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Direct Antimicrobial Resistance Prediction from MALDI-TOF mass spectra profile in clinical isolates through Machine Learning
Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.07.30.228411v1?rss=1
Authors: Weis, C., Cuenod, A., Rieck, B., Llinares-Lopez, F., Dubuis, O., Graf, S., Lang, C., Oberle, M., Soegaard, K. K., Osthoff, M., Borgwardt, K., Egli, A.
Abstract:
Early administration of effective antimicrobial treatments improves the outcome of infections. Culture-based antimicrobial resistance testing allows for tailored treatments, but takes up to 96h. We present a revolutionary approach to predict resistance with unmatched speed within 24h, using calibrated logistic regression and LightGBM-classifiers trained on species-specific MALDI-TOF mass spectrometry measurements. For this analysis, we created an unprecedented large, publicly-available dataset combining mass spectra and resistance information. Our models provide highly valuable treatment guidance 12-72h earlier than classical approaches. Rejection of uncertain predictions enables quality control and clinically-applicable sensitivities and specificities for the priority pathogens Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae.
Copy rights belong to original authors. Visit the link for more info
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By Multimodal LLCLink to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.07.30.228411v1?rss=1
Authors: Weis, C., Cuenod, A., Rieck, B., Llinares-Lopez, F., Dubuis, O., Graf, S., Lang, C., Oberle, M., Soegaard, K. K., Osthoff, M., Borgwardt, K., Egli, A.
Abstract:
Early administration of effective antimicrobial treatments improves the outcome of infections. Culture-based antimicrobial resistance testing allows for tailored treatments, but takes up to 96h. We present a revolutionary approach to predict resistance with unmatched speed within 24h, using calibrated logistic regression and LightGBM-classifiers trained on species-specific MALDI-TOF mass spectrometry measurements. For this analysis, we created an unprecedented large, publicly-available dataset combining mass spectra and resistance information. Our models provide highly valuable treatment guidance 12-72h earlier than classical approaches. Rejection of uncertain predictions enables quality control and clinically-applicable sensitivities and specificities for the priority pathogens Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae.
Copy rights belong to original authors. Visit the link for more info