title: Multiplex and quantifiable detection of nucleic acid from pathogenic fungi using padlock probes, generic real time PCR and specific suspension array readout.
abstract: A new concept for multiplex detection and quantification of microbes is here demonstrated on a range of infectious fungal species. Padlock probe methodology in conjunction with qPCR and Luminex technology was used for simultaneous detection of ten fungal species in one single experiment. By combining the multiplexing properties of padlock probes and Luminex detection with the well established quantitative characteristics of qPCR, quantitative microbe detection was done in 10-plex mode. A padlock probe is an oligonucleotide that via a ligation reaction forms circular DNA when hybridizing to specific target DNA. The region of the padlock probe that does not participate in target DNA hybridization contains generic primer sequences for amplification and a tag sequence for Luminex detection. This was the fundament for well performing multiplexing. Circularized padlock probes were initially amplified by rolling circle amplification (RCA), followed by a SybrGreen real time PCR which allowed an additive quantitative assessment of target DNA in the sample. Detection and quantification of amplified padlock probes were then done on color coded Luminex microspheres carrying anti-tag sequences. A novel technique, using labeled oligonucleotides to prevent reannealing of amplimers by covering the flanks of the address sequence, improved the signal to noise ratio in the detection step considerably. The method correctly detected fungi in a variety of clinical samples and offered quantitative information on fungal nucleic acid.
authors.affiliation: Uppsala University, Department of Medical Sciences, Sections of Clinical Virology and Clinical Bacteriology, Sweden.
authors.forename: Ronnie
authors.initials: R
authors.lastname: Eriksson
authors.forename: Magnus
authors.initials: M
authors.lastname: Jobs
authors.forename: Charlotta
authors.initials: C
authors.lastname: Ekstrand
authors.forename: Måns
authors.initials: M
authors.lastname: Ullberg
authors.forename: Björn
authors.initials: B
authors.lastname: Herrmann
authors.forename: Ulf
authors.initials: U
authors.lastname: Landegren
authors.forename: Mats
authors.initials: M
authors.lastname: Nilsson
authors.forename: Jonas
authors.initials: J
authors.lastname: Blomberg
mesh_terms: D015169:Colony Count, Microbial / Q000379:methods; D004271:DNA, Fungal / Q000235:genetics / Q000302:isolation & purification*; D005658:Fungi / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D009181:Mycoses / Q000175:diagnosis*; D015345:Oligonucleotide Probes / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity
chemical_list: D004271:DNA, Fungal; D015345:Oligonucleotide Probes