Vitek ms

The detection of B. cereus and S. aureus was performed by modifying the Korea food code (No.2022-76, 2022.10.25). To isolate B. cereus, detected shotgun metagenomics sequencing samples were streaked on Mannitol egg yolk polymyxin agar plates (MYP, Oxoid, UK) and the plates were incubated for 24 h at 30°C. In addition, the samples were incubated with Tryptic soy broth (TSB, Oxoid, UK) containing 10% sodium chloride for 24 h at 37°C to isolate S. aureus. And then, incubated samples were streaked on Baird Parker agar plates (BPA, Oxoid) and the plates were incubated for 24 h at 37°C. Typical colonies of each bacteria were selected and purified to obtain single colonies. These colonies were identified using MALDI-TOF MS (BioMérieux, VITEK MS versus Bruker MALDI Biotyper, France).

The comparator method(s) for organism identification were the site’s SOC, including traditional culture, FDA-cleared matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS) (i.e., bioMérieux Vitek MS and Bruker Biotyper), and automated phenotypic identification and antibiotic susceptibility platforms (e.g., Becton, Dickinson [BD] Phoenix, bioMérieux Vitek 2, and Siemens MicroScan). The phenotypic methods listed above varied at different sites and served as the site’s reference identification standard. Due to issues with organism misidentification, samples with a member of the Acinetobacter calcoaceticus-baumannii complex (15 (link)) or Candida parapsilosis (16 (link)) identified by SOC were confirmed using analytically validated PCR amplification assays followed by bidirectional sequencing (PCR/sequencing) or 16S sequencing by Laboratory Corporation of America Holdings (LabCorp [Burlington, NC]) according to FDA clinical trial instructions outlined in the 510k summary (10 ). The comparator methods for ARGs were analytically validated by real-time PCR amplification assay(s) followed by bidirectional sequencing, developed and performed by LabCorp.

The identification of all the isolates was also undertaken using two Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) systems—the bioMérieux Vitek MS (bioMérieux) and Bruker Autoflex Speed (Bruker Daltonics, Bremen, Germany). Preparation of A. lentulus isolates for MALDI-TOF MS identification was performed according to the manufacturer’s instructions with some modifications (Li et al., 2017 (link)). The acquisition and analysis of mass spectra were handled using software Myla (for Vitek MS, database version 3.2.0, bioMérieux) and Biotyper version 3.1 with the Filamentous Fungi Library 1.0 (for Autoflex Speed, Bruker Daltonics), again following the manufacturer’s instructions. All identification results displaying a single result with a confidence score ≥ 1.700 or a confidence value of 99.9% were considered acceptable for Bruker Biotyper MS and Vitek MS, respectively (Wang et al., 2016 (link); Zhou et al., 2016 (link)).