Multi-year comparison of VITEK MS performance for identification of rarely encountered pathogenic gram-positive organisms (GPOs) in a large integrated Canadian healthcare region

ABSTRACT This multi-year study (2014–2019) compared identification of rare and unusual gram-positive organisms (GPOs) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (VITEK MS; bioMérieux, Laval, Quebec) to 16S rRNA gene sequencing (16S) according to our laboratory routine workflow. 16S is done if initial MALDI-TOF MS results are discordant or wrong, or there are no results. GPO isolates were first analyzed by standard phenotypic methods and MALDI-TOF MS using direct deposit with full formic acid extraction; MALDI-TOF was repeated if no result occurred. Medically approved 16S analyses were done using fast protocols. Isolate sequences were analyzed using the Integrated Database Network System bacterial database (SmartGene, Lausanne, Switzerland). 655 GPO isolates were recovered from 648 specimens; >1 isolate was recovered from 7 (1%). A total of 451 (68.9%) aerobic gram-positive bacilli (GPBs) and 204 (31.1%) aerobic gram-positive cocci (GPCs) were mainly recovered from bloodstream infections (35%), sterile fluids and deep tissues (35%), and abscesses/deep wounds (17%). Accurate genus vs species identities were obtained for 59% and 49.4% GPB, and 81% and 53.9% GPC, respectively. Wrong or no results were obtained for 9% and 31% of GPB and 7% and 12% of GPC; 15% of GPBs and 5.3% of GPC identification errors occurred due to absence from the instrument’s database. VITEK MS performance remained stable for GPB and GPC isolates due to few species additions to the database. VITEK MS databases need to be continually updated to include an increasing number of rare and unusual GPOs causing invasive human infections. 16S remains important for identification of GPOs where MALDI-TOF fails.IMPORTANCEMALDI-TOF MS has transformed the identification of commonly encountered GPOs in the clinical laboratory, but rare and unusual bacteria continue to challenge the technology. This study verified the performance of VITEK MS for identification of a broad range of rare and unusual clinical GPO isolates by our large reference laboratory workflow over a multi-year period. Although most GPOs were accurately identified by MALDI-TOF MS, a small number of common GPC isolates (6.3%) (i.e., Enterococcus/Staphylococcus/Streptococcus) requiring sequencing for identification were studied. Approximately 13% of aerobic GPBs and 5.3% of GPCs could not be accurately identified by MALDI-TOF due to lack of an organism in the instrument’s database. MALDI-TOF MS databases should be continuously updated and validated, and laboratories should have a workflow for the identification of unusual or rarely encountered GPOs that includes 16S rRNA gene sequencing whenever MALDI-TOF cannot give a definitive identification.