Electrochemical detection of bacterial and/or fungal infections

• US 10,273,535 B2
• Filed: 08/03/2018
• Issued: 04/30/2019
• Est. Priority Date: 08/24/2017
• Status: Active Grant

• Current Assignee: Roche Molecular Systems Inc (Roche Holding AG)
• Original Assignee: Clinical Micro Sensors Inc. (Roche Holding AG)
• Inventors: Brown, Bradley Adam, Martinez, Milena Iacobelli, Freeman-Cook, Lisa Lynn, Harvey, John Jay, Shaw, Christine J., Al-Khouri, Anna Maria
• Primary Examiner(s): Priest, Aaron A
• Application Number:
  US16/054,960
• Publication Number:
  US 20190062803A1
• Time in Patent Office: 270 Days
• CPC Class Codes: B01L 2300/0627 Sensor or part of a sensor is integrated
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 3/5023 with a sample being transported to, and subsequently stored in an absorbent for analysis
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 1/6895 for plants, fungi or algae
• CPC Class Codes: C12Q 2527/143 Concentration of primer or probe
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G01N 27/3277 being a redox reaction, e.g. detection by cyclic voltammetry voltammetry per se G01N27/42, G01N27/48
• CPC Class Codes: G01N 27/48 using polarography, i.e. measuring changes in current under a slowly-varying voltage
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: G16H 15/00 ICT specially adapted for medical reports, e.g. generation or transmission thereof
• CPC Class Codes: G16H 80/00 ICT specially adapted for facilitating communication between medical practitioners or patients, e.g. for collaborative diagnosis, therapy or health monitoring
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

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.

Claims

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.