Comparison of VITEK 2 and Bruker Microflex LT MALDI-TOF MS for Routine Bacterial Identification in a Tertiary Hospital

To compare bacterial identification using the VITEK 2 Compact (bioMérieux) and Bruker Microflex LT matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems in routine clinical microbiology. This retrospective cross-sectional study included consecutive clinical isolates recovered between February and April 2022 from a 1355-bed academic center. Identification was performed using VITEK 2 GN/GP cards and the Bruker MALDI Biotyper workflow using a Microflex LT instrument. Identifications were compared at species and genus levels; concordance was defined as identical taxon names. Agreement was summarized as percent agreement (Wilson 95% confidence intervals (CI)) and Cohen’s kappa (κ); discordance was interpreted as between-system disagreement because no molecular adjudication was performed. A total of 1394 isolates were analyzed. Most isolates were obtained from urine-related specimens (n=563, 40.4%) and blood cultures (n=446, 32.0%). Species-level concordance between systems was 93.1% (95% CI, 91.7–94.3%; κ=0.923 (95% CI, 0.908–0.937)), and genus-level concordance was 98.3% (95% CI, 97.5–98.8%; κ=0.979 (95% CI, 0.970–0.987)). Among the 96 discordant species identifications, 72 (75.0%) occurred within the same genus, indicating disagreements concentrated in closely related taxa. The most frequent discordant pairs involved the Klebsiella genus and coagulase-negative Staphylococcus species; the single most common pair was Klebsiella pneumoniae versus Klebsiella variicola (n=12). VITEK 2 and Bruker Microflex LT MALDI-TOF MS demonstrated very high agreement for routine bacterial identification, with most discrepancies occurring among closely related taxa. When species-level precision is clinically critical (e.g., outbreaks or invasive infections), confirmatory approaches such as 16S rRNA sequencing and up-to-date databases may be required.