Identification of Mycobacterium abscessus subspecies by MALDI-TOF Mass Spectrometry and Machine Learning

Mycobacterium abscessus complex is one of the most common and pathogenic nontuberculous mycobacteria (NTM) isolated in clinical laboratories. It consists of three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. bolletii and M. abscessus subsp. massiliense. Due to their different antibiotic susceptibility pattern, a rapid and accurate identification method is necessary for their differentiation. Although matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has proven useful for NTM identification, the differentiation of M. abscessus subspecies is challenging. In this study, a collection of 244 clinical isolates of M. abscessus complex was used for MALDI-TOF MS analysis and for the development of machine learning predictive models. Overall, using a Random Forest model with several confidence criteria (samples by triplicate and similarity values >60%), a total of 95.8% of isolates were correctly identified at subspecies level. In addition, differences in culture media, colony morphology and geographic origin of the strains were evaluated, showing that the latter most affected the mass spectra of isolates. Finally, after studying all protein peaks previously reported for this complex, two novel peaks with potential for subspecies differentiation were found. Therefore, machine learning methodology has proven to be a promising approach for rapid and accurate identification of subspecies of the M. abscessus complex using MALDI-TOF MS.