Cell-free nucleic acids for the analysis of the human microbiome associated with respiratory infection
Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.
1. A method of detecting a microbe associated with a respiratory infection comprising:
a) providing a sample comprising cell-free nucleic acids, wherein the sample comprising cell-free nucleic acids is from a subject with a respiratory infection and is selected from the group consisting of plasma, serum, cerebrospinal fluid and synovial fluid and wherein the cell-free nucleic acids comprise cell-free nucleic acids free of viral particles;
b) performing high-throughput sequencing of the cell-free nucleic acids free of viral particles to generate sequence reads that comprise sequence reads from at least one microbe associated with the respiratory infection; and
c) detecting the at least one microbe associated with the respiratory infection.
2. The method of claim 1 , wherein the cell-free nucleic acids free of viral particles comprise cell-free DNA.
3. The method of claim 2 , further comprising selectively extracting the cell-free DNA from the sample comprising cell-free nucleic acids to obtain extracted cell-free DNA, wherein the high-throughput sequencing in (b) is performed on the extracted cell-free DNA.
4. The method of claim 1 , wherein the detecting the at least one microbe associated with the respiratory infection comprises determining a normalized quantity of the at least one microbe associated with the respiratory infection based on the sequence reads from the at least one microbe associated with the respiratory infection.
5. The method of claim 1 , wherein the cell-free nucleic acids comprise cell-free DNA, cell-free RNA, or a combination thereof, and further comprising attaching adapters to the cell-free DNA, cell-free RNA, or a combination thereof prior to (b) to produce nucleic acids attached to the adapters, wherein the nucleic acids attached to the adapters comprise nucleic acids from the at least one microbe associated with the respiratory infection and wherein (b) comprises sequencing the nucleic acids attached to the adapters.
6. The method of claim 1 , wherein the cell-free nucleic acids comprise RNA.
7. The method of claim 1 , further comprising extracting RNA from the sample to obtain extracted RNA, and wherein the high-throughput sequencing in (b) is performed on the extracted RNA.
8. The method of claim 1 , further comprising extracting cell-free RNA from the sample to obtain extracted cell-free RNA, and wherein the high-throughput sequencing in (b) is performed on the extracted cell-free RNA.
9. The method of claim 1 , further comprising identifying the at least one microbe associated with the respiratory infection at a strain or species level.
10. The method of claim 1 , wherein the respiratory infection is a lung infection.
11. The method of claim 1 , further comprising, prior to (b), amplifying a plurality of the cell-free nucleic acids.
12. The method of claim 11 , wherein the amplifying the plurality of the cell-free nucleic acids comprises performing non-biased amplification on the cell-free nucleic acids.
13. The method of claim 11 , wherein the amplifying the plurality of the cell-free nucleic acids comprises performing a PCR reaction with universal primers.
14. The method of claim 11 , wherein the amplifying the plurality of the cell-free nucleic acids comprises ligating adapters to the cell-free nucleic acids and amplifying with primers specific for the adapters.
15. The method of claim 1 , wherein the sample comprising cell-free nucleic acids is a plasma sample.
16. The method of claim 1 , wherein the at least one microbe associated with the respiratory infection comprises a virus.
17. The method of claim 1 , wherein the at least one microbe associated with the respiratory infection comprises a bacterium.
18. The method of claim 1 , wherein the at least one microbe associated with the respiratory infection comprises a fungus.
19. The method of claim 1 , wherein the at least one microbe associated with the respiratory infection comprises at least one fungus and at least one bacterium.
20. The method of claim 1 , wherein the at least one microbe associated with the respiratory infection comprises at least one microbe selected from the group consisting of: human respiratory syncytial virus, human rhinovirus, human influenza virus, human parainfluenza virus, coronavirus, human coronavirus, human SARS coronavirus, human enterovirus, measles virus, mumps virus, adenovirus, Pneumocystis, Pneumocystis jiroveci , Metapneumovirus, Staphylococcus, Staphylococcus aureus , Multi-drug resistant Staphylococcus aureus (MRSA), candida, Klebsiella pneumonia, Streptococcus pneumoniae , gram positive bacterium, gram negative bacterium, Legionella, Aspergillus, mycobacterium , Mycoplasmatales, Apergillus fumigatus , and Aspergillus niger.
21. The method of claim 1 , wherein the sequence reads are short sequence reads.
22. The method of claim 1 , further comprising quantifying an amount of the at least one microbe associated with the respiratory infection based on the sequence reads from the at least one microbe associated with the respiratory infection and detecting the respiratory infection in the subject with the respiratory infection based on the amount of the at least one microbe associated with the respiratory infection.
23. The method of claim 22 , further comprising administering an antimicrobial treatment to the subject with the respiratory infection to treat the respiratory infection, wherein the respiratory infection is detected based on the amount of the at least one microbe associated with the respiratory infection.
24. The method of claim 23 , wherein the antimicrobial treatment is an antiviral treatment.
25. The method of claim 23 , wherein the antimicrobial treatment is an antibiotic.
26. The method of claim 1 , further comprising obtaining a second sample from the subject with the respiratory infection at a second time point and performing (b) and (c) on the second sample.
27. The method of claim 26 , wherein the second time point is a time point following administration of an antimicrobial treatment to the subject with the respiratory infection, and wherein the method further comprises detecting a decrease in quantity of the at least one microbe in response to the antimicrobial treatment.
28. The method of claim 1 , wherein the sequence reads that comprise sequence reads from at least one microbe associated with the respiratory infection comprise at least 10 7 sequence reads.
29. The method of claim 1 , wherein the sequence reads that comprise sequence reads from at least one microbe associated with the respiratory infection comprise at least 10 8 sequence reads per sample.
30. The method of claim 1 , wherein the at least one microbe associated with the respiratory infection comprises a parasite.