66 Chapter 4 Supplementary data Supplementary Materials and methods Selection of training set strains A collection of deep-frozen E. coli strains was used that were cultured from routinely tested human specimens between January 2014 – March 2018 in the Radboudumc (Nijmegen, The Netherlands). Strains were routinely identified using the MALDITOF MS (BD Diagnostic Systems, Sparks, MD, USA) and susceptibility testing was performed using BD Phoenix System (BD Diagnostic Systems, Sparks, MD, USA). ESBL confirmation was performed using cefepime and cefepime + clavulanic acid, ESBL Confirm (Chrom. AmpC) Kit (98012) (Rosco Diagnostica A/S, Taastrup, Denmark) when ceftriaxone and/or ceftazidime MICs were > 1 mg/L according to EUCAST Clinical breakpoints - bacteria (v 9.0) (‘The European Committee on Antimicrobial Susceptibility Testing. Breakpoint Tables for Interpretation of MICs and Zone Diameters, Version 9.0, 2019.’, n.d.). A selection of E. coli strains with an ESBL negative phenotype and a cefoxitin MIC > 8 mg/L were selected as controls for further evaluation. Selection of validation set 1 strains We assessed all stored E. coli strains cultured between 2012 and 2015 at Amphia Hospital (Breda, The Netherlands), Elisabeth-TweeSteden Hospital (Tilburg, The Netherlands) and Bravis Hospital (Roosendaal and Bergen op Zoom, The Netherlands) which represents a Dutch hospital epidemiology to minimize selection bias. Strains identified as E. coli on the MALDI-TOF MS or VitekMS (bioMérieux, Marcy l’Etoile, France) were retrospectively selected from a collection of deep-frozen strains originated from blood cultures. ESBL confirmation was performed using the ESBL Confirm (Chrom. AmpC) Kit (98012). Selection was based upon ESBL negative phenotype and cefoxitin MIC > 8 mg/L BD obtained using BD Phoenix System or Vitek 2 (bioMérieux, Marcy l’Etoile, France). Strains were used as input for the validation of the algorithm. Selection of validation set 2 strains Three different institutes (department of Medical Microbiology, Erasmus MC, Rotterdam, The Netherlands; department of Medical Microbiology and Infection Control, Amsterdam UMC location VUmc, Amsterdam, The Netherlands; Central
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