Maldi tof ms system

The Quantitative determination kit for CEA and CA19-9 were from Roche Company (US), MB-WCX was from Bruker Company (Germany), Standard proteins and peptides were from Bruker Company (Germany), and MALDI-TOF MS system was from Bruker Company (Germany).

One hundred and thirty-eight S. aureus isolates were used in this study. Eighty-two of the strains were isolated from food samples in 2011–2019, and 56 strains were isolated from 20 SFP outbreaks in 2009–2016. All the isolates were identified as S. aureus using conventional microbiological methods including Gram staining and catalase and coagulase tests and then stored in a Brain Heart Infusion (BHI) medium with 40% glycerine at −80°C. Species was confirmed by Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) System (Bruker, Berlin, Germany) before further experiments.

Blood from neonates was cultured in BACTEC plus PEDS aerobic bottles and incubated in the Bactec FX (BD, Heidelberg, Germany). In case of positive blood cultures, plates were inoculated and, after 16–24 h of incubation at 37 °C, screened for S. aureus based on colony morphology. Identification was performed by means of a latex agglutination test (Slidex Staph Plus, bioMérieux, Marcy-l’Etoile, France) and/or via matrix-assisted laser desorption/ionisation, time-of-flight, mass spectrometry (MALDI-TOF MS system, Bruker). S. aureus isolates were stored at − 20 °C or – 80 °C until use. The VITEK 2 system (bioMérieux) was used for antimicrobial susceptibility testing (AST).

Blood culture bottles were incubated in the automatic VirtuoBacT/Alert system (bioMérieux, Inc., Marcy l’Etoile, France). Isolated colonies from blood cultures were identified using the Matrix-Assisted Laser Desorption Ionization–Time Of Fight Mass Spectrometry (MALDI-TOF MS) system (Bruker Daltonik GmbH, Bremen, Germany). Antimicrobial susceptibility was tested using the MicroScan WalkAway system (Beckman Coulter, Inc., Brea, CA, USA). The MICs of antibiotics were assessed by following EUCAST breakpoint tables for the interpretation of MICs and zone diameters, version 9.0, valid from 2 January 2019 [42 ].
Strains showing a carbapenem-resistant phenotype (according to EUCAST criteria [42 ]) were tested using the real-time PCR assay Xpert Carba-R kit for the GeneXpert system (Cepheid, Sunnyvale, CA, USA) to evaluate the presence of the blaVIM, blaIMP, blaKPC, blaOXA-48, and blaNDM carbapenemase genes.

Microorganisms obtained in our cultures were all identified using a MALDI TOF MS System (Bruker Daltonics, Bremen, Germany), while antimicrobial susceptibility testing (AST) was performed using Micronaut panels (Diagnostika Gmbh, Bornheim, Germany, now a subsidiary of Bruker Daltonics, Billerica, MA, USA) run on MICRO MIB (Bruker Daltonics, Billerica, MA, USA). For some BCs, particularly those from critically ill patients, a molecular assay was performed to produce a result quickly available to the clinician. The BCID syndromic panel was used, namely, ePlex^® Panels (GenMark Diagnostics, Inc., Carlsbad, CA, USA). The panels provide pathogen identification and the presence/absence of the main resistance genes after approximately 1 h and 15 min.

A total of 365 unique CRE clinical isolates were randomly selected for testing. This set comprised carbapenem-resistant (defined as nonsusceptibility [intermediate or resistant] to ≥1 carbapenem) isolates collected between 2007 and 2020 for an ongoing carbapenem-resistant Gram-negative pathogen surveillance study (originally obtained from Singapore General Hospital’s Diagnostic Bacteriology Laboratory) and those which were submitted to the Singapore General Hospital Pharmacy Research Laboratory for antibiotic combination testing. The study isolates were representative of the strains frequently encountered in our region, including bacterial isolates collected from nonresidents/foreign patients seeking treatment in Singapore (16 (link), 17 (link)).
The bacterial genus and species were identified and confirmed as per the institution’s microbiology laboratory routine procedures, i.e., using Vitek GNI+ cards with the Vitek 2 instrument (bioMérieux, Hazelwood, MO) and/or matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system (BrukerDaltonik GmbH, Germany). Isolates were preserved in Microbank cryovials (Pro-Lab Diagnostics, Richmond Hill, ON, Canada) at −80°C and subcultured twice on Trypticase soy agar + 5% sheep blood plates (BD, Sparks, MD) before experimental testing.

The identification of CRAB strains was based accordingly on local laboratory techniques. Blood culture bottles were incubated in the automatic BacT/ALERT Virtuo system (bioMérieux, Inc., Marcy l’Étoile, France). Isolated colonies from blood cultures or other positive cultures were identified using a MALDI-TOF MS system (Bruker Daltonik GmbH, Bremen, Germany). Antimicrobial susceptibility was tested using the MicroScan WalkAway system (Beckman Coulter, Inc., Brea, CA, USA). The determination of cefiderocol susceptibility, when available for the clinicians, was performed with the disc diffusion method. A zone diameter of ≥17 mm for the cefiderocol 30 μg disc corresponded to MIC values below the pharmacokinetic/pharmacodynamic breakpoint of S ≤ 2 mg/L. The MICs of antibiotics were assessed by following EUCAST criteria.²³