C V Weis1, C R Jutzeler2, K Borgwardt2. 1. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Switzerland. Electronic address: caroline.weis@bsse.ethz.ch. 2. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Switzerland.
Abstract
BACKGROUND: The matrix assisted laser desorption/ionization and time-of-flight mass spectrometry (MALDI-TOF MS) technology has revolutionized the field of microbiology by facilitating precise and rapid species identification. Recently, machine learning techniques have been leveraged to maximally exploit the information contained in MALDI-TOF MS, with the ultimate goal to refine species identification and streamline antimicrobial resistance determination. OBJECTIVES: The aim was to systematically review and evaluate studies employing machine learning for the analysis of MALDI-TOF mass spectra. DATA SOURCES: Using PubMed/Medline, Scopus and Web of Science, we searched the existing literature for machine learning-supported applications of MALDI-TOF mass spectra for microbial species and antimicrobial susceptibility identification. STUDY ELIGIBILITY CRITERIA: Original research studies using machine learning to exploit MALDI-TOF mass spectra for microbial specie and antimicrobial susceptibility identification were included. Studies focusing on single proteins and peptides, case studies and review articles were excluded. METHODS: A systematic review according to the PRISMA guidelines was performed and a quality assessment of the machine learning models conducted. RESULTS: From the 36 studies that met our inclusion criteria, 27 employed machine learning for species identification and nine for antimicrobial susceptibility testing. Support Vector Machines, Genetic Algorithms, Artificial Neural Networks and Quick Classifiers were the most frequently used machine learning algorithms. The quality of the studies ranged between poor and very good. The majority of the studies reported how to interpret the predictors (88.89%) and suggested possible clinical applications of the developed algorithm (100%), but only four studies (11.11%) validated machine learning algorithms on external datasets. CONCLUSIONS: A growing number of studies utilize machine learning to optimize the analysis of MALDI-TOF mass spectra. This review, however, demonstrates that there are certain shortcomings of current machine learning-supported approaches that have to be addressed to make them widely available and incorporated them in the clinical routine.
BACKGROUND: The matrix assisted laser desorption/ionization and time-of-flight mass spectrometry (MALDI-TOF MS) technology has revolutionized the field of microbiology by facilitating precise and rapid species identification. Recently, machine learning techniques have been leveraged to maximally exploit the information contained in MALDI-TOF MS, with the ultimate goal to refine species identification and streamline antimicrobial resistance determination. OBJECTIVES: The aim was to systematically review and evaluate studies employing machine learning for the analysis of MALDI-TOF mass spectra. DATA SOURCES: Using PubMed/Medline, Scopus and Web of Science, we searched the existing literature for machine learning-supported applications of MALDI-TOF mass spectra for microbial species and antimicrobial susceptibility identification. STUDY ELIGIBILITY CRITERIA: Original research studies using machine learning to exploit MALDI-TOF mass spectra for microbial specie and antimicrobial susceptibility identification were included. Studies focusing on single proteins and peptides, case studies and review articles were excluded. METHODS: A systematic review according to the PRISMA guidelines was performed and a quality assessment of the machine learning models conducted. RESULTS: From the 36 studies that met our inclusion criteria, 27 employed machine learning for species identification and nine for antimicrobial susceptibility testing. Support Vector Machines, Genetic Algorithms, Artificial Neural Networks and Quick Classifiers were the most frequently used machine learning algorithms. The quality of the studies ranged between poor and very good. The majority of the studies reported how to interpret the predictors (88.89%) and suggested possible clinical applications of the developed algorithm (100%), but only four studies (11.11%) validated machine learning algorithms on external datasets. CONCLUSIONS: A growing number of studies utilize machine learning to optimize the analysis of MALDI-TOF mass spectra. This review, however, demonstrates that there are certain shortcomings of current machine learning-supported approaches that have to be addressed to make them widely available and incorporated them in the clinical routine.
Authors: Eva Gato; Ignacio Pedro Constanso; Bruno Kotska Rodiño-Janeiro; Paula Guijarro-Sánchez; Tyler Alioto; Manuel Jesús Arroyo; Gema Méndez; Luis Mancera; Marta Gut; Ivo Gut; Miguel Álvarez-Tejado; Germán Bou; Marina Oviaño Journal: J Clin Microbiol Date: 2021-07-19 Impact factor: 5.948