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References
- Clinical metagenomic next-generation sequencing for pathogen detection.Annu Rev Pathol. 2019; 14: 319-338
- An outbreak of colistin-resistant Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae in The Netherlands (July to December 2013), with inter-institutional spread.Eur J Clin Microbiol Infect Dis. 2015; 34: 1647-1655
- Characterization of a CTX-M-15 producing Klebsiella pneumoniae outbreak strain assigned to a novel sequence type (1427).Front Microbiol. 2015; 6: 1250
- Applying rapid whole-genome sequencing to predict phenotypic antimicrobial susceptibility testing results among carbapenem-resistant Klebsiella pneumoniae clinical isolates.Antimicrob Agents Chemother. 2019; 63 ([pii:e01923-18])
- Actionable diagnosis of neuroleptospirosis by next-generation sequencing.N Engl J Med. 2014; 370: 2408-2417
- Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples.J Clin Microbiol. 2015; 53: 2230-2237
- Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples.J Clin Microbiol. 2017; 55: 1285-1298
- Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum.Int J Infect Dis. 2017; 62: 44-46
- Outbreak of adenovirus in a neonatal intensive care unit: critical importance of equipment cleaning during inpatient ophthalmologic examinations.Ophthalmology. 2019; 126: 137-143
- Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.Proc Natl Acad Sci U S A. 2012; 109: 3065-3070
- Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation.Clin Infect Dis. 2016; 63: 380-386
- Antibiotic/antimicrobial resistance 2019.(Available at:) (Accessed January 3, 2019)
- Diverse sources of C. difficile infection identified on whole-genome sequencing.N Engl J Med. 2013; 369: 1195-1205
- Whole-genome sequencing to determine origin of multinational outbreak of Sarocladium kiliense bloodstream infections.Emerg Infect Dis. 2016; 22: 476-481
- Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes.J Clin Microbiol. 2014; 52: 2365-2370
- Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-β-D-arabinose biosynthetic and utilization pathway genes.Nat Genet. 2013; 45: 1190-1197
- Genome-wide association study of HIV whole genome sequences validated using drug resistance.PLoS One. 2016; 11: e0163746
- Comparison of an in vitro diagnostic next-generation sequencing assay with Sanger sequencing for HIV-1 genotypic resistance testing.J Clin Microbiol. 2018; 56 ([pii:e00105-18])
- WGS accurately predicts antimicrobial resistance in Escherichia coli.J Antimicrob Chemother. 2015; 70: 2763-2769
- Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission.J Antimicrob Chemother. 2017; 72: 3025-3034
- Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae.Sci Rep. 2018; 8: 421
- Correlation between phenotypic antibiotic susceptibility and the resistome in Pseudomonas aeruginosa.Int J Antimicrob Agents. 2017; 50: 210-218
- Accuracy of different bioinformatics methods in detecting antibiotic resistance and virulence factors from Staphylococcus aureus whole-genome sequences.J Clin Microbiol. 2018; 56 ([pii:e01815-17])
- WGS to predict antibiotic MICs for Neisseria gonorrhoeae.J Antimicrob Chemother. 2017; 72: 1937-1947
- Using machine learning to predict antimicrobial MICs and associated genomic features for nontyphoidal Salmonella.J Clin Microbiol. 2019; 57 ([pii:e01260-18])
- Evaluation of whole-genome sequencing for mycobacterial species identification and drug susceptibility testing in a clinical setting: a large-scale prospective assessment of performance against line probe assays and phenotyping.J Clin Microbiol. 2018; 56 ([pii:e01480-17])
- Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.Lancet Infect Dis. 2015; 15: 1193-1202
- Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.Nat Commun. 2015; 6: 10063
- The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.Clin Microbiol Infect. 2017; 23: 2-22
- Application of next generation sequencing in clinical microbiology and infection prevention.J Biotechnol. 2017; 243: 16-24
- Lowering the barriers to routine whole-genome sequencing of bacteria in the clinical microbiology laboratory.J Clin Microbiol. 2018; 56 ([pii:e00813-18])
- The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility.Antimicrob Agents Chemother. 2015; 59: 427-436
- Rapid nanopore sequencing of plasmids and resistance gene detection in clinical isolates.J Clin Microbiol. 2017; 55: 3530-3543
- Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing.J Clin Microbiol. 2014; 52: 1182-1191
- Coinfection of Fusobacterium nucleatum and Actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing.J Clin Microbiol. 2014; 52: 1789-1792
- 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
- Validation of metagenomic next-generation sequencing tests for universal pathogen detection.Arch Pathol Lab Med. 2017; 141: 776-786
- Whole genome sequencing indicates Corynebacterium jeikeium comprises 4 separate genomospecies and identifies a dominant genomospecies among clinical isolates.Int J Med Microbiol. 2014; 304: 1001-1010
- Microbiome sequencing methods for studying human diseases.Methods Mol Biol. 2018; 1706: 77-90
- Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification---increased discrimination of closely related species.Sci Rep. 2017; 7: 3434
- Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis.MBio. 2015; 6 (e01491-15)
- BacCapSeq: a platform for diagnosis and characterization of bacterial infections.MBio. 2018; 9 ([pii:e02007-18])
- Investigation of the plasma virome from cases of unexplained febrile illness in Tanzania from 2013 to 2014: a comparative analysis between unbiased and VirCapSeq-VERT high-throughput sequencing approaches.mSphere. 2018; 3 ([pii:e00311-18])
- Detection of cytomegalovirus drug resistance mutations by next-generation sequencing.J Clin Microbiol. 2013; 51: 3700-3710
- Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease.Nat Microbiol. 2019; 4: 663-674
- Development and optimization of metagenomic next-generation sequencing methods for cerebrospinal fluid diagnostics.J Clin Microbiol. 2018; 56 ([pii:e00472-18])
- Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system.Neurol Neuroimmunol Neuroinflamm. 2016; 3: e251
- Chronic meningitis investigated via metagenomic next-generation sequencing.JAMA Neurol. 2018; 75: 947-955
- Rapid pathogen identification in bacterial pneumonia using real-time metagenomics.Am J Respir Crit Care Med. 2017; 196: 1610-1612
- Metagenomic approach for identification of the pathogens associated with diarrhea in stool specimens.J Clin Microbiol. 2016; 54: 368-375
- Direct detection and identification of prosthetic joint infection pathogens in synovial fluid by metagenomic shotgun sequencing.J Clin Microbiol. 2018; 56 ([pii:e00402-18])
- Identification of prosthetic joint infection pathogens using a shotgun metagenomics approach.Clin Infect Dis. 2018; 67: 1333-1338
- Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract.Nat Commun. 2018; 9: 2412
- Identifying corneal infections in formalin-fixed specimens using next generation sequencing.Invest Ophthalmol Vis Sci. 2018; 59: 280-288
- Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice.Clin Infect Dis. 2018; 67: S231-S240
- A variegated squirrel bornavirus associated with fatal human encephalitis.N Engl J Med. 2015; 373: 154-162
- A novel cause of chronic viral meningoencephalitis: Cache Valley virus.Ann Neurol. 2017; 82: 105-114
- Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.J Microbiol Methods. 2016; 127: 141-145
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.BMC Biol. 2014; 12: 87
- Diagnosis of Capnocytophaga canimorsus sepsis by whole-genome next-generation sequencing.Open Forum Infect Dis. 2016; 3: ofw144
- The challenge of diagnostic metagenomics.Expert Rev Mol Diagn. 2018; 18: 605-615
- Fatal Zika virus infection with secondary nonsexual transmission.N Engl J Med. 2016; 375: 1907-1909
- Evaluation of the CosmosID bioinformatics platform for prosthetic joint-associated sonicate fluid shotgun metagenomic data analysis.J Clin Microbiol. 2019; 57 ([pii:e01182-18])
- Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.Proc Natl Acad Sci U S A. 2018; 115: E12353-E12362
- Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases.Clin Infect Dis. 2018; 66: 778-788
- What is bioinformatics? An introduction and overview.Yearb Med Inform. 2001; : 83-99
- 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. 2018; 20: 4-27
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Footnotes
Disclosure Statement: P.J. Simner reports grants and personal fees from Accelerate Diagnostics, grants from BD Diagnostics, Inc, grants from bioMerieux, Inc, grants from Check-Points Diagnostics, BV, grants from Hardy Diagnostics, personal fees from Roche Diagnostics, personal fees from Opgen Inc, personal fees from CosmosID, outside the submitted work. P.J. Simner reports travel funds from Oxford Nanopore Technologies. S.L. Mitchell is a member of GenMark Diagnostic’s Scientific Advisory Board.
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