E test gradient strip method

Biochemical characteristics of the strains were investigated using API ZYM, 20A and 50CH strips (BioMérieux) according to the manufacturer's instructions. A 20‐min‐thermic shock of fresh colonies at 80°C was done in order to test sporulation. Catalase (BioMerieux) activity was determined in 3% hydrogen peroxide solution and oxidase activity was assessed using an oxidase reagent (Becton‐Dickinson).
Cellular fatty acid methyl ester (FAME) analysis was performed by gas chromatography/mass spectrometry (GC/MS). Two samples were prepared with approximately 17 mg of bacterial biomass per tube for strain Marseille‐P2849^T and 5 mg per tube for strain Marseille‐P3277^T. Briefly, fatty acid methyl esters were separated using an Elite 5‐MS column and monitored by mass spectrometry (Clarus 500—SQ 8 S, Perkin Elmer, Courtaboeuf, France) as previously described (Dione et al., 2016). Spectral database search was performed using MS Search 2.0 operated with the Standard Reference Database 1A (NIST, Gaithersburg, USA) and the FAMEs mass spectral database (Wiley, Chichester, UK).
Antibiotic susceptibility was tested using the E test gradient strip method (BioMerieux) to determine the minimal inhibitory concentration (MIC) of each tested antibiotic on blood Colombia agar media (BioMerieux, France).

Antimicrobial susceptibility testing was performed following the guidelines and interpretive criteria of the European Committee on Antimicrobial Susceptibility Testing (EUCAST).⁵⁰ The antibiotic test panel was chosen following the recommendations of Brook et al.^{51 (link)} for antimicrobials with an available EUCAST breakpoint (Supplementary Table S5a). Antibiotic susceptibility was determined with a minimum inhibitory concentration (MIC) procedure using the E-test gradient strip method (bioMérieux) accordingly to the manufacturer’s instructions. Additionally, strains of enterococci, streptococci and enterobacteria were analyzed for their sensitivity to the antimicrobials and concentrations recommended by EUCAST⁵⁰ and EFSA^{52 (link)} with the EUCAST standardized disk diffusion method (Supplementary Table S5c).