title: Rapid real-time nucleic Acid sequence-based amplification-molecular beacon platform to detect fungal and bacterial bloodstream infections.
abstract: Bloodstream infections (BSIs) are a significant cause of morbidity and mortality. Successful patient outcomes are diminished by a failure to rapidly diagnose these infections and initiate appropriate therapy. A rapid and reliable diagnostic platform of high sensitivity is needed for the management of patients with BSIs. The combination of an RNA-dependent nucleic acid sequence-based amplification and molecular beacon (NASBA-MB) detection system in multiplex format was developed to rapidly detect medically important BSI organisms. Probes and primers representing pan-gram-negative, pan-gram-positive, pan-fungal, pan-Candida, and pan-Aspergillus organisms were established utilizing 16S and 28S rRNA targets for bacteria and fungi, respectively. Two multiplex panels were developed to rapidly discriminate bacterial or fungal infections at the subkingdom/genus level with a sensitivity of 1 to 50 genomes. A clinical study was performed to evaluate the accuracy of this platform by evaluating 570 clinical samples from a tertiary-care hospital group using blood bottle samples. The sensitivity, specificity, and Youden's index values for pan-gram-positive detection and pan-gram-negative detection were 99.7%, 100%, 0.997 and 98.6%, 95.9%, 0.945, respectively. The positive predictive values (PPV) and the negative predictive values (NPV) for these two probes were 100, 90.7, and 99.4, 99.4, respectively. Pan-fungal and pan-Candida probes showed 100% sensitivity, specificity, PPV, and NPV, and the pan-Aspergillus probe showed 100% NPV. Robust signals were observed for all probes in the multiplex panels, with signal detection in <15 min. The multiplex real-time NASBA-MB assay provides a valuable platform for the rapid and specific diagnosis of bloodstream pathogens, and reliable pathogen identification and characterization can be obtained in under 3 h.
authors.affiliation: Public Health Research Institute, UMDNJ-New Jersey Medical School, Newark, NJ 07103, USA.
authors.forename: Yanan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Steven
authors.initials: S
authors.lastname: Park
authors.forename: Barry N
authors.initials: BN
authors.lastname: Kreiswirth
authors.forename: Christine C
authors.initials: CC
authors.lastname: Ginocchio
authors.forename: Raphaël
authors.initials: R
authors.lastname: Veyret
authors.forename: Ali
authors.initials: A
authors.lastname: Laayoun
authors.forename: Alain
authors.initials: A
authors.lastname: Troesch
authors.forename: David S
authors.initials: DS
authors.lastname: Perlin
mesh_terms: D016470:Bacteremia / Q000175:diagnosis*; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001769:Blood / Q000382:microbiology*; D017931:DNA Primers / Q000235:genetics; D005658:Fungi / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D009181:Mycoses / Q000175:diagnosis*; D015345:Oligonucleotide Probes / Q000235:genetics; D011237:Predictive Value of Tests; D012329:RNA, Bacterial / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D021161:Self-Sustained Sequence Replication / Q000379:methods*; D012680:Sensitivity and Specificity
chemical_list: D017931:DNA Primers; D015345:Oligonucleotide Probes; D012329:RNA, Bacterial; D012331:RNA, Fungal; D012336:RNA, Ribosomal, 16S; D012339:RNA, Ribosomal, 28S