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References from Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation. Local targets link to admitted publications; unresolved targets remain external evidence.
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Unresolved reference
External reference
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Characterization of the gut microbiome using 16S or shotgun metagenomics
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Characterization of the 18S rRNA gene for designing universal eukaryote specific primers
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ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases
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Towards standards for human fecal sample processing in metagenomic studies
2017 · External reference
Shotgun metagenomics, from sampling to analysis
2017 · External reference
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16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform
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The challenge and potential of metagenomics in the clinic
2016 · External reference
Impact of sample type and DNA isolation procedure on genomic inference of microbiome composition
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Assessing the accuracy of quantitative molecular microbial profiling
10.3390/ijms151121476 · 2014 · External reference
Application of metagenomic sequencing to food safety: detection of Shiga Toxin-producing Escherichia coli on fresh bagged spinach
10.1128/aem.02601-15 · 2015 · External reference
Primer and platform effects on 16S rRNA tag sequencing
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Unresolved reference
2010 · External reference
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CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
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Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
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2016 · External reference
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10.1128/aem.01541-09 · External reference
Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology
10.1099/00207713-44-4-846 · 1994 · External reference
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
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10.1128/aem.03006-05
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Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases
10.1093/cid/cix881 · 2018 · External reference
Multiplexed molecular diagnostics for respiratory, gastrointestinal, and central nervous system infections
10.1093/cid/ciw494 · 2016 · External reference
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Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach
10.1128/jcm.00273-11 · 2011 · External reference
Is there still room for novel viral pathogens in pediatric respiratory tract infections?
10.1371/journal.pone.0113570 · 2014 · External reference
Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains
10.1016/j.diagmicrobio.2015.06.017 · 2015 · External reference
Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel
10.1128/jcm.03060-15 · 2016 · External reference
Herpes zoster laryngitis in a patient treated with fingolimod
10.1016/j.jiac.2016.07.011 · 2016 · External reference
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Metataxonomic and metagenomic approaches vs. culture-based techniques for clinical pathology
10.3389/fmicb.2016.00484 · 2016 · External reference
Metagenomics study of viral pathogens in undiagnosed respiratory specimens and identification of Human Enteroviruses at a Thailand hospital
10.4269/ajtmh.16-0062 · 2016 · External reference
Rapid pathogen identification in bacterial pneumonia using real-time metagenomics
10.1164/rccm.201703-0537le · 2017 · External reference
Metagenomic analysis identified human Rhinovirus B91 infection in an adult suffering from severe pneumonia
10.1164/rccm.201609-1908le · 2017 · External reference
A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach
10.1007/s00705-017-3367-4 · 2017 · External reference
10.1093/infdis/jix148
10.1093/infdis/jix148 · External reference
Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique
10.1007/s11427-016-0244-8 · 2017 · External reference
Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection
10.1371/journal.pone.0177340 · 2017 · External reference
Incidence, risk factors, and attributable mortality of secondary infections in the intensive care unit after admission for sepsis
10.1001/jama.2016.2691 · 2016 · External reference
Targeted next-generation sequencing of the 16S–23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species
10.1038/s41598-017-03458-6 · 2017 · External reference
A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
10.1038/s41598-017-05772-5 · 2017 · External reference
Thoracic empyema caused by Prevotella spp. diagnosed using 16S rDNA sequence analysis
10.1111/crj.12106 · 2015 · External reference
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10.1186/1471-2105-10-421 · 2009 · External reference
10.1016/s0022-2836(05)80360-2
10.1016/s0022-2836(05)80360-2 · External reference
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External reference
Comparison of two NGS platforms for metagenomic analysis of clinical samples
2017 · External reference
Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients
2017 · External reference
Actionable diagnosis of Neuroleptospirosis by next-generation sequencing
10.1056/nejmoa1401268 · 2014 · External reference
Acute West Nile Virus meningoencephalitis diagnosed via metagenomic deep sequencing of Cerebrospinal Fluid in a renal transplant patient
10.1111/ajt.14058 · 2017 · External reference
Neurobrucellosis: unexpected answer from metagenomic next-generation sequencing
2016 · External reference
Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing
10.1093/cid/ciu912 · 2015 · External reference
Hepatitis E Virus–associated meningoencephalitis in a lung transplant recipient diagnosed by clinical metagenomic sequencing
10.1093/ofid/ofx121 · 2017 · External reference
Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing
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Diagnosis of fatal human case of St. Louis encephalitis virus infection by metagenomic sequencing, California, 2016
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Human pegivirus detected in a patient with severe encephalitis using a metagenomic pan-virus array
10.1016/j.jcv.2016.01.013 · 2016 · External reference
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10.1016/s0140-6736(16)30386-5 · External reference
Fatal Psychrobacter sp. infection in a pediatric patient with meningitis identified by metagenomic next-generation sequencing in cerebrospinal fluid
10.1007/s00203-015-1168-2 · 2016 · External reference
Central nervous system infection diagnosis by next-generation sequencing: a glimpse into the future?
2017 · External reference
Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: unexpected detection of human herpesvirus 1 while searching for RNA pathogens
10.1016/j.jviromet.2015.09.010 · 2015 · External reference
Rapid detection of Powassan virus in a patient with encephalitis by metagenomic sequencing
2017 · External reference
Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system
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Comprehensive metagenomic approach for detecting causative microorganisms in culture-negative infective endocarditis
10.1016/j.ijcard.2013.12.197 · 2014 · External reference
Metagenomic analysis for detecting pathogens in culture-negative infective endocarditis
10.1016/j.jiac.2015.08.007 · 2015 · External reference
Viral communities associated with human pericardial fluids in idiopathic pericarditis
10.1371/journal.pone.0093367 · 2014 · External reference
The development and application of a molecular community profiling strategy to identify polymicrobial bacterial DNA in the whole blood of septic patients
10.1186/s12866-015-0557-7 · 2015 · External reference
Identification by highly sensitive 16S metagenomic sequencing of an unusual case of polymicrobial bacteremia
10.1016/j.jinf.2017.05.005 · 2017 · External reference
Diagnosis of bacterial bloodstream infections: a 16S metagenomics approach
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Next-generation sequencing diagnostics of bacteremia in septic patients
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Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
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Metagenomic approach for identification of the pathogens associated with diarrhea in stool specimens
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Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Cote d'Ivoire: a proof-of-concept study
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Towards diagnostic metagenomics of Campylobacter in fecal samples
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Rapid MinION metagenomic profiling of the preterm infant gut microbiota to aid in pathogen diagnostics
2017 · External reference
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Metagenomic DNA sequencing for the diagnosis of intraocular infections
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Diagnosis of a malayan filariasis case using a shotgun diagnostic metagenomics assay
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Identifying corneal infections in formalin-fixed specimens using next generation sequencing
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Pathogens in urine from a female patient with overactive bladder syndrome detected by culture-independent high throughput sequencing: a case report
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Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing
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A novel prosthetic joint infection pathogen, Mycoplasma salivarium, identified by metagenomic shotgun sequencing
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Molecular diagnosis of orthopedic-device-related infection directly from sonication fluid by metagenomic sequencing
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Comprehensive diagnosis of bacterial infection associated with acute cholecystitis using metagenomic approach
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Messages from the first International Conference on Clinical Metagenomics (ICCMg)
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