The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood

• Published in: PloS one 2016-07, Vol.11 (7), p.e0158186-e0158186
• Main Authors: Metzgar, David, Frinder, Mark W, Rothman, Richard E, Peterson, Stephen, Carroll, Karen C, Zhang, Sean X, Avornu, Gideon D, Rounds, Megan A, Carolan, Heather E, Toleno, Donna M, Moore, David, Hall, Thomas A, Massire, Christian, Richmond, Gregory S, Gutierrez, Jose R, Sampath, Rangarajan, Ecker, David J, Blyn, Lawrence B
• Format: Article
• Language: English
• Subjects: Algorithms; Anti-Bacterial Agents - therapeutic use; Antibiotics; Assaying; Bacteria; Bacteria - isolation & purification; Bacterial artificial chromosomes; Bacterial Infections - blood; Biological Assay - methods; Biology and Life Sciences; Blood; Candida; Candida - isolation & purification; Candidiasis - blood; Care and treatment; Causes of; Contaminants; Culture; Deoxyribonucleic acid; Diagnosis; DNA; DNA Primers; DNA probes; Drug resistance; Drug Resistance, Bacterial; Drug Resistance, Fungal; Emergency medical care; Genetic testing; Hospitals; Humans; Identification; Identification methods; Infections; Ionization; Laboratories; Limit of Detection; Mass spectrometry; Mass spectroscopy; Medicine; Medicine and Health Sciences; Microorganisms; Mortality; Multidrug resistance; Mycobacterium; Organisms; Physical Sciences; Polymerase Chain Reaction; Primers; Public health; Reproducibility of Results; Research and Analysis Methods; Scientific imaging; Sensitivity and Specificity; Sepsis; Sepsis - blood; Sepsis - microbiology; Spectrometry, Mass, Electrospray Ionization; Yeast
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0158186

Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours. The IRIDICA BAC BSI Assay is not available in the United States.