Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

Hasman, Henrik; Saputra, Dhany; Sicheritz-Pontén, Thomas; Lund, Ole; Svendsen, Christina Aaby; Frimodt‐Møller, Niels; Aarestrup, Frank Møller

doi:10.1128/jcm.01369-14

Cited by 72 publications

(96 citation statements)

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“…Rapid WGS has also been utilized to detect and characterize bacteria directly from clinical samples, to identify bacteria from polymicrobial urine samples, as well as detect pathogenic bacteria from culture-negative samples. [20] Also in a recent case report, NGS was used to diagnose a patient with a rare bacterial meningoencephalitis caused by leptospirosis, a condition that was undetectable using current clinical assays. [21] Whole genome sequencing provides the highest resolution possible for identification and discrimination of bacteria; and may in fact revolutionise bacterial systematics and taxonomy.…”

Section: Detection and Identification Of Bacteriamentioning

confidence: 99%

Bacterial whole genome sequencing: The future of clinical bacteriology

Aliyu¹

2014

Ann Nigerian Med

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Section: Detection and Identification Of Bacteriamentioning

confidence: 99%

Bacterial whole genome sequencing: The future of clinical bacteriology

Aliyu¹

2014

Ann Nigerian Med

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“…The genome sequence assemblies were analysed using the Bacterial Analysis Pipeline 5 . To determine the taxonomic identity of isolate the pipeline utilizes a k-mer based approach 8 . Subsequently, a genomic MLSTtyping is performed based on the allele and sequence profiles from PubMLST 9 .…”

Section: Whole Genome Sequence Analysismentioning

confidence: 99%

“…Intravitreal injection with anti-vascular endothelial growth factor (anti-VEGF) has revolutionized 59 the treatment of wet age-related macular degeneration, as well as diabetic maculopathy, and retinal 60 vein occlusions during the last decade. It is the fastest growing procedure in ophthalmology and it 61 was estimated that the number of intravitreal injections in the US would reach nearly 6 million in 62 2016 8 . The risk of endophthalmitis after intravitreal injection is approximately 4.9 per 10,000 63 intravitreal injections 9 .…”

mentioning

confidence: 99%

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

Kirstahler

Bjerrum

Friis-Møller

et al. 2017

Preprint

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Advances in genomics have the potential to revolutionize clinical diagnostics. Here, we 20 examine the microbiome of vitreous (intraocular body fluid) from patients who developed 21 endophthalmitis following cataract surgery or intravitreal injection. Endophthalmitis is an 22 inflammation of the intraocular cavity and can lead to a permanent loss of vision. As 23 controls, we included vitreous from endophthalmitis-negative patients, balanced salt 24 solution used during vitrectomy, and DNA extraction blanks. We compared two DNA 25 isolation procedures and found that an ultraclean production of reagents appeared to 26 reduce background DNA in these low microbial biomass samples. We created a curated 27 microbial genome database (>5700 genomes) and designed a metagenomics workflow 28 with filtering steps to reduce DNA sequences originating from: i) human hosts, ii) 29 ambiguousness/contaminants in public microbial reference genomes, and iii) the 30 environment. Our metagenomic read classification revealed in nearly all cases the same 31 microorganism than was determined in cultivation-and mass spectrometry-based 32 analyses. For some patients, we identified the sequence type of the microorganism and 33 antibiotic resistance genes through analyses of whole genome sequence (WGS) 34 assemblies of isolates and metagenomic assemblies. Together, we conclude that 35 genomics-based analyses of human ocular body fluid specimens can provide actionable 36 information relevant to infectious disease management.

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“…High (99.7%) accordance between pheno-and genotypic resistance was demonstrated between 200 bacterial isolates belonging to four different species, 19 and the same predicted susceptibility profiles have been obtained using direct sequencing on clinical specimens and sequencing of single isolates. 20 The disadvantage of WGS is that it fails to reveal as yet undescribed resistance genotypes, and the actual phenotype may not always be deduced from sequencing data. For example, detection of nonfunctional pseudogenes or repressed efflux systems may lead to false positive (R) results.…”

Section: Antimicrobial Susceptibility Testingmentioning

confidence: 99%

Diagnostic microbiology in veterinary dermatology: present and future

Guardabassi

Damborg

Stamm

et al. 2017

Veterinary Dermatology

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Background -The microbiology laboratory can be perceived as a service provider rather than an integral part of the healthcare team.Objectives -The aim of this review is to discuss the current challenges of providing a state-of-the-art diagnostic veterinary microbiology service including the identification (ID) and antimicrobial susceptibility testing (AST) of key pathogens in veterinary dermatology.Methods -The Study Group for Veterinary Microbiology (ESGVM) of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) identified scientific, technological, educational and regulatory issues impacting the predictive value of AST and the quality of the service offered by microbiology laboratories.Results -The advent of mass spectrometry has significantly reduced the time required for ID of key pathogens such as Staphylococcus pseudintermedius. However, the turnaround time for validated AST methods has remained unchanged for many years. Beyond scientific and technological constraints, AST methods are not harmonized and clinical breakpoints for some antimicrobial drugs are either missing or inadequate. Small laboratories, including in-clinic laboratories, are usually not adequately equipped to run up-to-date clinical microbiologic diagnostic tests.Conclusions and clinical importance -ESGVM recommends the use of laboratories employing mass spectrometry for ID and broth micro-dilution for AST, and offering assistance by expert microbiologists on pre-and post-analytical issues. Setting general standards for veterinary clinical microbiology, promoting antimicrobial stewardship, and the development of new, validated and rapid diagnostic methods, especially for AST, are among the missions of ESGVM.

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Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

Abstract: A row for sample number 16 was erroneously included, and thus the agreement between the results for single isolates and direct sequencing is not correct for any of the subsequently listed samples. The body of the table should read as follows:

Cited by 72 publications

References 0 publications

Bacterial whole genome sequencing: The future of clinical bacteriology

Bacterial whole genome sequencing: The future of clinical bacteriology

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

Diagnostic microbiology in veterinary dermatology: present and future

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