Microflex mass spectrophotometer

For MALDI-TOF MS identification, ribosomal protein extraction was performed as described by Hijazin et al. [11 (link)]. The protein spectra were captured by a Microflex™ mass spectrophotometer (Bruker Daltonics, Inc., Billerica, MA, USA) and FlexControl™ v3.4 (Bruker Daltonics, Inc., Billerica, MA, USA) software using the MTB_autoX method. The spectrophotometer was externally calibrated using the Bacterial Test Standard (BTS—Bruker Daltonics, Inc., Billerica, MA, USA). The microbial identification was performed by BioTyper™ 3.0 (Bruker Daltonics, Inc., Billerica, MA, USA) using the manufacturer’s criteria: the species were assigned with log score values ≥ 2.0; scores ≥ 1.7 and <2.0 determined only genus identification.

For E. coli isolation, swabs were streaked on MacConkey agar and Chromagar™ Orientation (Difco, Sparks, MD, USA) and incubated at 37 °C for 24 h under aerobic conditions. Suspected bacterial colonies were sub-cultured in 3.0 mL of Brain Heart Infusion (BHI) broth (Difco, Sparks, MD, USA), and aliquots were taken from this culture for DNA extraction and strain identification using Matrix Associated Laser Desorption-Ionization—Time of Flight (MALDI-TOF) mass spectrometry.
For MALDI-TOF MS, ribosomal protein extraction was performed as described by Hijazin et al. [13 (link)]. The Microflex™ mass spectrophotometer (Bruker Daltonics, Inc., Billerica, MA, USA) from the Environmental Company of the State of São Paulo (CETESB) was used. The protein spectra were captured by the FlexControl™ (Bruker Daltonics, Inc., Billerica, MA, USA) using the MTB_autoX method. The spectrophotometer was externally calibrated using the Bacterial Test Standard (BTS—Bruker Daltonics, Inc., Billerica, MA, USA). The microbial identification was performed by BioTyper™ 3.0 (Bruker Daltonics, Inc., Billerica, MA, USA) using the following manufacturer criteria: species were assigned log score values ≥ 2.0, while scores between ≥ 1.7 and <2.0 determined only genus identification.