacteria;
c. categorizing the data from group (v) as either positive or negative for fungus;
d. reporting the infection by the species or genus of the gram-positive bacteria; and
e. reporting the co-infection as a gram-negative bacterial infection and/or a fungal infection but not reporting the co-infection species data.
2. The method of claim 1 , wherein the sample comprises viable gram-positive bacteria and non-viable gram-positive bacteria.
3. The method of claim 2 , wherein the viable gram-positive bacteria are present in the sample at a lower concentration than the non-viable gram-positive bacteria.
4. The method of claim 2 , wherein the data is obtained after the sample is subjected to a single detuned multiplex end-point polymerase chain reaction (PCR), the PCR comprising about 30 to about 35 cycles.
5. The method of claim 1 , wherein the gram-positive bacteria are Bacillus cereus, Micrococcus, Bacillus subtilis, Staphylococcus, Staphylococcus aureus, Propionibacterium acnes, Staphylococcus epidermidis, Staphylococcus lugdunensis, Enterococcus faecalis, Streptococcus, Enterococcus faecium, Streptococcus agalactiae, Lactobacillus, Listeria, Streptococcus pneumoniae, Listeria monocytogenes , or Streptococcus pyogenes.
6. The method of claim 1 , further comprising categorizing the data from group (i) and group (ii) as either resistant or sensitive to methicillin or vancomycin.
7. The method of claim 1 , wherein reporting in steps d and e comprises automatically generating and sending a detection report to a laboratory information system (LIS) interchange.
8. The method of claim 1 , wherein the data is obtained by detecting electrochemical signals.
9. The method of claim 1 , wherein the method is carried out in a sample-to-answer system, wherein the sample-to-answer system is configured to (i) receive a test order from a hospital laboratory information system (LIS), (ii) generate a detection report and (iii) automatically send the detection report to the hospital LIS.
10. The method of claim 1 , wherein the method is carried out in a sample-to-answer system, wherein the sample-to-answer system is configured to connect to more than one hospital LIS.
11. The method of claim 1 , further comprising: assessing, in a second portion of the sample, data that detects:
i. gram-negative bacteria in the sample by its genus,
ii. the gram-negative bacteria in the sample by its species,
iii. gram-positive bacteria,
iv. the gram-positive bacteria by its species, and
v. fungus in the sample by its species,
wherein data that detects gram-positive bacteria by its species and fungus in the sample by its species is second portion co-infection species data;
b. categorizing the data from group (iii) and (iv) as either positive or negative for gram-positive bacteria in the second portion;
c. categorizing the data from group (v) as either positive or negative for fungus in the second portion;
d. reporting the infection as a gram-positive bacterial infection in the second portion; and
e. reporting the co-infection by the species or genus of the gram-negative bacteria and/or as a fungal infection in the second portion but not reporting the second portion co-infection species data.
12. The method of claim 1 , further comprising:
assessing, in a second portion of the sample, data that detects fungus in the sample by its species; and
reporting the co-infection by the species or genus of the fungus.
13. A method to diagnose a gram-negative bacterial infection and a gram-positive bacterial and/or fungal co-infection in a patient the method comprising:
a. assessing, in a sample identified by a gram-stain culture as gram-negative, data that detects:
i. gram-negative bacteria in the sample by its genus,
ii. the gram-negative bacteria in the sample by its species,
iii. gram-positive bacteria,
iv. the gram-positive bacteria by its species, and
v. fungus in the sample by its species,
wherein data that detects gram-positive bacteria by its species and fungus in the sample by its species is co-infection species data;
b. categorizing the data from group (iii) and group (iv) as either positive or negative for gram-positive bacteria;
c. categorizing the data from group (v) as either positive or negative for fungus;
d. reporting the infection by the species or genus of the gram-negative bacteria; and
e. reporting the co-infection as a gram-positive bacterial infection and/or a fungal infection but not reporting the co-infection species data.
14. The method of claim 13 , wherein the sample comprises viable and non-viable gram-positive bacteria.
15. The method of claim 13 , further comprising:
assessing, in a second portion of the sample, data that detects:
i. gram-positive bacteria in the sample by its genus,
ii. the gram-positive bacteria in the sample by its species,
iii. gram-negative bacteria,
iv. the gram-negative bacteria by its species, and
v. fungus in the sample by its species,
wherein data that detects gram-negative bacteria by its species and fungus in the sample by its species is second portion co-infection species data;
b. categorizing the data from group (iii) and group (iv) as either positive or negative for gram-negative bacteria in the second portion;
c. categorizing the data from group (v) as either positive or negative for fungus in the second portion;
d. reporting the infection as a gram-negative bacterial infection in the second portion; and
e. reporting the co-infection by the species or genus of the gram-positive bacteria and/or as a fungal infection in the second portion but not reporting the second portion co-infection species data.
16. The method of claim 13 , further comprising:
assessing, in a second portion of the sample, data that detects fungus in the sample by its species; and
reporting the infection by the species or genus of the fungus.
17. The method of claim 13 , wherein the data is obtained by detecting electrochemical signals.
18. The method of claim 13 , further comprising categorizing the data from group (i) and group (ii) as either resistant or sensitive to CTX-M, IMP, KPC, NDM, OXA, or VIM.
19. The method of claim 13 , wherein reporting in steps d and e comprises automatically generating and sending a detection report to a LIS interchange.
20. The method of claim 13 , wherein the method is carried out in a sample-to-answer system wherein the sample-to-answer system is configured to (i) receive a test order from a hospital LIS, (ii) generate a detection report and (iii) automatically send the detection report to the hospital LIS.