MALDI-TOF MS Biomarkers Associated with Antimicrobial Resistance in Enterococcus faecium: Current Evidence, Methodological Challenges, and Future Perspectives

Enterococcus faecium is a major healthcare-associated pathogen whose increasing resistance to clinically important antimicrobials has created a need for faster susceptibility-testing approaches. This narrative review critically evaluated the available evidence on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) biomarkers for predicting antimicrobial resistance in E. faecium. PubMed/MEDLINE, Scopus, and Web of Science Core Collection were searched from database inception to 15 July 2026, without language or publication-date restrictions. Seventeen studies met the eligibility criteria. Most investigated vancomycin resistance or the presence of vanA and vanB, whereas fewer addressed ampicillin resistance, resistance to other antimicrobials, or lineage discrimination. Several individual peaks and machine-learning models showed high discriminatory performance within their respective study populations. However, direct comparisons were limited by substantial heterogeneity in isolate collections, culture conditions, sample-preparation protocols, MALDI-TOF MS platforms, spectral-processing pipelines, feature-selection methods, and validation strategies. Most reported biomarkers lacked molecular annotation, and some previously proposed signals could not be reproduced in independent collections, suggesting that certain peaks may reflect clonal lineage rather than a direct resistance mechanism. External and multicenter validation also remained limited. MALDI-TOF MS-based resistance prediction therefore represents a promising rapid screening or decision-support approach but cannot currently replace reference phenotypic antimicrobial susceptibility testing. Future research should prioritize standardized experimental and analytical workflows, isolate-level data partitioning, geographically diverse multicenter cohorts, independent external validation, and integrated proteomic and genomic characterization of candidate biomarkers.