Microbiome Diagnostics

• US 20180030516A1
• Filed: 02/26/2016
• Published: 02/01/2018
• Est. Priority Date: 02/27/2015
• Status: Abandoned Application

• Current Assignee: Alere, Inc. (Abbott Laboratories Incorporated)
• Original Assignee: Alere, Inc. (Abbott Laboratories Incorporated)
• Inventors: Nawana, Namal, Fister, III, Julius C.
• Application Number:
  US15/553,704
• Publication Number:
  US 20180030516A1
• Time in Patent Office: Days
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

A method for determining data related to a microbiome of a human includes isothermally amplifying polynucleotides of at least N different microorganisms present in a sample obtained from the human, wherein N>1, determining, based on the amplified polynucleotides, microbiome data comprising data indicative of at least one of a presence and an abundance of each of the N microorganisms, and determining, based on the microbiome data and prior data related to the N microorganisms, data related to a condition of the animal.

Claims

1. A method, comprising:

a) amplifying polynucleotides of at least N different microorganisms present in a sample obtained from an animal, wherein N>

1;

b) determining, based on the amplified polynucleotides, microbiome data comprising data indicative of at least one of a presence and an abundance of each of the N microorganisms; and

c) determining, based on the microbiome data and on prior data related to the N microorganisms, data related to a condition of the animal.

2. The method of claim 1, wherein the animal is a human.

3. The method of claim 1, further comprising determining a treatment for the condition based on the microbiome data and the prior data.

4. The method of claim 3, further comprising administering the treatment to the animal.

5. The method of claim 1, wherein the amplification is performed isothermally.

6. The method of claim 5, wherein the amplification is performed without subjecting the polynucleotides to a temperature in excess of about 75°

C.

7. The method of claim 1, wherein the amplification is performed without first subjecting the polynucleotides to a temperature sufficient to denature double stranded polynucleotides present in the sample.

8. The method of claim 1, wherein the amplification is performed using recombinase polymerase amplification or nicking and extension amplification reaction.

9. The method of claim 1, wherein the amplification is performed in a total time T of about 30 minutes or less.

10. The method of claim 1, wherein N is at least 5.

11. The method of claim 1, wherein the prior data are indicative of a correlation between the presence or abundance of the microorganisms in humans and the presence, absence or severity of or a tendency toward the condition in such humans.

26. The method of claim 1, wherein based on the microorganisms identified offering to said subject a range of one or more products that may benefit the wellbeing of the subject.

27. The method of claim 26, wherein the offering of products comprises offering cosmetic products for application to the facial area, offering anti-perspirant products, offering deodorant products.

28. The method of claim 27, wherein the offering of products comprises offering a probiotic, offering a pre-biotic, offering an antibiotic.

12-15. -15. (canceled)

16. A method of screening a sample obtained from a human subject at point of care or point of presence to determine the identity of one or more microorganisms present or potentially present in the sample, the method comprising the steps;

obtaining a sample from the human subject;

processing the sample;

applying the processed sample to an assay device;

operating the assay device to perform at least one isothermal nucleic acid amplification cycle to amplify the nucleic acid content of the sample;

performing further isothermal nucleic acid amplification cycles to amplify defined sequences if present know to be associated with particular microorganisms;

identifying the microorganisms present in the sample based on the amplified nucleic acid; and

reporting to a user the specie or species of microorganism present in the sample.

17. The method of claim 16, wherein the step of processing the sample comprises lysing the sample to release nucleic acid contents;

filtering the sample to remove debris which may interfere with nucleic acid amplification; and

optionally concentrating the sample.

18. The method of claim 16, wherein the step of applying the processed sample to an assay device comprises delivering the processed sample to a reaction chamber to initiate isothermal nucleic acid amplification.

19. The method of claim 16, wherein the process of isothermal nucleic acid amplification comprises recombinase polymerase amplification (RPA), nicking and extension amplification reaction (NEAR).

20. The method of claim 16, wherein screening of the sample is performed to identify one or more microorganisms known to be present on the skin of a human being.

21. The method of claim 16, wherein screening of the sample is performed to identify one or more microorganisms known to be present on or around the eye of a human being.

22. The method of claim 16, wherein screening of the sample is performed to identify one or more microorganisms known to be present in the upper respiratory tract of a human being.

23. The method of claim 16, wherein screening of the sample is performed to identify one or more microorganisms known to be present in the intestinal tract of a human being.

24. The method of claim 16, wherein screening of the sample is performed to identify one or more microorganisms known to be present in the oral cavity of a human being.

25. The method of claim 16, wherein screening of the sample is performed to identify one or more microorganisms known to be present in the genitourinary tract of a human being.

32. The method of claim 16, wherein from the output of the method, selecting a compound that is synergistic with the microbial species or a compound produced by the microbial species.

33. The method of claim 16, wherein based on the result of the method, selecting a compound to treat the medical condition, physical condition, or according to individual'"'"'s responsiveness to the therapeutic use of the compound.

34. The method of claim 16, wherein the data associated with an individual'"'"'s microbiome comprises data about the environment.

35. The method of claim 34, wherein the selected compound is compatible with the environment.

36. The method of claim 16, wherein the isothermal amplification of DNA is performed using a cassette.

37. The method of claim 16, wherein the isothermal amplification is multiplexed amplification of a single sample.

38. The method of claim 16, wherein a single sample is divided into a plurality of sample fractions, wherein each fraction is combined with reagents for isothermal amplification and primers specific to at least one microorganism.

39. The method of claim 16, wherein the step of detecting comprises detecting a 10⁶ fold amplification, a 10⁷ fold amplification, a 10⁸ fold amplification, a 10⁹ fold amplification, a 10¹⁰ fold amplification, a 10¹¹ fold amplification, a 10¹² fold amplification of the target nucleic acid sequence.

40. The method of claim 16, wherein the method is performed at point of care, or point of retail.

41. The method of claim 16, wherein the sample is selected from the group comprising;

blood, plasma, serum, urine, saliva, tear fluid, seminal fluid, a vaginal swab, a nasal swab, a rectal swab, a skin swab, an in ear swab, a cheek swab, a throat swab, a fecal sample, cerebrospinal fluid.

42. The method of claim 16, wherein the method comprises determining the susceptibility of an individual to a therapy based on synergism of compound with the microbial species identified on said individual.

43. The method of claim 16, wherein the compound used to treat the medical or physical condition affects the count of a bacterium found in the individual'"'"'s microbiome profile.

44. The method of claim 43 wherein the compound used to treat comprises a pre-biotic, a pro-biotic or an antibiotic.

29. A method of determining the microbiome profile of an individual comprising receiving a sample from the individual, performing isothermal nucleic acid amplification of a nucleic acid associated with at least one microorganism, and detecting the amplified nucleic acid product, wherein the detected products are used to build a profile of the individual'"'"'s microbiome.

30. The method of claim 29, wherein the step of determining the microbiome profile is completed in 15 minutes or less, 10 minutes or less, five minutes or less, 3 minutes or less.

31. The method of claim 29, further comprising providing a set of algorithms for linking the data associated with the individual'"'"'s microbiome to a certain medical condition, physical condition, or likely responsiveness to a certain therapy.

45-111. -111. (canceled)