Utilizing Negative Markers for Identifying Mycobacteria Species based on Mass Spectrometry with Machine Learning Methods

Abstract

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a useful tool for rapid identification of microorganisms based on the protein mass profile represented in a mass spectrum of the microorganism. Typically, markers that are specific for particular microorganisms are extracted from the mass information obtained by MALDI-TOF MS, and a machine learning technique is applied to the markers. Identification of mycobacteria is of high clinical importance in that different pathogens must be treated with different antibiotics, but is still challenging because spectral patterns of different mycobacteria appear similar. In this paper, we propose a novel approach to use both positive and negative markers in order to enhance discrimination between the spectral patterns of different mycobacteria. We apply the proposed method to classify species in the Mycobacterium abscessus and Mycobacterium fortuitum groups. Experimental results demonstrate that, when combined with various classifier techniques, our method significantly improves the accuracy of mycobacteria identification.