Sensitive and fast identification of bacteria in blood samples by immunoaffinity mass spectrometry for quick BSI diagnosis

Abstract

Bloodstream infections rank among the most serious causes of morbidity and mortality in hospitalized patients, partly due to the long period (up to one week) required for clinical diagnosis. In this work, we have developed a sensitive method to quickly and accurately identify bacteria in human blood samples by combining optimized matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS) and efficient immunoaffinity enrichment/separation. A library of bacteria reference mass spectra at different cell numbers was firstly built. Due to a reduced sample spot size, the reference spectra could be obtained from as few as 10 to 10² intact bacterial cells. Bacteria in human blood samples were then extracted using antibodies-modified magnetic beads for MS fingerprinting. By comparing the sample spectra with the reference spectra based on a cosine correlation, bacteria with concentrations as low as 500 cells per mL in blood serum and 8000 cells per mL in whole blood were identified. The proposed method was further applied to positive clinical blood cultures (BCs) provided by a local hospital, where Escherichia coli and Staphylococcus aureus were identified. Because of the method's high sensitivity, the BC time required for diagnosis can be greatly reduced. As a proof of concept, whole blood spiked with a low initial concentration (10² or 10³ cells per mL) of bacteria was cultured in commercial BC bottles and analysed by the developed method after different BC times. Bacteria were successfully identified after 4 hours of BC. Therefore, an entire diagnostic process could be accurately accomplished within half a day using the newly developed method, which could facilitate the timely determination of appropriate anti-bacterial therapy and decrease the risk of mortality from bloodstream infections.

Fig. 1. Direct MALDI-TOF MS fingerprinting of intact (A) E. coli, (B) B. subtilis, and (C) S. aureus with reduced sample spot size at different cell numbers: 10⁵ cells (10⁸ cells per mL × 1 μL), 10⁴ cells (10⁷ cells per mL × 1 μL), 10³ cells (10⁶ cells per mL × 1 μL), 10² cells (10⁵ cells per mL × 1 μL), and 10 cells (10⁴ cells per mL × 1 μL).

Scheme 1. Schematic representation of the immunoaffinity MALDI-TOF MS procedure.

Fig. 2. Immunoaffinity MALDI-TOF mass spectra (in blue) for a low concentration of (A) E. coli, (B) B. subtilis, and (C) S. aureus in blood serum (500 cells per mL) or whole blood (8000 cells per mL), and comparisons with the reference spectra (in green) of the corresponding species at 10 cells with similarity scores calculated using the cosine correlation method (r.int: relative intensity).

Fig. 3. Immunoaffinity MALDI-TOF mass spectra (in blue) obtained from four positive BC bottles and comparison with the reference spectra (in green) with similarity scores calculated using the cosine correlation method.

Fig. 4. Immunoaffinity MALDI-TOF mass spectra obtained from BC bottles with initial E. coli concentrations of (A) 10² cells per mL and (B) 10³ cells per mL in 5 mL of blood after different BC times: 0 h, 2 h, 4 h, 6 h, 8 h and 10 h.