Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA.
Roby P BhattacharyyaMark WalkerRich BoykinSophie S SonJamin LiuAustin C HacheyPeijun MaLidan WuKyungyong ChoiKaelyn C CumminsMaura BensonJennifer SkerryHyunryul RyuSharon Y WongMarcia B GoldbergJongyoon HanVirginia M PierceLisa A CosimiNoam ShoreshJonathan LivnyJoseph BeechemDeborah T HungPublished in: Scientific reports (2019)
Rapid bacterial identification remains a critical challenge in infectious disease diagnostics. We developed a novel molecular approach to detect and identify a wide diversity of bacterial pathogens in a single, simple assay, exploiting the conservation, abundance, and rich phylogenetic content of ribosomal RNA in a rapid fluorescent hybridization assay that requires no amplification or enzymology. Of 117 isolates from 64 species across 4 phyla, this assay identified bacteria with >89% accuracy at the species level and 100% accuracy at the family level, enabling all critical clinical distinctions. In pilot studies on primary clinical specimens, including sputum, blood cultures, and pus, bacteria from 5 different phyla were identified.
Keyphrases
- high throughput
- nucleic acid
- infectious diseases
- single molecule
- loop mediated isothermal amplification
- machine learning
- gram negative
- label free
- deep learning
- cystic fibrosis
- mycobacterium tuberculosis
- randomized controlled trial
- clinical trial
- single cell
- bioinformatics analysis
- cancer therapy
- living cells
- genetic diversity
- drug delivery
- fine needle aspiration
- double blind