Machine learning for microbial identification and antimicrobial susceptibility testing on MALDI-TOF mass spectra
| Autor: | Caroline Weis, Catherine R. Jutzeler, Karsten M. Borgwardt |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Microbiology (medical) Computer science Antimicrobial treatment 030106 microbiology MEDLINE Antimicrobial susceptibility Microbial Sensitivity Tests Antimicrobial resistance Machine learning computer.software_genre Original research Field (computer science) Machine Learning 03 medical and health sciences 0302 clinical medicine Study Eligibility Criteria MALDI-TOF MS Humans Antimicrobial susceptibility testing 030212 general & internal medicine Bacteria Artificial neural network business.industry Microbial identification General Medicine Anti-Bacterial Agents Support vector machine Identification (information) Infectious Diseases Spectrometry Mass Matrix-Assisted Laser Desorption-Ionization Artificial intelligence business computer |
| Zdroj: | Clinical Microbiology and Infection, 26 (10) Clinical Microbiology and Infection |
| ISSN: | 1198-743X 1470-9465 |
| DOI: | 10.1016/j.cmi.2020.03.014 |
| Popis: | 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. Clinical Microbiology and Infection, 26 (10) ISSN:1470-9465 ISSN:1198-743X |
| Databáze: | OpenAIRE |
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