PATHDET is a web application for “PATHogen DETection” from extracellular DNA/RNA via high-throughput sequencing data for infectious diseases. Dev by @cikazda.
RIEM, Nagoya Univ., Japan
Joined January 2020
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You can access the PATHDET REPORT (demo).
pathdet.hgc.jp/file_upload/d…
Demo data is from S. maltophilia bacteremia.
#pathdet #demo #infections
PATHDET retweeted
Our study analyzing both pathogen detection and host gene expression in HLH patients has been published. Cell-free RNA profiling suggested mitochondrial RNAs as potential biomarkers of virus-associated HLH.
#mNGS #cfRNA #PATHDET
doi.org/10.1002/jmv.71122
PATHDET retweeted
国立感染症研究所の病原体ゲノム解析研究センターでは、感染症を引き起こす細菌・真菌・ウイルス等のゲノム配列解析と情報提供を通じて、我が国の感染症対策の基盤となるゲノム研究を推進しています。#国立健康危機管理研究機構 #JIHS #国立感染症研究所 #NIID
PATHDET retweeted
mNGS found Prevotella spp. in culture-negative pus samples in muscle abscesses.#metagenome #NGS #pathdet
sciencedirect.com/science/ar…
PATHDET retweeted
mNGS, using PATHDET pipeline, revealed Fusobacterium arthritis. #ngs #metagenome @pathdet
The contribution of metagenomic next-generation sequencing to a diagnosis of gas-producing Fusobacterium-induced septic hip arthritis: A case report
sciencedirect.com/science/ar…
PATHDET retweeted
PATHDET detected GAS in a pleural fluid using metagenomic NGS.
Severe Parapneumonic Effusion in a Child With Respiratory Syncytial Virus and Streptococcus pyogenes Coinfection cureus.com/articles/327252-s…
PATHDET web server is still under maintenance, but the analysis is available on our local env.; infectious diseases researchers who need metagenomic NGS analysis are welcome to contact us.
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PATHDET conducted metagenomic analysis in this study.
Published online! Nanopore sequencing could comprehensively detect RNA viral pathogens in BALF samples with equivalent sensitivity and genome coverage as Illumina sequencing. sciencedirect.com/science/ar…
#nanopore #infection #metagenome #respiratory
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PATHDET contributed to the detection of #Ureaplasma in this study. #metagenome #newborn #chorioamnionitis
We found, #Ureaplasma in the newborn's gastric fluid was connected to their mother's chorioamnionitis in cases of #newborn respiratory distress, according to #NGS. #metagenomics
doi.org/10.1080/14767058.202…
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PATHDET retweeted
Is that just me, or Today's poster session @MicroTas2022 was quiet? Anyway, if you want yo chat about any of our posters, please DM! 🙏
Also please admire our colour matching poster selection 🤩
#microtas2022 #microfluidics #LabOnAChip
PATHDET retweeted
Performance of Nanopore and Illumina metagenomic sequencing for pathogen detection and transcriptome analysis in infantile central nervous system infections
✅ Just Accepted
🔓 Open Access
🔗 bit.ly/3roQ6v9
PATHDET pipeline was used for metagenomic analysis for Illumina and Nanopore sequence data. An online version is now undergoing an update.
We showed that #nanopore sequencing can be used for both #metagenomic and host #transcriptomic analysis from a single clinical sample with #infectious diseases. @OFIDJournal doi.org/10.1093/ofid/ofac504
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PATHDET retweeted
I'm excited to speak at the free #WSCSpotlight on April 27! I will discuss our @iSEP_SEQ 'microfluidics + sequencing' approach to diagnose sepsis.
Join me and 35+ speakers discussing diagnostic approaches for #sepsis. For more info and free registration wscspotlight.org
For server maintenance, PATHDET will not be available on the web to March 25th. If you need immediate analysis, please contact us by e-mail.
The metagenomic NGS for pediatric febrile neutropenia by PATHDET was published in the OFID Volume 8 Issue 11 November 2021. doi.org/10.1093/ofid/ofab223
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PATHDET is not available during am 9:00 Sep 29th - pm 18:00 on Sep 30th (Japan Standard Time) due to server maintenance.
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The analysis of 112 febrile neutropenic children's blood by PATHDET was reported in the OFID. doi.org/10.1093/ofid/ofab223
#pathogendetection #metagenome
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