PATHOGEN DIAGNOSIS BY METAGENOMIC NANOPORE SEQUENCING: A REVIEW
Main Article Content
Keywords
Metagenomics, Nanopore Sequencing, Next Generation Sequencing, Pathogens, Antibiotics
Abstract
All microorganisms contain genetic material (DNA or RNA), thereby making sequencing a useful technique for the identification of microbes. Identification of microorganisms in its natural environment is known as metagenomics. The expense of next generation sequencing has been reduced by a certain size since its invention in 2004, but soon developed as a powerful molecular technique for identification and characterization of microbes from clinical samples from patients. Nanopore Sequencing, a next generation sequencing approach has proved as an innovative molecular technique that upgrades the capacity to identify pathogens. The technique involves the sequencing of a single strand using protein nanopores and adaptable electronic gadgets. The current review deals with how nanopore sequencing plays an important role in metagenomics and few real time examples on how it enables to reduce the consumption of antibiotics.
References
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2. Rondon, M R et al. “Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms.” Applied and environmental microbiology vol. 66,6 (2000): 2541-7. doi:10.1128/AEM.66.6.2541-2547.2000
3. Sanger, F., Air, G., Barrell, B. et al. Nucleotide sequence of bacteriophage φX174 DNA. Nature 265, 687–695 (1977). https://doi.org/10.1038/265687a0
4. Liles, Mark R et al. “A census of rRNA genes and linked genomic sequences within a soil metagenomic library.” Applied and environmental microbiology vol. 69,5 (2003): 2684-91. doi:10.1128/AEM.69.5.2684-2691.2003
5. Maxam, A M, and W Gilbert. “A new method for sequencing DNA.” Proceedings of the National Academy of Sciences of the United States of America vol. 74,2 (1977): 560-4. doi:10.1073/pnas.74.2.560
6. Air, G M et al. “Nucleotide and amino acid sequences of gene G of omegaX174.” Journal of molecular biology vol. 108,3 (1976): 519-33. doi:10.1016/s0022-2836(76)80134-9
7. Metzker, Michael L. “Emerging technologies in DNA sequencing.” Genome research vol. 15,12 (2005): 1767-76. doi:10.1101/gr.3770505
8. Branton, D., Deamer, D., Marziali, A. et al. The potential and challenges of nanopore sequencing. Nat Biotechnol 26, 1146–1153 (2008). https://doi.org/10.1038/nbt.1495
9. Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat Biotechnol 34, 518–524 (2016). https://doi.org/10.1038/nbt.3423
10. Kasianowicz JJ, Brandin E, Branton D, Deamer DW. 1996. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U.S.A. 1996, 93(24): 13770-13773, https://doi.org/10.1073/pnas.93.24.13770
11. Cherf, G., Lieberman, K., Rashid, H. et al. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nat Biotechnol 30, 344–348 (2012). https://doi.org/10.1038/nbt.2147
12. Ayub, M., & Bayley, H. (2012). Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore. Nano letters, 12(11), 5637–5643. https://doi.org/10.1021/nl3027873
13. Manrao, E., Derrington, I., Laszlo, A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol 30, 349–353 (2012). https://doi.org/10.1038/nbt.2171
14. Zhao, Q et al. “Detecting SNPs using a synthetic nanopore.” Nano letters vol. 7,6 (2007): 1680-5. doi:10.1021/nl070668c
15. Hoenen, Thomas et al. “Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool.” Emerging infectious diseases vol. 22,2 (2016): 331-4. doi:10.3201/eid2202.151796
16. Bleeker-Rovers, Chantal P et al. “A prospective multicenter study on fever of unknown origin: the yield of a structured diagnostic protocol.” Medicine vol. 86,1 (2007): 26-38. doi:10.1097/MD.0b013e31802fe858
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18. Wilson, Michael R et al. “Actionable diagnosis of neuroleptospirosis by next-generation sequencing.” The New England journal of medicine vol. 370,25 (2014): 2408-17. doi:10.1056/NEJMoa1401268
19. Chiu, Charles Y. “Viral pathogen discovery.” Current opinion in microbiology vol. 16,4 (2013): 468-78. doi:10.1016/j.mib.2013.05.001
20. Cummings, Lisa A et al. “Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples.” Clinical chemistry vol. 62,11 (2016): 1465-1473. doi:10.1373/clinchem.2016.258806
21. Salipante, Stephen J et al. “Coinfection of Fusobacterium nucleatum and Actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing.” Journal of clinical microbiology vol. 52,5 (2014): 1789-92. doi:10.1128/JCM.03133-13
22. Gire, Stephen K et al. “Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.” Science (New York, N.Y.) vol. 345,6202 (2014): 1369-72. doi:10.1126/science.1259657
23. Salipante, Stephen J et al. “Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.” Journal of clinical microbiology vol. 53,4 (2015): 1072-9. doi:10.1128/JCM.03385-14
24. Deurenberg, Ruud H et al. “Application of next generation sequencing in clinical microbiology and infection prevention.” Journal of biotechnology vol. 243 (2017): 16-24. doi:10.1016/j.jbiotec.2016.12.022
25. Sahoo, M. K., Lefterova, M. I., Yamamoto, F., Waggoner, J. J., Chou, S., Holmes, S. P., Anderson, M. W., & Pinsky, B. A. (2013). Detection of cytomegalovirus drug resistance mutations by next-generation sequencing. Journal of clinical microbiology, 51(11), 3700–3710. https://doi.org/10.1128/JCM.01605-13
26. Pennisi, E. Search for pore-fection. Science 2012, 336(6081): 534–537. DOI: 10.1126/science.336.6081.534
27. Song, L et al. “Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore.” Science (New York, N.Y.) vol. 274,5294 (1996): 1859-66. doi:10.1126/science.274.5294.1859
28. Kasianowicz, J. J., Brandin, E., Branton, D., and Deamer, D. W. (1996). Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U.S.A. 93, 13770–13773.
29. Gouaux, J E et al. “Subunit stoichiometry of staphylococcal alpha-hemolysin in crystals and on membranes: a heptameric transmembrane pore.” Proceedings of the National Academy of Sciences of the United States of America vol. 91,26 (1994): 12828-31. doi:10.1073/pnas.91.26.12828
30. Gouaux, E. “alpha-Hemolysin from Staphylococcus aureus: an archetype of beta-barrel, channel-forming toxins.” Journal of structural biology vol. 121,2 (1998): 110-22. doi:10.1006/jsbi.1998.3959
31. Deamer, David. “Nanopore analysis of nucleic acids bound to exonucleases and polymerases.” Annual review of biophysics vol. 39 (2010): 79-90. doi:10.1146/annurev.biophys.093008.131250
32. Bayley, Hagan. “Sequencing single molecules of DNA.” Current opinion in chemical biology vol. 10,6 (2006): 628-37. doi:10.1016/j.cbpa.2006.10.040
33. Eme, L., Spang, A., Lombard, J. et al. Archaea and the origin of eukaryotes. Nat Rev Microbiol 15, 711–723 (2017). https://doi.org/10.1038/nrmicro.2017.133
34. Filloux, Denis et al. “Nanopore-based detection and characterization of yam viruses.” Scientific reports vol. 8,1 17879. 14 Dec. 2018, doi:10.1038/s41598-018-36042-7
35. Batavska J. et al., “Metagenomic arbovirus detection using MinION nanopore sequencing”. Journal of Virological Methods. 2018, 249: 79-84. https://doi.org/10.1016/j.jviromet.2017.08.019
36. Jain, M., Olsen, H.E., Paten, B. et al. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 17, 239 (2016). https://doi.org/10.1186/s13059-016-1103-0
37. Finn, S., Condell, O., McClure, P., Amézquita, A., & Fanning, S. (2013). Mechanisms of survival, responses and sources of Salmonella in low-moisture environments. Frontiers in microbiology, 4, 331. https://doi.org/10.3389/fmicb.2013.00331
38. Lawson, C.E., Harcombe, W.R., Hatzenpichler, R. et al. Common principles and best practices for engineering microbiomes. Nat Rev Microbiol 17, 725–741 (2019). https://doi.org/10.1038/s41579-019-0255-9
39. Song, S., Jarvie, T., Hattori, M. Our. Second Genome—Human Metagenome: How Next-Generation Sequencer Changes our Life Through Microbiology- Chapter Three - Advances in Microbial Physiology, 2013, 62: 119-144, https://doi.org/10.1016/B978-0-12-410515-7.00003-2
40. Blomström, Anne-Lie. “Viral metagenomics as an emerging and powerful tool in veterinary medicine.” The Veterinary Quart 2011, 31(3): 107-14. doi:10.1080/01652176.2011.604971
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Nov 30, 2019
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Nataraja B.T., Rathna Kumari B.M., Mohan Kumar B.S., & Uddappanda Bopaiah Roy. (2019). PATHOGEN DIAGNOSIS BY METAGENOMIC NANOPORE SEQUENCING: A REVIEW. Journal of Population Therapeutics and Clinical Pharmacology, 26(4), 141-149. https://doi.org/10.53555/jptcp.v26i4.7240
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Author Biographies
Nataraja B.T.
Department of Microbiology, Government Science College, Chitradurga, Karnataka, India
Rathna Kumari B.M.
Department of Botany, Government First Grade College, Vijayanagara, Bengaluru, Karnataka, India
Mohan Kumar B.S.
Department of Zoology, Maharani’s Science College for Women, Bengaluru, Karnataka, India
Uddappanda Bopaiah Roy
Department of Zoology, Government Science College, Bengaluru, Karnataka, India
How to Cite
Nataraja B.T., Rathna Kumari B.M., Mohan Kumar B.S., & Uddappanda Bopaiah Roy. (2019). PATHOGEN DIAGNOSIS BY METAGENOMIC NANOPORE SEQUENCING: A REVIEW. Journal of Population Therapeutics and Clinical Pharmacology, 26(4), 141-149. https://doi.org/10.53555/jptcp.v26i4.7240