Skip to main content
SpringerLink
Log in

Genomic Applications in the Clinical Management of Infectious Diseases

  • Chapter
  • First Online:
Genomic Applications in Pathology

  • 1817 Accesses

Abstract

Next-generation sequencing (NGS) technologies are increasingly being used for diagnosis and monitoring of infectious diseases. Here, we review the application of NGS in clinical microbiology focusing on genotypic resistance testing, direct detection of unknown disease-associated pathogens in clinical specimens, investigation of microbial population diversity in the human host, and strain typing. We have organized this chapter into three main sections: (1) applications in clinical virology; (2) applications in clinical bacteriology, mycobacteriology, and mycology; and (3) validation, quality control, and maintenance of proficiency. Though many challenges remain, NGS continues to hold enormous promise for clinical infectious diseases testing.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Loman NJ, Constantinidou C, Chan JZ, et al. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol. 2012;10(9):599–606.

    Article  CAS  PubMed  Google Scholar 

  2. Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N. Application of next-generation sequencing technologies in virology. J Gen Virol. 2012;93(Pt 9):1853–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Weinstock GM. Genomic approaches to studying the human microbiota. Nature. 2012;489(7415):250–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Vrancken B, Lequime S, Theys K, Lemey P. Covering all bases in HIV research: unveiling a hidden world of viral evolution. AIDS Rev. 2010;12(2):89–102.

    PubMed  Google Scholar 

  5. Gibson RM, Schmotzer CL, Quinones-Mateu ME. Next-generation sequencing to help monitor patients infected with HIV: ready for clinical use? Curr Infect Dis Rep. 2014;16(4):401.

    Article  PubMed  Google Scholar 

  6. Dunn DT, Coughlin K, Cane PA. Genotypic resistance testing in routine clinical care. Curr Opin HIV AIDS. 2011;6(4):251–7.

    Article  PubMed  Google Scholar 

  7. Cortez KJ, Maldarelli F. Clinical management of HIV drug resistance. Viruses. 2011;3(4):347–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Simen BB, Simons JF, Hullsiek KH, et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis. 2009;199(5):693–701.

    Article  PubMed  Google Scholar 

  9. Lataillade M, Chiarella J, Yang R, et al. Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naive subjects in the CASTLE study. PLoS One. 2010;5(6):e10952.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Li JZ, Paredes R, Ribaudo HJ, et al. Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: a systematic review and pooled analysis. JAMA. 2011;305(13):1327–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Gorzer I, Guelly C, Trajanoski S, Puchhammer-Stockl E. The impact of PCR-generated recombination on diversity estimation of mixed viral populations by deep sequencing. J Virol Methods. 2010;169(1):248–52.

    Article  CAS  PubMed  Google Scholar 

  12. Harismendy O, Ng PC, Strausberg RL, et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 2009;10(3):R32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Mild M, Hedskog C, Jernberg J, Albert J. Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation. PLoS One. 2011;6(7):e22741.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res. 2007;17(8):1195–201.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci U S A. 2011;108(50):20166–71.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Clutter DS, Zhou S, Varghese V, et al. Prevalence of drug-resistant minority variants in untreated HIV-1-infected individuals with and those without transmitted drug resistance detected by Sanger sequencing. J Infect Dis. 2017;216(3):387–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Vandenbroucke I, Van Marck H, Mostmans W, et al. HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays. AIDS Res Ther. 2010;7:4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Sahoo MK, Lefterova MI, Yamamoto F, et al. Detection of cytomegalovirus drug resistance mutations by next-generation sequencing. J Clin Microbiol. 2013;51(11):3700–10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Tzou PL, Ariyaratne P, Varghese V, et al. Comparison of an in vitro diagnostic next-generation sequencing assay with Sanger sequencing for HIV-1 genotypic resistance testing. J Clin Microbiol. 2018;56(6):pii: e00105-18.

    Article  Google Scholar 

  20. Swenson LC, Mo T, Dong WW, et al. Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis. 2011;203(2):237–45.

    Article  PubMed  PubMed Central  Google Scholar 

  21. Kagan RM, Johnson EP, Siaw M, et al. A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients. PLoS One. 2012;7(9):e46334.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Le T, Chiarella J, Simen BB, et al. Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use. PLoS One. 2009;4(6):e6079.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Codoner FM, Pou C, Thielen A, et al. Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects. PLoS One. 2011;6(5):e19461.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kotton CN, Kumar D, Caliendo AM, et al. International consensus guidelines on the management of cytomegalovirus in solid organ transplantation. Transplantation. 2010;89(7):779–95.

    Article  PubMed  Google Scholar 

  25. Ljungman P, Reusser P, de la Camara R, et al. Management of CMV infections: recommendations from the infectious diseases working party of the EBMT. Bone Marrow Transplant. 2004;33(11):1075–81.

    Article  CAS  PubMed  Google Scholar 

  26. Lurain NS, Chou S. Antiviral drug resistance of human cytomegalovirus. Clin Microbiol Rev. 2010;23(4):689–712.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Chou S, Ercolani RJ, Sahoo MK, Lefterova MI, Strasfeld LM, Pinsky BA. Improved detection of emerging drug-resistant mutant cytomegalovirus subpopulations by deep sequencing. Antimicrob Agents Chemother. 2014;58(8):4697–702.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Li F, Kenyon KW, Kirby KA, Fishbein DP, Boeckh M, Limaye AP. Incidence and clinical features of ganciclovir-resistant cytomegalovirus disease in heart transplant recipients. Clin Infect Dis. 2007;45(4):439–47.

    Article  CAS  PubMed  Google Scholar 

  29. Limaye AP, Corey L, Koelle DM, Davis CL, Boeckh M. Emergence of ganciclovir-resistant cytomegalovirus disease among recipients of solid-organ transplants. Lancet. 2000;356(9230):645–9.

    Article  CAS  PubMed  Google Scholar 

  30. Myhre HA, Haug Dorenberg D, Kristiansen KI, et al. Incidence and outcomes of ganciclovir-resistant cytomegalovirus infections in 1244 kidney transplant recipients. Transplantation. 2011;92(2):217–23.

    Article  CAS  PubMed  Google Scholar 

  31. Chou S. Comparison of cytomegalovirus terminase gene mutations selected after exposure to three distinct inhibitor compounds. Antimicrob Agents Chemother. 2017;61(11)

    Google Scholar 

  32. Chou S. Rapid in vitro evolution of human cytomegalovirus UL56 mutations that confer letermovir resistance. Antimicrob Agents Chemother. 2015;59(10):6588–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Chou S. A third component of the human cytomegalovirus terminase complex is involved in letermovir resistance. Antivir Res. 2017;148:1–4.

    Article  CAS  PubMed  Google Scholar 

  34. Tang MW, Liu TF, Shafer RW. The HIVdb system for HIV-1 genotypic resistance interpretation. Intervirology. 2012;55(2):98–101.

    Article  PubMed  Google Scholar 

  35. Woods CK, Brumme CJ, Liu TF, et al. Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool. J Clin Microbiol. 2012;50(6):1936–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Petty TJ, Cordey S, Padioleau I, et al. Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study. J Clin Microbiol. 2014;52(9):3351–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Chiu CY. Viral pathogen discovery. Curr Opin Microbiol. 2013;16(4):468–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Barzon L, Lavezzo E, Militello V, Toppo S, Palu G. Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci. 2011;12(11):7861–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Rector A, Tachezy R, Van Ranst M. A sequence-independent strategy for detection and cloning of circular DNA virus genomes by using multiply primed rolling-circle amplification. J Virol. 2004;78(10):4993–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. de Vries M, Deijs M, Canuti M, et al. A sensitive assay for virus discovery in respiratory clinical samples. PLoS One. 2011;6(1):e16118.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Pyrc K, Jebbink MF, Berkhout B, van der Hoek L. Detection of new viruses by VIDISCA. Virus discovery based on cDNA-amplified fragment length polymorphism. Methods Mol Biol. 2008;454:73–89.

    Article  CAS  PubMed  Google Scholar 

  42. Depledge DP, Palser AL, Watson SJ, et al. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One. 2011;6(11):e27805.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Duncavage EJ, Magrini V, Becker N, et al. Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue. J Mol Diagn. 2011;13(3):325–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Wylie TN, Wylie KM, Herter BN, Storch GA. Enhanced virome sequencing using targeted sequence capture. Genome Res. 2015;25(12):1910–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Briese T, Kapoor A, Mishra N, et al. Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis. MBio. 2015;6(5):e01491-15.

    Article  PubMed  PubMed Central  Google Scholar 

  46. Gu W, Crawford ED, O'Donovan BD, et al. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 2016;17:41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Bhaduri A, Qu K, Lee CS, Ungewickell A, Khavari PA. Rapid identification of non-human sequences in high-throughput sequencing datasets. Bioinformatics. 2012;28(8):1174–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Kostic AD, Ojesina AI, Pedamallu CS, et al. PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol. 2011;29(5):393–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL. Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis. 2012;6(2):e1485.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Berthet N, Reinhardt AK, Leclercq I, et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Mol Biol. 2008;9:77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Cheval J, Sauvage V, Frangeul L, et al. Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol. 2011;49(9):3268–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95(6):315–27.

    Article  CAS  PubMed  Google Scholar 

  53. Falkow S. Molecular Koch’s postulates applied to bacterial pathogenicity – a personal recollection 15 years later. Nat Rev Microbiol. 2004;2(1):67–72.

    Article  CAS  PubMed  Google Scholar 

  54. Koser CU, Ellington MJ, Cartwright EJ, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog. 2012;8(8):e1002824.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Clarridge JE 3rd. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004;17(4):840–62. table of contents

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Balajee SA, Sigler L, Brandt ME. DNA and the classical way: identification of medically important molds in the 21st century. Med Mycol. 2007;45(6):475–90.

    Article  CAS  PubMed  Google Scholar 

  57. Klindworth A, Pruesse E, Schweer T, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1.

    Article  CAS  PubMed  Google Scholar 

  58. Kuczynski J, Lauber CL, Walters WA, et al. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet. 2012;13(1):47–58.

    Article  CAS  Google Scholar 

  59. Cox MJ, Cookson WO, Moffatt MF. Sequencing the human microbiome in health and disease. Hum Mol Genet. 2013;22(R1):R88–94.

    Article  CAS  PubMed  Google Scholar 

  60. Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One. 2011;6(12):e27310.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Haas BJ, Gevers D, Earl AM, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011;21(3):494–504.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37(Database issue):D141–5.

    Article  CAS  PubMed  Google Scholar 

  66. Bokulich NA, Subramanian S, Faith JJ, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2013;10(1):57–9.

    Article  CAS  PubMed  Google Scholar 

  67. Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–6.

    CAS  PubMed  Google Scholar 

  68. McDonald D, Price MN, Goodrich J, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6(3):610–8.

    Article  CAS  PubMed  Google Scholar 

  69. Salipante SJ, Sengupta DJ, Rosenthal C, et al. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLoS One. 2013;8(5):e65226.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Salipante SJ, Hoogestraat DR, Abbott AN, et al. Coinfection of Fusobacterium nucleatum and Actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing. J Clin Microbiol. 2014;52(5):1789–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Srinivasan S, Hoffman NG, Morgan MT, et al. Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria. PLoS One. 2012;7(6):e37818.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Zhao J, Schloss PD, Kalikin LM, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A. 2012;109(15):5809–14.

    Article  PubMed  PubMed Central  Google Scholar 

  73. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008;6(11):e280.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Morgan XC, Tickle TL, Sokol H, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13(9):R79.

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Naccache SN, Federman S, Veeraraghavan N, et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014;24(7):1180–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014;370(25):2408–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Flygare S, Simmon K, Miller C, et al. Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol. 2016;17(1):111.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Group NHW, Peterson J, Garges S, et al. The NIH Human Microbiome Project. Genome Res. 2009;19(12):2317–23.

    Article  CAS  Google Scholar 

  79. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Long SW, Williams D, Valson C, et al. A genomic day in the life of a clinical microbiology laboratory. J Clin Microbiol. 2013;51(4):1272–7.

    Article  PubMed  PubMed Central  Google Scholar 

  81. Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet. 2012;13(9):601–12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Jenkins SG, Schuetz AN. Current concepts in laboratory testing to guide antimicrobial therapy. Mayo Clin Proc. 2012;87(3):290–308.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Koser CU, Ellington MJ, Peacock SJ. Whole-genome sequencing to control antimicrobial resistance. Trends Genet. 2014;30(9):401–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Gupta SK, Padmanabhan BR, Diene SM, et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother. 2014;58(1):212–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Warner DF, Mizrahi V. Complex genetics of drug resistance in Mycobacterium tuberculosis. Nat Genet. 2013;45(10):1107–8.

    Article  CAS  PubMed  Google Scholar 

  87. Heysell SK, Houpt ER. The future of molecular diagnostics for drug-resistant tuberculosis. Expert Rev Mol Diagn. 2012;12(4):395–405.

    Article  CAS  PubMed  Google Scholar 

  88. MacCannell D. Bacterial strain typing. Clin Lab Med. 2013;33(3):629–50.

    Article  PubMed  Google Scholar 

  89. Rehm HL, Bale SJ, Bayrak-Toydemir P, et al. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013;15(9):733–47.

    Article  PubMed  PubMed Central  Google Scholar 

  90. College of American Pathologists. Molecular pathology checklist. Next generation sequencing. Northfield: College of American Pathologists; 2014. p. 8.

    Google Scholar 

  91. Schlaberg R, Chiu CY, Miller S, et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch Pathol Lab Med. 2017;141(6):776–86.

    Article  CAS  PubMed  Google Scholar 

  92. Food and Drug Administration. High-throughput sequencing technologies for microbial identification and detection of antimicrobial resistance markers. 2014.

    Google Scholar 

  93. Doan T, Acharya NR, Pinsky BA, et al. Metagenomic DNA sequencing for the diagnosis of intraocular infections. Ophthalmology. 2017;124(8):1247–8.

    Article  PubMed  Google Scholar 

  94. Graf EH, Simmon KE, Tardif KD, et al. Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel. J Clin Microbiol. 2016;54(4):1000–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Lefterova MI, Suarez CJ, Banaei N, Pinsky BA. Next-generation sequencing for infectious disease diagnosis and management: a report of the Association for Molecular Pathology. J Mol Diagn. 2015;17(6):623–34.

    Article  CAS  PubMed  Google Scholar 

  96. Feng H, Shuda M, Chang Y, Moore PS. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science. 2008;319(5866):1096–100.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Palacios G, Druce J, Du L, et al. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med. 2008;358(10):991–8.

    Article  CAS  PubMed  Google Scholar 

  98. Briese T, Paweska JT, McMullan LK, et al. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog. 2009;5(5):e1000455.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Yozwiak NL, Skewes-Cox P, Gordon A, et al. Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua. J Virol. 2010;84(18):9047–58.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Yongfeng H, Fan Y, Jie D, et al. Direct pathogen detection from swab samples using a new high-throughput sequencing technology. Clin Microbiol Infect. 2011;17(2):241–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. McMullan LK, Frace M, Sammons SA, et al. Using next generation sequencing to identify yellow fever virus in Uganda. Virology. 2012;422(1):1–5.

    Article  CAS  PubMed  Google Scholar 

  102. Wamala JF, Malimbo M, Okot CL, et al. Epidemiological and laboratory characterization of a yellow fever outbreak in northern Uganda, October 2010-January 2011. Int J Infect Dis. 2012;16(7):e536–42.

    Article  PubMed  Google Scholar 

  103. Wilson MR, Zimmermann LL, Crawford ED, et al. Acute West Nile virus meningoencephalitis diagnosed via metagenomic deep sequencing of cerebrospinal fluid in a renal transplant patient. Am J Transplant. 2017;17(3):803–8.

    Article  CAS  PubMed  Google Scholar 

  104. Wilson MR, Suan D, Duggins A, et al. A novel cause of chronic viral meningoencephalitis: Cache Valley virus. Ann Neurol. 2017;82(1):105–14.

    Article  PubMed  PubMed Central  Google Scholar 

  105. Kuroda M, Sekizuka T, Shinya F, et al. Detection of a possible bioterrorism agent, Francisella sp., in a clinical specimen by use of next-generation direct DNA sequencing. J Clin Microbiol. 2012;50(5):1810–2.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Mongkolrattanothai K, Naccache SN, Bender JM, et al. Neurobrucellosis: unexpected answer from metagenomic next-generation sequencing. J Pediatric Infect Dis Soc. 2017;6(4):393–8.

    PubMed  PubMed Central  Google Scholar 

  107. Wilson MR, Shanbhag NM, Reid MJ, et al. Diagnosing Balamuthia mandrillaris encephalitis with metagenomic deep sequencing. Ann Neurol. 2015;78(5):722–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Frey KG, Herrera-Galeano JE, Redden CL, et al. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood. BMC Genomics. 2014;15:96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

Material and references were used from Lefterova MI, Banaei N, and Pinsky BA. Genomic Applications in the Clinical Management of Infectious Diseases. In: Netto GJ, Schrijver I, eds. Genomic Applications in Pathology. 1st Ed. Springer. 2015. The authors thank the AMP NGS in ID Work Group, a joint project of the AMP Infectious Diseases Subdivision Leadership and Clinical Practice Committee for their contributions to the previous version of this manuscript [95].

Author information

Authors and Affiliations

  1. Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA

    Martina I. Lefterova, Carlos J. Suarez, Niaz Banaei & Benjamin A. Pinsky

  2. Guardant Health, Redwood City, CA, USA

    Martina I. Lefterova

  3. Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA

    Niaz Banaei & Benjamin A. Pinsky

Authors
  1. Martina I. Lefterova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Carlos J. Suarez
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Niaz Banaei
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Benjamin A. Pinsky
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Benjamin A. Pinsky .

Editor information

Editors and Affiliations

  1. Professor and Chair of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA

    George Jabboure Netto

  2. Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Clinical Professor of Pathology, University of Chicago Pritzker School of Medicine, Evanston, IL, USA

    Karen L. Kaul

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Lefterova, M.I., Suarez, C.J., Banaei, N., Pinsky, B.A. (2019). Genomic Applications in the Clinical Management of Infectious Diseases. In: Netto, G., Kaul, K. (eds) Genomic Applications in Pathology. Springer, Cham. https://doi.org/10.1007/978-3-319-96830-8_37

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-96830-8_37

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-96829-2

  • Online ISBN: 978-3-319-96830-8

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation