Quantification of bacterial DNA in blood using droplet digital PCR: a pilot study

Bloodstream infections (BSIs) caused by bacteria associated with sepsis are among the leading causes of mortality, particularly in critically ill patients [1,2]. The gold standard method for the microbiological diagnosis of BSIs is still blood culture, which is slow, cannot detect viruses, and only yield positive results in one-third of suspected BSIs and sepsis cases [1,3]. Droplet digital PCR (ddPCR) is a next-generation PCR method, with great precision and accuracy, that allows absolute quantification of target gene(s) without a standard curve and little interference from normal PCR inhibitors[4]. These characteristics make ddPCR an ideal method for the detection and quantification of pathogens directly from blood or other clinical samples [4] in patients with suspected BSI and sepsis. The aim of this work was to use genus/species specific genes ddPCR assays to detect and quantify bacterial DNA from four of the most common BSIs pathogens in blood. Here we demonstrate the quantification capacity and specificity of two duplex ddPCR assays that allow the detection and quantification of Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus and Enterococcus spp directly from blood.