Virtuo

During the study period the BACT/ALERT 3D and VIRTUO systems (both bioMérieux, Marcy-l’Étoile, France) were used to incubate aerobic and anaerobic blood culture flasks either with charcoal or raisins. Identification of ESBL-PE in bloodstream isolates was performed by standard culture methods in accordance to the guidelines of the Clinical and Laboratory Standards Institute [15 ]. Species were identified either with MALDI-TOF mass spectrometry (Bruker Daltonics, Bremen, Germany) or biochemically with the VITEK 2 system (bioMérieuex). Specific species within the K. pneumoniae group (K. pneumoniae, K. variicola, K. quasipneumoniae, and K. quasivariicola) could not be separated. The VITEK 2 system was also used for susceptibility testing. ESBL production was based on the detection of resistance to cefpodoxime, ceftriaxone, ceftazidime or aztreonam. Phenotypic confirmation of the ESBL test result was conducted by Etest strips (bioMérieuex) using cefotaxime, ceftazidime or cefepime, each tested with and without clavulanic acid or with Neo-Sensitabs discs (Rosco, Taastrup, Denmark). Minimum inhibitory concentration (MIC) breakpoints were interpreted according to EUCAST guidelines (www.eucast.org). ESBL was reported when at least two of three test substances showed evidence for ESBL.

CFS specimens were processed according to standard microbiological procedures, including Gram stain and culture [19 (link)]. Multiplex PCR using the BioFire FilmArray^® Meningitis/Encephalitis (ME) PCR Panel (Biomerieux, Salt Lake City, USA) was implemented in the routine in September 2016 and from that date was performed according to the manufacturer’s protocol and the laboratory diagnostic algorithm on CSF samples with ≥100 cells/mm³. The panel was used to detect 14 pathogens, including the following bacterial species: Escherichia coli, H. influenzae, Listeria monocytogenes, N. meningitidis, Streptococcus agalactiae, and S. pneumoniae. Blood cultures were performed by conventional systems, BacT/Alert 3D or Virtuo (BioMérieux, Durham, CA, USA). Isolates obtained from routine cultures were identified using standard methods and MALDI-TOF (Bruker, Bremen, Germany).