2 ml microcentrifugation tube

Standard procedures were used to cultivate bacterial cultures. Escherichia coli was cultured overnight in tryptic soy broth (TSB; Sigma-Aldrich, St. Louis, Missouri, USA). An aliquot of 2 ml of the bacterial cell culture was triple washed by spinning down the E. coli culture in a 2 ml microcentrifugation tube (Eppendorf AG, Hamburg, Germany) for 5 min at 3500 rpm. After each cycle, the supernatant TSB was removed, and the bacterial culture resuspended in 1 ml phosphate-buffered saline (PBS). The obtained bacterial concentration was 10⁸ CFU/ml. To prevent further bacterial growth during transfer experiments, microcentrifugation tubes were stored temporarily on ice.

To quantify the amount of DNA particles from each swab after having performed the experiments, the cotton swab was placed in a 2 ml microcentrifugation tube (Eppendorf AG, Hamburg, Germany) with 200 μl of mQ water (Fig. 1). Each sample was ultrasonicated for 1 min and vortexed for 10 s. To release the DNA from the silica coating, 1%vol of a highly diluted solution of buffered oxide etch (BOE) with 0.03 wt% ammonium hydrogen difluorid (NH4FHF, pure, Merck) and 0.02 wt% ammonium fluoride (NH4F, puriss., Sigma-Aldrich, St. Louis, Missouri, USA) were added to the sample. The resulting suspension was then analysed by quantitative PCR (LightCycler® 96) in a multiplex setup with three sequence-specific fluorescent probes (SPED1: Hex, SPED2: Texas Red, SPED3: FAM). All three fluorescent probes could be detected simultaneously and allowed to quantify each particle separately. The qPCR total reaction volume was 12.5 μl consisting of 2.5 μl sample solution, 0.2 μl of each primer (3x forward and reverse),0.125 μl of each probe (Microsynth AG) and Mastermix 2x (GoTaq® Probe, Promega). The qPCR program consisted of a preincubation step for 600 s at 95 °C, followed by a 2-step cycling for 15 s at 95 °C and for 60 s at 56 °C. For quantification, a dilution series with known concentration of particles was performed.