title: Universal microbial diagnostics using random DNA probes.
abstract: Early identification of pathogens is essential for limiting development of therapy-resistant pathogens and mitigating infectious disease outbreaks. Most bacterial detection schemes use target-specific probes to differentiate pathogen species, creating time and cost inefficiencies in identifying newly discovered organisms. We present a novel universal microbial diagnostics (UMD) platform to screen for microbial organisms in an infectious sample, using a small number of random DNA probes that are agnostic to the target DNA sequences. Our platform leverages the theory of sparse signal recovery (compressive sensing) to identify the composition of a microbial sample that potentially contains novel or mutant species. We validated the UMD platform in vitro using five random probes to recover 11 pathogenic bacteria. We further demonstrated in silico that UMD can be generalized to screen for common human pathogens in different taxonomy levels. UMD's unorthodox sensing approach opens the door to more efficient and universal molecular diagnostics.
authors.affiliation: Rice University, Houston, TX 77005, USA.
authors.forename: Amirali
authors.initials: A
authors.lastname: Aghazadeh
authors.affiliation: Rice University, Houston, TX 77005, USA.
authors.forename: Adam Y
authors.initials: AY
authors.lastname: Lin
authors.affiliation: Rice University, Houston, TX 77005, USA.
authors.forename: Mona A
authors.initials: MA
authors.lastname: Sheikh
authors.affiliation: Rice University, Houston, TX 77005, USA.
authors.forename: Allen L
authors.initials: AL
authors.lastname: Chen
authors.affiliation: Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Atkins
authors.affiliation: Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Coreen L
authors.initials: CL
authors.lastname: Johnson
authors.affiliation: Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Joseph F
authors.identifier: 0000-0002-4046-6898
authors.initials: JF
authors.lastname: Petrosino
authors.affiliation: Rice University, Houston, TX 77005, USA.
authors.forename: Rebekah A
authors.initials: RA
authors.lastname: Drezek
authors.affiliation: Rice University, Houston, TX 77005, USA.
authors.forename: Richard G
authors.identifier: 0000-0002-0721-8999
authors.initials: RG
authors.lastname: Baraniuk
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D015342:DNA Probes / Q000235:genetics*; D004269:DNA, Bacterial / Q000145:classification / Q000235:genetics*; D006801:Humans; D007239:Infections / Q000175:diagnosis* / Q000235:genetics / Q000382:microbiology; D016133:Polymerase Chain Reaction
chemical_list: D015342:DNA Probes; D004269:DNA, Bacterial
keywords: Microbial diagnostics; compressive sensing; molecular beacons