Diafiltration MALDI-TOF mass spectrometry method for culture-independent detection and identification of pathogens directly from urine specimens

Objectives: With the aim of rapid, culture-independent identification of microorganisms directly from urine specimens, we developed a diafiltration matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method. Methods: In this procedure, urine specimens are desalted, fractionated, and concentrated prior to MS analysis. The analytic performance characteristics of the diafiltration method were assessed in a prospective trial whereby 100 fresh urine specimens were processed using diafiltration MALDI-TOF MS. Concomitant with this, conventional culture was performed with results blinded to the MS operator. Results: The diafiltration method correctly identified urine specimens positive for uropathogens (Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis) and correctly classified all specimens negative for clinically relevant bacteriuria, including a subset of contaminated urine specimens and a subset with growth of clinically insignificant flora. The sensitivity and specificity of the assay were 67% and 100%, respectively. The detection limit of this method was 105 to 106 colony-forming units/mL. Conclusions: Using the diafiltration method, we were able to improve the turnaround time for microorganism identification from 24 to 48 hours (for conventional culture) to 2 to 3 hours. Although methodological refinements are under way to further improve the clinical sensitivity and turnaround time, the 100% positive predictive value of this method suggests that it could be used to guide the selection of antimicrobial agents.