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Allen E.K.,University of Virginia | Pitkaranta A.,University of Helsinki | Maki M.,Mobidiag Ltd | Hendley J.O.,University of Virginia | And 3 more authors.
International Forum of Allergy and Rhinology | Year: 2013

Background: Patients  with  viral respiratory infections/viral rhinitis/common colds are often treated with antibiotic; however, there is little information on whether or how bacterial microbiota in the nose and nasopharynx might influence the course of viral illnesses. Methods: To initiate investigation of possible interaction between viral respiratory illness and microbiota of the nose/nasopharynx, we used microarray technology to examine 100 nasal lavage fluid (NLF) samples for bacterial species and recorded the bacterial titer of culturable bacteria. Rhinovirus illnesses were induced by self-inoculation using the "finger to nose or eye natural transmission route" in 10 otherwise healthy young adults. NLF samples were collected during wellness and at specific time points following experimental rhinovirus inoculation. Results: The rhinovirus infection rate was 70%. There were no consistent changes in the prevalence of different bacterial species determined by microarray and bacterial titer by culture methods during rhinovirus infection. The bacterial profile in NLF samples showed high variability between volunteers but low variability in multiple NLFs obtained before and following infection from the same volunteer. Streptococcus epidermidis/coagulase-negative staphylococcus (CNS) were identified in all 10 subjects. One or more bacterial sinus/otitis pathogens were identified by microarray in 6 of the 10 volunteers. The microarray identified a few bacteria not included in traditional bacterial cultures. Conclusion: Our pilot study showed that each of the 10 volunteers had a unique bacterial profile in the nose by microarray analysis and that bacterial load did not change during experimental rhinovirus colds. Larger scale studies are warranted. © 2013 The Authors. International Forum of Allergy & Rhinology published by Wiley Periodicals, Inc., on behalf of ARS-AAOA, LLC. Source

Viitala S.M.,University of Eastern Finland | Viitala S.M.,Biocenter Kuopio | Jaaskelainen A.J.,University of Helsinki | Kelo E.,Reagena Ltd | And 7 more authors.
Diagnostic Microbiology and Infectious Disease | Year: 2013

Microarrays are widely used in high-throughput DNA and RNA hybridization tests and recently adopted to protein and small molecule interaction studies in basic research and diagnostics. Parallel detection of serum antibodies and antigens has several potential applications in epidemiologic research, vaccine development, and in the diagnosis of allergies, autoimmunity, and infectious diseases. This study demonstrates an immobilization method for immunoassay-based microarray in conventional 96-well polystyrene plates for a serologic diagnostic method combined with quantitative C-reactive protein (CRP) assay. A synthetic peptide (HIV-1), a recombinant protein (Puumala hantavirus nucleocapsid), and purified virus preparations (Sindbis and adenoviruses) were used as antigens for virus-specific antibody detection and monoclonal anti-CRP antibody for antigen detection. The microarray was based on conventional enzyme immunoassays and densitometry from photographed results. Peptide and recombinant antigens functioned well, while whole virus antigens gave discrepant results in 1 out of 23 samples from the reference method, tested with human sera with various antibody responses. The CRP results were in concordance in the concentration range 0.5-150 mg/L with 2 commercially available CRP assays: ReaScan rapid test (R2 = 0.9975) and Cobas 6000 analyzer (R2 =0.9595). The results indicate that microtiter plates provide a promising platform for further development of microarrays for parallel antibody and antigen detection. © 2013 Elsevier Inc. Source

Hinic V.,University of Basel | Aittakorpi A.,Mobidiag Ltd | Suter S.,University of Basel | Turan S.,University of Basel | And 3 more authors.
Journal of Microbiological Methods | Year: 2014

The performance of Prove-it™ Bone&Joint, a novel microarray-based assay for direct pathogen detection from clinical samples was assessed. In culture-positive samples, Prove-it™ performed similarly with broad-range bacterial PCR in osteoarticular (sensitivity 62.9% vs. 57.7%) and non-osteoarticular samples (54.6% vs. 56.8%). Prove-it™ is a rapid tool providing preliminary results while awaiting culture results. © 2014 Elsevier B.V. Source

Tapiovaara L.,University of Helsinki | Lehtoranta L.,University of Helsinki | Swanljung E.,University of Helsinki | Makivuokko H.,Valio Ltd. | And 4 more authors.
International Journal of Pediatric Otorhinolaryngology | Year: 2014

Objective: Probiotics may have potency in reducing upper respiratory infections, in particular in children. We studied findings from middle ear effusion (MEE) samples after randomized, placebo-controlled 3-week oral administration of probiotic Lactobacillus rhamnosus GG (L. GG). Methods: 40 children referred to tympanostomy were randomized to receive either L. GG or placebo (1:1) for 3 weeks before surgery. MEE samples were collected from 13 children (in total, 25 samples, 19 from the L. GG group and 6 from the placebo group) and analyzed for L. GG and pathogenic bacterial and viral findings. Results: L. GG was present in 5 of the 25 MEE samples (4 from the L. GG group). Haemophilus infuenzae was the most prominent pathogen in 12 samples (10 from the L. GG group). Rhinovirus was present in 12 samples (10 from the L. GG group) and enterovirus in 1 sample (L. GG group). Conclusions: L. GG was present in the middle ear of children suffering from otitis media with effusion, but did not reduce the presence of pathogenic bacteria or viruses. © 2014 Elsevier Ireland Ltd. Source

Laakso S.,Mobidiag Ltd | Kirveskari J.,University of Helsinki | Tissari P.,University of Helsinki | Maki M.,Mobidiag Ltd
PLoS ONE | Year: 2011

Background: High incidence of septic patients increases the pressure of faster and more reliable bacterial identification methods to adapt patient management towards focused and effective treatment options. The aim of this study was to assess two automated DNA extraction solutions with the PCR and microarray-based assay to enable rapid and reliable detection and speciation of causative agents in the diagnosis of sepsis. Methodology/Principal Findings: We evaluated two automated DNA instruments NucliSENS® easyMAG® and NorDiag Arrow for the preparation of blood culture samples. A set of 91 samples flagged as positive during incubation was analyzed prospectively with the high-throughput generation of Prove-it™ Sepsis assay designed to identify over 60 Gram-negative and Gram-positive bacterial species as well as methicillin resistance marker from a blood culture. Bacterial findings were accurately reported from 77 blood culture samples, whereas 14 samples were reported as negative, containing bacteria not belonging to the pathogen panel of the assay. No difference was observed between the performance of NorDiag Arrow or NucliSENS® easyMAG® with regard to the result reporting of Prove-it™ Sepsis. In addition, we also assessed the quality and quantity of DNA extracted from the clinical Escherichia coli isolate with DNA extraction instruments. We observed only minor differences between the two instruments. Conclusions: Use of automated and standardized sample preparation methods together with rapid, multiplex pathogen detection offers a strategy to speed up reliably the diagnostics of septic patients. Both tested DNA extraction devices were shown to be feasible for blood culture samples and the Prove-it™ Sepsis assay, providing an accurate identification of pathogen within 4,5 hours when the detected pathogen was in the repertoire of the test. © 2011 Laakso et al. Source

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