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

• Published in: Journal of clinical microbiology Vol. 61; no. 1; p. e0111022
• Main Authors: Rodríguez-Temporal, David, Herrera, Laura, Alcaide, Fernando, Domingo, Diego, Héry-Arnaud, Genevieve, van Ingen, Jakko, Van den Bossche, An, Ingebretsen, André, Beauruelle, Clémence, Terschlüsen, Eva, Boarbi, Samira, Vila, Neus, Arroyo, Manuel J, Méndez, Gema, Muñoz, Patricia, Mancera, Luis, Ruiz-Serrano, María Jesús, Rodríguez-Sánchez, Belén
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 26.01.2023
• Subjects: Clinical Microbiology; Editor's Pick; Humans; Life Sciences; Mycobacteriology and Aerobic Actinomycetes; Mycobacterium; Mycobacterium abscessus; Mycobacterium Infections, Nontuberculous - diagnosis; Mycobacterium Infections, Nontuberculous - microbiology; Nontuberculous Mycobacteria; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods; Mycobacterium massiliense; MALDI-TOF; subspecies differentiation; Mycobacterium bolletii; mass spectrometry; machine learning; Mycobacterium abscessus
• ISSN: 0095-1137; 1098-660X
• DOI: 10.1128/jcm.01110-22

Mycobacterium abscessus is one of the most common and pathogenic nontuberculous mycobacteria (NTM) isolated in clinical laboratories. It consists of three subspecies: M. abscessus subsp. , M. abscessus subsp. , and M. abscessus subsp. . 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 325 clinical isolates of M. abscessus was used for MALDI-TOF MS analysis and for the development of machine learning predictive models based on MALDI-TOF MS protein spectra. Overall, using a random forest model with several confidence criteria (samples by triplicate and similarity values >60%), a total of 96.5% of isolates were correctly identified at the subspecies level. Moreover, an improved model with Spanish isolates was able to identify 88.9% of strains collected in other countries. In addition, differences in culture media, colony morphology, and geographic origin of the strains were evaluated, showing that the latter had an impact on the protein spectra. Finally, after studying all protein peaks previously reported for this species, 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 M. abscessus using MALDI-TOF MS.