Accurate and rapid identification of bacterial species from positive blood cultures with a DNA-based microarray platform: an observational study.
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.
Tissari
Päivi
P
Division of Clinical Microbiology, Helsinki University Hospital Laboratory, Helsinki, Finland.
Zumla
Alimuddin
A
Tarkka
Eveliina
E
Mero
Sointu
S
Savolainen
Laura
L
Vaara
Martti
M
Aittakorpi
Anne
A
Laakso
Sanna
S
Lindfors
Merja
M
Piiparinen
Heli
H
Mäki
Minna
M
Carder
Caroline
C
Huggett
Jim
J
Gant
Vanya
V
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
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D046915:Penicillin-Binding Proteins; C487789:mecA protein, Staphylococcus aureus; D027101:DNA Topoisomerase IV; D027081:DNA Gyrase