Application of a MALDI-TOF analysis platform (ClinProTools) for rapid and preliminary report of MRSA sequence types in Taiwan

Abstract

BackgroundThe accurate and rapid preliminarily identification of the types of methicillin-resistant Staphylococcus aureus (MRSA) is crucial for infection control. Currently, however, expensive, time-consuming, and labor-intensive methods are used for MRSA typing. By contrast, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a potential tool for preliminary lineage typing. The approach has not been standardized, and its performance has not been analyzed in some regions with geographic barriers (e.g., Taiwan Island).MethodsThe mass spectra of 306 MRSA isolates were obtained from multiple reference hospitals in Taiwan. The multilocus sequence types (MLST) of the isolates were determined. The spectra were analyzed for the selection of characteristic peaks by using the ClinProTools software. Furthermore, various machine learning (ML) algorithms were used to generate binary and multiclass models for classifying the major MLST types (ST5, ST59, and ST239) of MRSA.ResultsA total of 10 peaks with the highest discriminatory power (m/z range: 2,082–6,594) were identified and evaluated. All the single peaks revealed significant discriminatory power during MLST typing. Moreover, the binary and multiclass ML models achieved sufficient accuracy (82.80–94.40% for binary models and >81.00% for multiclass models) in classifying the major MLST types.ConclusionsA combination of MALDI-TOF MS analysis and ML models is a potentially accurate, objective, and efficient tool for infection control and outbreak investigation.

Rapidly predicting vancomycin resistance ofEnterococcus faeciumthrough MALDI-TOF MS spectrum obtained in real-world clinical microbiology laboratory

“…14–16 On the basis of the massive data produced by MALDI-TOF MS, moreover, some studies have demonstrated that subspecies typing could be predicted from a specific pattern of MS spectra only. 17,19 Furthermore, other studies have shown a good correlation between AST and specific patterns of MS spectra. 18,23–25,48 However, some issues have limited the generalization of these results.…”

“…A log score (generated through Biotyper 3.1) larger than 2 was used for confirming E. faecium . 17–19 We tested vancomycin susceptibility of E. faecium by using the paper disc method. The details of E. faecium identification and AST are given in the eMethods in the Supplement.…”

“…These ML algorithms have demonstrated their successful applications (either classification or prediction) in clinical practice. 17–19,27,28,35,36 The details of these ML algorithms and model training processes are attached in the eMethods in the Supplement.…”

“…14–16 In addition to species identification, MALDI-TOF MS has been promising in other applications, such as strain typing or AST. 17–19 MALDI-TOF MS can generate massive data comprising hundreds of peak signals on the spectra. 17,20 The complex data of MALDI-TOF spectra are overwhelming to even an experienced medical staff.…”

“…17–19 MALDI-TOF MS can generate massive data comprising hundreds of peak signals on the spectra. 17,20 The complex data of MALDI-TOF spectra are overwhelming to even an experienced medical staff. 19 Studies have attempted to identify the characteristic peak through visual inspection.…”