title: Accurate and rapid identification of bacterial species from positive blood cultures with a DNA-based microarray platform: an observational study.
abstract: BACKGROUND
  New DNA-based microarray platforms enable rapid detection and species identification of many pathogens, including bacteria. We assessed the sensitivity, specificity, and turnaround time of a new molecular sepsis assay.
  
  
  METHODS
  2107 positive blood-culture samples of 3318 blood samples from patients with clinically suspected sepsis were investigated for bacterial species by both conventional culture and Prove-it sepsis assay (Mobidiag, Helsinki, Finland) in two centres (UK and Finland). The assay is a novel PCR and microarray method that is based on amplification and detection of gyrB, parE, and mecA genes of 50 bacterial species. Operators of the test assay were not aware of culture results. We calculated sensitivity, specificity, and turnaround time according to Clinical and Laboratory Standards Institute recommendations.
  
  
  RESULTS
  1807 of 2107 (86%) positive blood-culture samples included a pathogen covered by the assay. The assay had a clinical sensitivity of 94.7% (95% CI 93.6-95.7) and a specificity of 98.8% (98.1-99.2), and 100% for both measures for meticillin-resistant Staphylococcus aureus bacteraemia. The assay was a mean 18 h faster than was the conventional culture-based method, which takes an additional 1-2 working days. 34 of 3284 (1.0%) samples were excluded because of technical and operator errors.
  
  
  CONCLUSIONS
  Definitive identification of bacterial species with this microarray platform was highly sensitive, specific, and faster than was the gold-standard culture-based method. This assay could enable fast and earlier evidence-based management for clinical sepsis.
authors.affiliation: Division of Clinical Microbiology, Helsinki University Hospital Laboratory, Helsinki, Finland.
authors.forename: Päivi
authors.initials: P
authors.lastname: Tissari
authors.forename: Alimuddin
authors.initials: A
authors.lastname: Zumla
authors.forename: Eveliina
authors.initials: E
authors.lastname: Tarkka
authors.forename: Sointu
authors.initials: S
authors.lastname: Mero
authors.forename: Laura
authors.initials: L
authors.lastname: Savolainen
authors.forename: Martti
authors.initials: M
authors.lastname: Vaara
authors.forename: Anne
authors.initials: A
authors.lastname: Aittakorpi
authors.forename: Sanna
authors.initials: S
authors.lastname: Laakso
authors.forename: Merja
authors.initials: M
authors.lastname: Lindfors
authors.forename: Heli
authors.initials: H
authors.lastname: Piiparinen
authors.forename: Minna
authors.initials: M
authors.lastname: Mäki
authors.forename: Caroline
authors.initials: C
authors.lastname: Carder
authors.forename: Jim
authors.initials: J
authors.lastname: Huggett
authors.forename: Vanya
authors.initials: V
authors.lastname: Gant
mesh_terms: D016470:Bacteremia / Q000382:microbiology*; D001419:Bacteria / Q000302:isolation & purification*; D001426:Bacterial Proteins / Q000032:analysis; D001431:Bacteriological Techniques; D027081:DNA Gyrase / Q000032:analysis; D027101:DNA Topoisomerase IV / Q000032:analysis; D004269:DNA, Bacterial / Q000032:analysis*; D024881:Drug Resistance, Bacterial / Q000235:genetics; D005798:Genes, Bacterial; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis; D046915:Penicillin-Binding Proteins; D016133:Polymerase Chain Reaction; D012680:Sensitivity and Specificity
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D046915:Penicillin-Binding Proteins; C487789:mecA protein, Staphylococcus aureus; D027101:DNA Topoisomerase IV; D027081:DNA Gyrase