A novel diagnostic approach may reduce inappropriate antibiotic use for acute respiratory infections

Hudson, Lori L.; Woods, Christopher W.; Ginsburg, Geoffrey S.

doi:10.1586/14787210.2014.881717

Cited by 5 publications

(3 citation statements)

References 16 publications

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“…Host gene expression profiling, part of Taxonomer’s integrated analysis architecture, is of growing interest for infectious diseases testing [ 21 ]. While host gene expression profiles can differentiate viral from bacterial infections using blood samples [ 17 – 19 ], Taxonomer enables simultaneous pathogen detection and gene expression profiling from the site of infection.…”

Section: Discussionmentioning

confidence: 99%

“…procalcitonin), or microarray-based host transcript expression profiling from blood leukocytes [ 17 – 19 ]. The greater sensitivity and unbiased nature of RNA sequencing (RNA-seq) enables simultaneous pathogen detection and host-expression response profiling, which in theory could be used to better inform treatment, potentially overcoming many of the limitations of current approaches [ 20 , 21 ], even in the absence of a definitive diagnosis of a pathogen.…”

Section: Introductionmentioning

confidence: 99%

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Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling

et al. 2016

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BackgroundHigh-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption.ResultsWe present Taxonomer, an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. To facilitate data-sharing across geographic distances in outbreak settings, Taxonomer is publicly available through a web-based user interface.ConclusionsTaxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0969-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling

et al. 2016

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“…Approximately 75% of all antibiotics prescribed in the ambulatory setting are for acute respiratory tract (ARI) infections, and albeit their use is associated with a significant symptomatic effect, their use is inappropriate because the vast majority of these infections are viral [2]. In addition, clinical and microbiological evaluations are neither sensitive nor specific to differentiate bacterial from viral respiratory tract infections [3], and thus of limited value for directing therapy.…”

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confidence: 99%