Vitek 2 microbial identification system

Of all Gram-positive isolates obtained from blood cultures up to 5 days before and/or during vancomycin treatment of study patients were identified from the databases of the Department of Clinical Microbiology. Microorganisms were identified by the VITEK 2 microbial identification system, (bioMérieux, Lyon, France). MICs were determined using E-tests (AB Biodisk, Sweden and Liofilchem, Italy). The interpretative criteria recommended by the CLSI (2010) and by EUCAST (2011, 2012) were applied.
Additionally, vancomycin MIC data of all CoNS strains isolated from blood cultures of patients aged <90 days, admitted to our hospital during the study period, were extracted from the database of the Clinical Microbiology Department.

Presence of CRE and associated MICs were identified using the Vitek^®2 Microbial Identification System (bioMérieux) in the University of Florida (UF) Health Shands Hospital Clinical Microbiology Laboratory. MICs were subsequently confirmed via Etest (bioMérieux). Organisms were further analysed via the Xpert^® Carba-R (Cepheid) to detect the presence of carbapenemase genes.¹⁶ As part of standard daily hospital infection control activities, all Gram-negative bacterial isolates found by the hospital microbiology laboratory to have resistance to carbapenem were identified through an automated infection control/laboratory surveillance system, and basic data on patient location and movement during hospitalization were collected. This resulted in identification of 11 NDM-carrying strains across a 1 year time period; sequence data were obtained for all 11 strains, as described below. A subset of patients infected with NDM strains were enrolled in an institutional review board-approved study at the University of Florida that permitted collection of additional clinical and epidemiological data from patients infected with antimicrobial-resistant bacterial strains. Informed consent was not required for the use of de-identified samples.

The nasal sampling procedure for the screening of S. aureus nasal carriage was standardized to ensure accurate sample collection and completion of microbiological procedures. For each subject, a nasal swab specimen was collected from the anterior nares using Copan eSwab Liquid Amies preservation medium (eSwab Collection and Preservation System, Copan Italia, Brescia, Italy). Samples were collected by rotating a sterile cotton swab five times in both anterior nares. These swabs were then transported at room temperature and processed within 4 h. Samples were first cultured on blood agar plates for 24 h at 35 °C. Gram-positive, β-hemolytic, coagulase-positive isolates were confirmed as S. aureus using a Vitek®2 microbial identification system (bioMérieux, Marcy l’Etoile, France) according to the manufacturer’s instructions.

A total of 184 consecutive Enterobacter isolates identified as E. cloacae complex with a VITEK 2 system were collected from Kaohsiung Medical University Hospital (KMUH), a 1720-bed medical center in Kaohsiung, Taiwan, from December 1, 2013, to June 14, 2014. The identification of bacterial isolates was performed using the VITEK 2 microbial identification system (bioMérieux, Hazelwood, MO, USA). Isolates were stored at −80 °C in GermBank stocks (CMP^TM Culture Media, New Taipei City, Taiwan) until processing.