Rapid identification of microorganisms isolated from throat swab specimens of community-acquired pneumonia patients by two MALDI-TOF MS systems

The rapid and reliable identification of pathogens is crucial for confirming infections concomitant with community-acquired pneumonia (CAP), guiding antimicrobial therapy, and epidemiologic surveillance. In this study, 2 matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems coupled to the Biotyper or SARAMIS database were used to identify strains isolated from the throat swab samples of 70 CAP patients. The analysis of 16S rRNA gene sequencing was used as the reference method. A total of 212 suspicious colonies representing 12 genera and 30 species were identified. Of these, 99.1% (total 210/212 and 202/212 in Biotyper and 193/212 in SARAMIS) were successfully identified with 93.4% (total 198 /212 and 190/212 in Biotyper and 149/212 in SARAMIS) identified at the species level. The integrity and comprehensiveness of the databases are the main reason for the significant differences in the identification of isolates between the Biotyper and SARAMIS systems. As a rapid, economical, and high-throughput method, MALDI-TOF MS is an effective alternative identification method that can aid in the diagnosis and surveillance of CAP.