Clinical metagenomics (original) (raw)

• Zhao, F. & Bajic, V. B. The value and significance of metagenomics of marine environments. Genomics Proteomics Bioinformatics 13, 271–274 (2015).
  Article PubMed PubMed Central Google Scholar
• Ufarte, L., Laville, E., Duquesne, S. & Potocki-Veronese, G. Metagenomics for the discovery of pollutant degrading enzymes. Biotechnol. Adv. 33, 1845–1854 (2015).
  Article CAS PubMed Google Scholar
• Greay, T. L. et al. Recent insights into the tick microbiome gained through next-generation sequencing. Parasit. Vectors 11, 12 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Guegan, M. et al. The mosquito holobiont: fresh insight into mosquito-microbiota interactions. Microbiome 6, 49 (2018).
  Article PubMed PubMed Central Google Scholar
• Lloyd-Price, J., Abu-Ali, G. & Huttenhower, C. The healthy human microbiome. Genome Med. 8, 51 (2016).
  Article PubMed PubMed Central Google Scholar
• Pallen, M. J. Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections. Parasitology 141, 1856–1862 (2014).
  Article CAS PubMed Google Scholar
• Chan, J. Z. et al. Metagenomic analysis of tuberculosis in a mummy. N. Engl. J. Med. 369, 289–290 (2013).
  Article CAS PubMed Google Scholar
• Chiu, C. Y. Viral pathogen discovery. Curr. Opin. Microbiol. 16, 468–478 (2013). This review covers one of the earliest applications of metagenomic sequencing for use in the detection and discovery of novel viral pathogens.
  Article CAS PubMed PubMed Central Google Scholar
• Moustafa, A. et al. The blood DNA virome in 8,000 humans. PLOS Pathog. 13, e1006292 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Rascovan, N., Duraisamy, R. & Desnues, C. Metagenomics and the human virome in asymptomatic individuals. Annu. Rev. Microbiol. 70, 125–141 (2016).
  Article CAS PubMed Google Scholar
• Somasekar, S. et al. Viral surveillance in serum samples from patients with acute liver failure by metagenomic next-generation sequencing. Clin. Infect. Dis. 65, 1477–1485 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Hampton-Marcell, J. T., Lopez, J. V. & Gilbert, J. A. The human microbiome: an emerging tool in forensics. Microb. Biotechnol. 10, 228–230 (2017).
  Article PubMed PubMed Central Google Scholar
• Miller, M. B. & Tang, Y. W. Basic concepts of microarrays and potential applications in clinical microbiology. Clin. Microbiol. Rev. 22, 611–633 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Streit, W. R. & Schmitz, R. A. Metagenomics—the key to the uncultured microbes. Curr. Opin. Microbiol. 7, 492–498 (2004).
  Article CAS PubMed Google Scholar
• Rota, P. A. et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300, 1394–1399 (2003).
  Article CAS PubMed Google Scholar
• Sotiriou, C. & Pusztai, L. Gene-expression signatures in breast cancer. N. Engl. J. Med. 360, 790–800 (2009).
  Article CAS PubMed Google Scholar
• Palmer, C. et al. Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res. 34, e5 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Voelkerding, K. V., Dames, S. A. & Durtschi, J. D. Next-generation sequencing: from basic research to diagnostics. Clin. Chem. 55, 641–658 (2009).
  Article CAS PubMed Google Scholar
• Wilson, M. R. et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N. Engl. J. Med. 370, 2408–2417 (2014). This case report describes the first use of clinical metagenomics for actionable diagnosis and treatment in a critically ill patient with a mysterious neurological infection.
  Article CAS PubMed PubMed Central Google Scholar
• Nutman, A. & Marchaim, D. ‘How to do it’-molecular investigation of a hospital outbreak. Clin. Microbiol. Infect. https://doi.org/10.1016/j.cmi.2018.09.017 (2018).
  Article PubMed Google Scholar
• Loman, N. J. et al. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 309, 1502–1510 (2013). This study describes the use of metagenomic sequencing and comparative bacterial genome analysis to investigate a global public health outbreak.
  Article CAS PubMed Google Scholar
• Oniciuc, E. A. et al. The present and future of whole genome sequencing (WGS) and whole metagenome sequencing (WMS) for surveillance of antimicrobial resistant microorganisms and antimicrobial resistance genes across the food chain. Genes (Basel) 9, E268 (2018).
  Google Scholar
• Stefan, C., Koehler, J. & Minogue, T. Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes. Sci. Rep. 6, 25904 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Gliddon, H. D., Herberg, J. A., Levin, M. & Kaforou, M. Genome-wide host RNA signatures of infectious diseases: discovery and clinical translation. Immunology 153, 171–178 (2018).
  Article CAS PubMed Google Scholar
• Langelier, C. et al. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc. Natl Acad. Sci. USA 115, E12353–E12362 (2018). This study integrates microbial metagenomic and host response NGS data to improve accuracy in diagnosing lower respiratory tract infections.
  Article CAS PubMed PubMed Central Google Scholar
• Lin, L. & Zhang, J. Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol. 18, 2 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Greninger, A. The challenge of diagnostic metagenomics. Expert Rev. Mol. Diagn. 18, 605–615 (2018).
  Article CAS PubMed Google Scholar
• Khare, R. et al. Comparative evaluation of two commercial multiplex panels for detection of gastrointestinal pathogens by use of clinical stool specimens. J. Clin. Microbiol. 52, 3667–3673 (2014).
  Article PubMed PubMed Central Google Scholar
• Leber, A. L. et al. Multicenter evaluation of BioFire FilmArray meningitis/encephalitis panel for detection of bacteria, viruses, and yeast in cerebrospinal fluid specimens. J. Clin. Microbiol. 54, 2251–2261 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Ruggiero, P., McMillen, T., Tang, Y. W. & Babady, N. E. Evaluation of the BioFire FilmArray respiratory panel and the GenMark eSensor respiratory viral panel on lower respiratory tract specimens. J. Clin. Microbiol. 52, 288–290 (2014).
  Article PubMed PubMed Central Google Scholar
• Tang, Y. W. et al. Clinical evaluation of the Luminex NxTAG respiratory pathogen panel. J. Clin. Microbiol. 54, 1912–1914 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Lefterova, M. I., Suarez, C. J., Banaei, N. & Pinsky, B. A. Next-generation sequencing for infectious disease diagnosis and management: a report of the association for molecular pathology. J. Mol. Diagn. 17, 623–634 (2015).
  Article CAS PubMed Google Scholar
• Blauwkamp, T. A. et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat. Microbiol. https://doi.org/10.1038/s41564-018-0349-6 (2019). This paper describes the analytical and clinical validation of an mNGS assay for sepsis.
  Article PubMed Google Scholar
• Deurenberg, R. H. et al. Application of next generation sequencing in clinical microbiology and infection prevention. J. Biotechnol. 243, 16–24 (2017).
  Article CAS PubMed Google Scholar
• Gargis, A. S., Kalman, L. & Lubin, I. M. Assuring the quality of next-generation sequencing in clinical microbiology and public health laboratories. J. Clin. Microbiol. 54, 2857–2865 (2016).
  Article PubMed PubMed Central Google Scholar
• Miller, S. et al. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Preprint at bioRxiv https://doi.org/10.1101/330381 (2019). This paper describes the clinical validation of an mNGS assay for diagnosis of meningitis and encephalitis from cerebrospinal fluid.
  Article Google Scholar
• Schlaberg, R. et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch. Pathol. Lab Med. 141, 776–786 (2017). This paper summarizes the clinical validation of two mNGS assays for neurological infections and pneumonia.
  Article CAS PubMed Google Scholar
• Rampini, S. K. et al. Broad-range 16S rRNA gene polymerase chain reaction for diagnosis of culture-negative bacterial infections. Clin. Infect. Dis. 53, 1245–1251 (2011).
  Article CAS PubMed Google Scholar
• Salipante, S. J. et al. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLOS ONE 8, e65226 (2013). This paper describes the use of targeted 16S rRNA NGS for diagnosis of polymicrobial bacterial infections.
  Article CAS PubMed PubMed Central Google Scholar
• Wagner, K., Springer, B., Pires, V. P. & Keller, P. M. Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture. Sci. Rep. 8, 6964 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Basein, T. et al. Clinical utility of universal PCR and its real-world impact on patient management. Open Forum Infect. Dis 4, S627 (2017).
  Article PubMed Central Google Scholar
• Corless, C. E. et al. Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J. Clin. Microbiol. 38, 1747–1752 (2000).
  CAS PubMed PubMed Central Google Scholar
• Quick, J. et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat. Protoc. 12, 1261–1276 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Faria, N. R. et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546, 406–410 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Grubaugh, N. et al. Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature 546, 401–405 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Thézé, J. et al. Genomic epidemiology reconstructs the introduction and spread of Zika virus in central America and Mexico. Cell Host Microbe 23, 855–864 (2018). This study introduces the use of the metagenomic sequencing with spiked primer enrichment technique for simultaneous targeted and untargeted pathogen detection and genome assembly.
  Article CAS PubMed PubMed Central Google Scholar
• Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228–232 (2016). This study describes deployment of a portable nanopore sequencer for real-time actionable sequencing of clinical samples during the Ebola outbreak in West Africa.
  Article CAS PubMed PubMed Central Google Scholar
• Garcia-Garcia, G. et al. Assessment of the latest NGS enrichment capture methods in clinical context. Sci. Rep. 6, 20948 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Briese, T. et al. Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis. mBio 6, e01491-15 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Metsky, H. C. et al. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat. Biotechnol. 37, 160–168 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Naccache, S. et al. Distinct Zika virus lineage in Salvador, Bahia, Brazil. Emerg. Infect. Dis. 22, 1788–1792 (2016).
  Article PubMed PubMed Central Google Scholar
• Wylie, T. N., Wylie, K. M., Herter, B. N. & Storch, G. A. Enhanced virome sequencing using targeted sequence capture. Genome Res. 25, 1910–1920 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Presidential Council. National action plan for combating antibiotic-resistant bacteria (The White House, Washington, 2015).
• Quince, C., Walker, A., Simpson, J., Loman, N. & Segata, N. Shotgun metagenomics, from sampling to analysis. Nat. Biotechnol. 35, 833–844 (2017).
  Article CAS PubMed Google Scholar
• Snitkin, E. et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci. Transl Med. 4, 148ra116 (2012). This study is the first to demonstrate the potential of whole-genome bacterial sequencing using NGS to track transmission of a hospital outbreak of carbapenem-resistant K. pneumoniae.
  Article PubMed PubMed Central Google Scholar
• Naccache, S. et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 24, 1180–1192 (2014). This paper describes the sequence-based ultrarapid pathogen identification metagenomic analysis pipeline for use in infectious disease diagnostics.
  Article CAS PubMed PubMed Central Google Scholar
• Hong, D. et al. Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease. Diagn. Microbiol. Infect. Dis. 92, 210–213 (2018).
  Article CAS PubMed Google Scholar
• Schlaberg, R. et al. Viral pathogen detection by metagenomics and pan-viral group polymerase chain reaction in children with pneumonia lacking identifiable etiology. J. Infect. Dis. 215, 1407–1415 (2017).
  Article CAS PubMed Google Scholar
• Jovel, J. et al. Characterization of the gut microbiome using 16S or shotgun metagenomics. Front. Microbiol. 7, 459 (2016).
  Article PubMed PubMed Central Google Scholar
• Young, V. The role of the microbiome in human health and disease: an introduction for clinicians. BMJ 356, j831 (2017).
  Article PubMed Google Scholar
• Samarkos, M., Mastrogianni, E. & Kampouropoulou, O. The role of gut microbiota in Clostridium difficile infection. Eur. J. Intern. Med. 50, 28–32 (2018).
  Article PubMed Google Scholar
• Shogbesan, O. et al. A Systematic review of the efficacy and safety of fecal microbiota transplant for Clostridium difficile infection in immunocompromised patients. Can. J. Gastroenterol. Hepatol. 2018, 1394379 (2018).
  Article PubMed PubMed Central Google Scholar
• van Nood, E. et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N. Engl. J. Med. 368, 407–415 (2013). This paper demonstrates the therapeutic potential of manipulating the microbiome with donor faecal transplantation to treat refractory C. difficile disease.
  Article CAS PubMed Google Scholar
• Boulangé, C., Neves, A., Chilloux, J., Nicholson, J. & Dumas, M. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Med. 8, 42 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Kukurba, K. & Montgomery, S. RNA sequencing and analysis. Cold Spring Harb. Protoc. 2015, 951–969 (2015).
  Article PubMed PubMed Central Google Scholar
• Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009). This Review provides an overview of RNA-seq for transcriptomics and its applications.
  Article CAS PubMed PubMed Central Google Scholar
• Ahn, S. et al. Gene expression-based classifiers identify Staphylococcus aureus infection in mice and humans. PLOS ONE 8, e48979 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Bouquet, J. et al. Longitudinal transcriptome analysis reveals a sustained differential gene expression signature in patients treated for acute Lyme disease. mBio 7, e00100–00116 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Zaas, A., Aziz, H., Lucas, J., Perfect, J. & Ginsburg, G. Blood gene expression signatures predict invasive candidiasis. Sci. Transl Med. 2, 21ra17 (2010).
  Article CAS PubMed Google Scholar
• Anderson, S. et al. Diagnosis of childhood tuberculosis and host RNA expression in Africa. N. Engl. J. Med. 370, 1712–1723 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Singhania, A. et al. A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection. Nat. Commun. 9, 2308 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Zak, D. E. et al. A blood RNA signature for tuberculosis disease risk: a prospective cohort study. Lancet 387, 2312–2322 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• HIPC-CHI Signatures Project Team & HIPC-I Consortium. Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses. Sci. Immunol. 2, eaal4656 (2017).
  Article PubMed Central Google Scholar
• Woods, C. et al. A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2. PLOS ONE 8, e52198 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Zaas, A. et al. Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans. Cell Host Microbe 6, 207–217 (2009). This paper is one of the earliest to demonstrate the potential use of host gene expression signatures to diagnose infections.
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, Y. et al. Identifying and analyzing different cancer subtypes using RNA-seq data of blood platelets. Oncotarget 8, 87494–87511 (2017).
  PubMed PubMed Central Google Scholar
• McClain, M. et al. A Genomic signature of influenza infection shows potential for presymptomatic detection, guiding early therapy, and monitoring clinical responses. Open Forum Infect. Dis 3, ofw007 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Sweeney, T., Wong, H. & Khatri, P. Robust classification of bacterial and viral infections via integrated host gene expression diagnostics. Sci. Transl Med. 8, 346ra391 (2016).
  Article CAS Google Scholar
• Emerson, J. B. et al. Schrodinger’s microbes: tools for distinguishing the living from the dead in microbial ecosystems. Microbiome 5, 86 (2017).
  Article PubMed PubMed Central Google Scholar
• Banerjee, A. et al. RNA-seq analysis of peripheral blood mononuclear cells reveals unique transcriptional signatures associated with disease progression in dengue patients. Transl Res. 186, 62–78 (2017).
  Article CAS PubMed Google Scholar
• Lee, H. J. et al. Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria. Sci. Transl Med. 10, eaar3619 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Marques, A. Laboratory diagnosis of Lyme disease: advances and challenges. Infect. Dis. Clin. North Am. 29, 295–307 (2015).
  Article PubMed PubMed Central Google Scholar
• Debiasi, R. & Tyler, K. Molecular methods for diagnosis of viral encephalitis. Clin. Microbiol. Rev. 17, 903–925 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Landry, M. & St George, K. Laboratory diagnosis of Zika virus infection. Arch. Pathol. Lab Med. 141, 60–67 (2017).
  Article PubMed Google Scholar
• Nakagawa, H. & Fujita, M. Whole genome sequencing analysis for cancer genomics and precision medicine. Cancer Sci. 109, 513–522 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Feng, H., Shuda, M., Chang, Y. & Moore, P. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319, 1096–1100 (2008). This paper describes the discovery of a novel polyomavirus associated with a rare skin cancer using NGS.
  Article CAS PubMed PubMed Central Google Scholar
• Allegretti, M. et al. Tearing down the walls: FDA approves next generation sequencing (NGS) assays for actionable cancer genomic aberrations. J. Exp. Clin. Cancer Res. 37, 47 (2018).
  Article PubMed PubMed Central Google Scholar
• Saha, A., Kaul, R., Murakami, M. & Robertson, E. S. Tumor viruses and cancer biology: modulating signaling pathways for therapeutic intervention. Cancer Biol. Ther. 10, 961–978 (2010).
  Article CAS PubMed Google Scholar
• Kanwal, F. et al. Risk of hepatocellular cancer in HCV patients treated with direct-acting antiviral agents. Gastroenterology 153, 996–1005 (2017).
  Article CAS PubMed Google Scholar
• Burd, E. Validation of laboratory-developed molecular assays for infectious diseases. Clin. Microbiol. Rev. 23, 550–576 (2010). This paper summarizes the essential requirements for validation of infectious disease assays in a clinical laboratory.
  Article CAS PubMed PubMed Central Google Scholar
• Food and Drug Administration. Infectious disease next generation sequencing based diagnostic devices: microbial identification and detection of antimicrobial resistance and virulence markers (FDA, 2016). This draft guidance from the FDA covers considerations for validation and approval of sequencing-based diagnostic devices for infectious diseases.
• DuPont, H. L., Levine, M. M., Hornick, R. B. & Formal, S. B. Inoculum size in shigellosis and implications for expected mode of transmission. J. Infect. Dis. 159, 1126–1128 (1989).
  Article CAS PubMed Google Scholar
• Corman, V. M. et al. Assay optimization for molecular detection of Zika virus. Bull. World Health Organ. 94, 880–892 (2016).
  Article PubMed PubMed Central Google Scholar
• Hasan, M. et al. Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing. J. Clin. Microbiol. 54, 919–927 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Matranga, C. et al. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol. 15, 519 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• O’Neil, D., Glowatz, H. & Schlumpberger, M. Ribosomal RNA depletion for efficient use of RNA-seq capacity. Curr. Protoc. Mol. Biol. 103, 4.19.1–4.19.8 (2013).
  Google Scholar
• Gu, W. 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. 17, 41 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Feehery, G. et al. A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PLOS ONE 8, e76096 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Charalampous, T. et al. Rapid diagnosis of lower respiratory infection using nanopore-based clinical metagenomics. Preprint at bioRxiv https://doi.org/10.1101/387548 (2018).
  Article Google Scholar
• Thoendel, M. et al. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing. J. Microbiol. Methods 127, 141–145 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Salter, S. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Li, R. et al. Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water. Sci. Rep. 7, 5752 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Naccache, S. et al. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Clin. Infect. Dis. 60, 919–923 (2015).
  Article PubMed PubMed Central Google Scholar
• Strong, M. et al. Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLOS Pathog. 10, e1004437 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• McIntyre, A. et al. Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. Genome Biol. 18, 182 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Jackson, S. A., Kralj, J. G. & Lin, N. J. Report on the NIST/DHS/FDA workshop: standards for pathogen detection for biosurveillance and clinical applications (National Institute for Standards and Technology, 2018).
• Pine, P. et al. Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design. BMC Biotechnol. 16, 54 (2016).
  Article PubMed PubMed Central Google Scholar
• Avraham, R. et al. A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes. Nat. Protoc. 11, 1477–1491 (2016).
  Article PubMed Google Scholar
• Flygare, S. et al. Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol. 17, 111 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Kim, D., Song, L., Breitwieser, F. & Salzberg, S. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 26, 1721–1729 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Wood, D. & Salzberg, S. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).
  Article PubMed PubMed Central Google Scholar
• Roy, S. et al. Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: a joint recommendation of the Association for Molecular Pathology and the College of American Pathologists. J. Mol. Diagn. 20, 4–27 (2018). This draft guidance from the Association for Molecular Pathology and College of American Pathologists reviews standards and guidelines for validation of NGS bioinformatics pipelines.
  Article CAS PubMed Google Scholar
• Goldberg, B., Sichtig, H., Geyer, C., Ledeboer, N. & Weinstock, G. Making the leap from research laboratory to clinic: challenges and opportunities for next-generation sequencing in infectious disease diagnostics. mBio 6, e01888-15 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Goodacre, N., Aljanahi, A., Nandakumar, S., Mikailov, M. & Khan, A. S. A reference viral database (RVDB) to enhance bioinformatics analysis of high-throughput sequencing for novel virus detection. mSphere 3, e00069-18 (2018).
  Article PubMed PubMed Central Google Scholar
• May, M. Automated sample preparation. NIST Special Publication 1222, 1–17 (2016).
  Article Google Scholar
• Levy, S. E. & Myers, R. M. Advancements in next-generation sequencing. Annu. Rev. Genomics Hum. Genet. 17, 95–115 (2016).
  Article CAS PubMed Google Scholar
• Castro-Wallace, S. L. et al. Nanopore DNA sequencing and genome assembly on the International Space Station. Sci. Rep. 7, 18022 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Simner, P. J., Miller, S. & Carroll, K. C. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clin. Infect. Dis. 66, 778–788 (2018). This is a concise yet comprehensive review of some of the clinical applications of mNGS for diagnosis of infectious diseases.
  Article CAS PubMed Google Scholar
• Afshinnekoo, E., Ahsanuddin, S. & Mason, C. E. Globalizing and crowdsourcing biomedical research. Br. Med. Bull. 120, 27–33 (2016).
  Article PubMed Google Scholar
• Brooks, J. P. et al. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol. 15, 66 (2015).
  Article PubMed PubMed Central Google Scholar
• Boja, E. et al. Right data for right patient-a precisionFDA NCI-CPTAC multi-omics mislabeling challenge. Nat. Med. 24, 1301–1302 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• McDonald, D. et al. American gut: an open platform for citizen science microbiome research. mSystems 3, e00031-18 (2018).
  Article PubMed PubMed Central Google Scholar
• Babayan, A. & Pantel, K. Advances in liquid biopsy approaches for early detection and monitoring of cancer. Genome Med. 10, 21 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Norton, M. E. et al. Cell-free DNA analysis for noninvasive examination of trisomy. N. Engl. J. Med. 372, 1589–1597 (2015).
  Article CAS PubMed Google Scholar
• Jain, M., Olsen, H., Paten, B. & Akeson, M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 17, 239 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Greninger, A. et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 7, 99 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Mitsuhashi, S. et al. A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer. Sci. Rep. 7, 5657 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Kerkhof, L., Dillon, K., Häggblom, M. & McGuinness, L. Profiling bacterial communities by MinION sequencing of ribosomal operons. Microbiome 5, 116 (2017).
  Article PubMed PubMed Central Google Scholar
• Tyler, A. et al. Evaluation of Oxford Nanopore’s MinION sequencing device for microbial whole genome sequencing applications. Sci. Rep. 8, 10931 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Oikonomopoulos, S., Wang, Y., Djambazian, H., Badescu, D. & Ragoussis, J. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations. Sci. Rep. 6, 31602 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Street, T. et al. Molecular diagnosis of orthopedic-device-related infection directly from sonication fluid by metagenomic sequencing. J. Clin. Microbiol. 55, 2334–2347 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Gardy, J. & Loman, N. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat. Rev. Genet. 19, 9–20 (2018). This Review describes efforts to deploy genomics globally for real-time, global pathogen surveillance.
  Article CAS PubMed Google Scholar
• Loose, M., Malla, S. & Stout, M. Real-time selective sequencing using nanopore technology. Nat. Methods 13, 751–754 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Stakaityte, G. et al. Merkel cell polyomavirus: molecular insights into the most recently discovered human tumour virus. Cancers (Basel) 6, (1267–1297 (2014).
  Google Scholar
• Brinkmann, A. et al. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics. PLOS Negl. Trop. Dis. 11, e0006075 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Quan, J. et al. FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Preprint at bioRxiv https://doi.org/10.1101/426338 (2018).
  Article Google Scholar
• Langelier, C. et al. Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients. Am. J. Respir. Crit. Care Med. 197, 524–528 (2018).
  Article PubMed PubMed Central Google Scholar
• Zinter, M. S. et al. Pulmonary metagenomic sequencing suggests missed infections in immunocompromised children. Clin. Infect. Dis https://doi.org/10.1093/cid/ciy802 (2018).
  Article Google Scholar
• Zhou, Y. et al. Metagenomic approach for identification of the pathogens associated with diarrhea in stool specimens. J. Clin. Microbiol. 54, 368–375 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Ivy, M. I. et al. Direct detection and identification of prosthetic joint infection pathogens in synovial fluid by metagenomic shotgun sequencing. J. Clin. Microbiol. 56, e00402-18 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Milani, C. et al. Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study. Sci. Rep. 6, 25945 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Tang, K. W. & Larsson, E. Tumour virology in the era of high-throughput genomics. Philos. Trans. R. Soc. Lond. B Biol. Sci. 372, 20160265 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Aravanis, A. M., Lee, M. & Klausner, R. D. Next-generation sequencing of circulating tumor DNA for early cancer detection. Cell 168, 571–574 (2017).
  Article CAS PubMed Google Scholar