Review: Identification and diagnosis of hospital-important microorganisms using MALDITOF and metagenomic NGS.

Abstract

The identification and diagnosis of pathogenic microorganisms are important for the treatment, management, and prognosis of hospital infections. However, many microorganisms are difficult to identify using conventional diagnostic methods. Advanced techniques such as MALDI-TOF MS and mNGS offer advantages for identifying microorganisms of hospital importance. MALDI-TOF MS is a rapid and precise method that creates a mass spectral fingerprint for microbial identification down to strain levels. This technique is quick, sensitive, and economical, allowing the identification of different types of microorganisms. MALDI-TOF MS can only identify new microorganisms if the spectral database contains peptide mass fingerprints of specific strains, which is a limitation of the technique. Meanwhile, metagenomics allows the analysis of DNA segments from multiple microorganisms within a community, either through amplicon-based or shotgun sequencing. Advances in clinical next-generation metagenomic sequencing (mNGS) increase diagnostic capacity by rapidly detecting rare pathogens and antibiotic resistance genes. This technique presents some limitations in its accuracy and logistical complexity but can perform comprehensive analyses of microbial communities. Both methods complement traditional diagnostic techniques, and their integration into clinical microbiology improves pathogen identification, guides treatment strategies, and supports outbreak investigations. This review summarizes MALDI-TOF MS and metagenomics as alternative methods for identifying and diagnosing microorganisms in hospitals