TY - JOUR
T1 - Discrimination of Methicillin-Resistant Staphylococcus aureus by MALDI-TOF Mass Spectrometry with Machine Learning Techniques in Patients with Staphylococcus aureus Bacteremia
AU - Kong, Po Hsin
AU - Chiang, Cheng Hsiung
AU - Lin, Ting Chia
AU - Kuo, Shu Chen
AU - Li, Chien Feng
AU - Hsiung, Chao A.
AU - Shiue, Yow Ling
AU - Chiou, Hung Yi
AU - Wu, Li Ching
AU - Tsou, Hsiao Hui
N1 - Funding Information:
Funding: This study was supported by grants PH-110-GP-02 and PH-111-GP-02 from the National Health Research Institutes, a nonprofit foundation dedicated to medical research and improved healthcare in Taiwan.
Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2022/5
Y1 - 2022/5
N2 - Early administration of proper antibiotics is considered to improve the clinical outcomes of Staphylococcus aureus bacteremia (SAB), but routine clinical antimicrobial susceptibility testing takes an additional 24 h after species identification. Recent studies elucidated matrix-assisted laser desorption/ionization time-of-flight mass spectra to discriminate methicillin-resistant strains (MRSA) or even incorporated with machine learning (ML) techniques. However, no universally applicable mass peaks were revealed, which means that the discrimination model might need to be established or calibrated by local strains’ data. Here, a clinically feasible workflow was provided. We collected mass spectra from SAB patients over an 8-month duration and preprocessed by binning with reference peaks. Machine learning models were trained and tested by samples independently of the first six months and the following two months, respectively. The ML models were optimized by genetic algorithm (GA). The accuracy, sensitivity, specificity, and AUC of the independent testing of the best model, i.e., SVM, under the optimal parameters were 87%, 75%, 95%, and 87%, respectively. In summary, almost all resistant results were truly resistant, implying that physicians might escalate antibiotics for MRSA 24 h earlier. This report presents an attainable method for clinical laboratories to build an MRSA model and boost the performance using their local data.
AB - Early administration of proper antibiotics is considered to improve the clinical outcomes of Staphylococcus aureus bacteremia (SAB), but routine clinical antimicrobial susceptibility testing takes an additional 24 h after species identification. Recent studies elucidated matrix-assisted laser desorption/ionization time-of-flight mass spectra to discriminate methicillin-resistant strains (MRSA) or even incorporated with machine learning (ML) techniques. However, no universally applicable mass peaks were revealed, which means that the discrimination model might need to be established or calibrated by local strains’ data. Here, a clinically feasible workflow was provided. We collected mass spectra from SAB patients over an 8-month duration and preprocessed by binning with reference peaks. Machine learning models were trained and tested by samples independently of the first six months and the following two months, respectively. The ML models were optimized by genetic algorithm (GA). The accuracy, sensitivity, specificity, and AUC of the independent testing of the best model, i.e., SVM, under the optimal parameters were 87%, 75%, 95%, and 87%, respectively. In summary, almost all resistant results were truly resistant, implying that physicians might escalate antibiotics for MRSA 24 h earlier. This report presents an attainable method for clinical laboratories to build an MRSA model and boost the performance using their local data.
KW - antimicrobial susceptibility testing
KW - binning method
KW - machine learning
KW - MALDI-TOF MS
KW - methicillin-resistant Staphylococcus aureus
KW - Staphylococcus aureus bacteremia
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U2 - 10.3390/pathogens11050586
DO - 10.3390/pathogens11050586
M3 - Article
AN - SCOPUS:85130682180
SN - 2076-0817
VL - 11
JO - Pathogens
JF - Pathogens
IS - 5
M1 - 586
ER -