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9 protocols using bhi agar

1

Preparation of Candida Strains for Research

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Three different Candida strains were used including C. tropicalis T26, C. tropicalis U71 and C. tropicalis V89. All strains were clinical isolates and previously characterized as highly biofilm forming (Sahal and Bilkay, 2018) . Identification was done using the 18S Ribosomal RNA Gene Sequence Analysis (Ref Gen Biotechnology Co. Ltd., 2017; Ankara, Turkey).
All Candida strains were first grown on Brain Heart Infusion (BHI) agar (Lab M Ltd, Lancashire, UK) for 24 h at 37 °C. For pre-culture preparations, single colonies were inoculated into 10 mL BHI broth (Lab M Ltd, Lancashire, UK) and incubated overnight at 37 °C. This preculture was used to inoculate a second culture of 200 mL BHI broth, which was subsequently grown for 24 h at 37 °C. Cells were harvested by centrifugation at 3220g for 10 min at 5 °C (Eppendorf 5810R, with an Eppendorf Swing-bucket rotor A-4-62, Hamburg, Germany) and washed 3 times with 10 mM potassium phosphate buffer (pH 7). Cells were counted in a thoma counting chamber and diluted appropriately to obtain the cell concentrations required for the experiments.
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2

Deferred Inhibition Spray Assay for S. aureus Resistance

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A deferred inhibition spray assay was performed to determine whether S. aureus clones had developed resistance to the toxin-producing S. epidermidis strains. The assay was performed on 10 clones from each experiment. A 25-μL spot (approximately 108 cells) of an overnight bacterial culture was pipetted onto the centre of an agar plate containing 15 mL of BHI agar (Lab M). The plates were incubated for 18 h at 37°C before 250 μL of a 10-fold diluted overnight culture of a different strain (106 cfu) was sprayed over the plate. The plates were incubated for a further 18 h after when the size of the inhibition zones produced by the central spot on the overlaid strain was assessed. The clarity of the inhibition zone was scored based on a simple scoring system of 1–4, 4 being completely clear and 1 being no detectable zone. The areas of any detectable zones were also recorded by measuring the diameter of the inhibition zone and the central colony.
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3

Enzymatic Characterization of S. aureus MRSA Strain

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For this study, S. aureus DPC5246 (Teagasc, Cork) was used to assess enzymatic ability. This MRSA strain was routinely cultured in Brain Heart Infusion broth (BHI; Sigma Aldrich, Gillingham, UK) or Muller Hinton Broth (MHB; Sigma Aldrich) at 37 °C with shaking, as well as on BHI agar plates or mannitol salt agar (MSA) plates (Lab M, Heywood, UK). Biofilm cultivations of S. aureus DPC5246 were carried out using BHI broth supplemented with 1% glucose (BHIg). Recombinant E. coli BL21 (DE3) Star (Novagen, London, UK) containing the constructs pET28a-CHAPk and pET28a-CHAPk-SH3blys were routinely grown in Luria-Bertani (LB) broth, and agar (Sigma Aldrich) supplemented with 50 μg/mL of kanamycin (Sigma Aldrich).
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4

Determination of Bacterial Load on Face Masks

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Brain Heart Infusion (BHI) agar (LAB M, Lancashire, UK) and Lysogeny Broth (LB) agar (Carlroth, Karlsruhe, Germany) plates (composition given in Supplementary Table 2), containing 1.5% (v/w) agar, were used to determine the bacterial load on the face masks before and after wearing and cleaning. The bacterial load was determined in colony forming units per ml (CFU/ml) of resuspension medium and recalculated to CFU/mask. The face mask suspension was diluted 10 times and 100 μl of undiluted and diluted suspensions were plated out on both growth media. Plates were incubated overnight at 37°C in aerobic conditions. CFUs were counted and a total of 47 colonies were isolated, subjected to colony PCR and identified using Sanger sequencing as described below. For isolation, colonies were transferred to BHI or LB liquid medium, grown statically at 37°C overnight and used for making glycerol stocks in 25% v/v glycerol stored at −80°C. To determine antibiotic resistance, the isolates were plated out on LB or BHI agar containing ampicillin and erythromycin, each at 100 μg/mL; final concentration.
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5

Antimicrobial Susceptibility Evaluation

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All chemicals were purchased from Merck (Sigma-Aldrich, Ireland), unless otherwise stated. The Jurkat cell line was purchased from the European Collection of Authenticated Cell Cultures (ECACC, UK). Bacterial cultures included Escherichia coli (#DSM3008; DSMZ, Germany), Listeria monocytogenes 36 (link) and Group B Streptococcus (GBS) 37 (link) . Antimicrobial agents included Gentamicin (10 µg) and Penicillin G (10U) (Oxoid, Thermofisher scientific, Ireland). Ringers tablets, brain heart infusion (BHI) broth and BHI agar were purchased from LAB M, UK.
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6

Listeria monocytogenes GAD system strains

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L. monocytogenes WT strains of EGD-e, 10403S and LO28 and their isogenic mutants in different genes of the GAD system (Table 1) were used in this study. Stock cultures were stored at -80°C in 15% (v/v) dimethyl sulfoxide (DMSO) (Sigma-Aldrich, Dorset, United Kingdom).
Prior to experiments, stock cultures were streaked onto brain heart infusion (BHI) agar (LAB M, Lancashire, United Kingdom) and incubated at 37°C overnight.
A single colony was transferred to 3 ml of either sterile BHI broth (LAB M) for EGD-e and 10403S or tryptone soy broth (Lab M) supplemented with 0.6% (w/v) of yeast extract (TSBY) for LO28 and incubated at 37°C with shaking (160 rpm). Bacteria were allowed to grow until stationary phase and used to inoculate the experimental culture with a 1% inoculum (v/v). These cultures were prepared in 250 ml conical flasks containing 20 ml of the same medium as used for the inoculum and incubated overnight at 37°C with shaking (120 rpm).
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7

Cultivation and Storage of C. acnes and S. epidermidis

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C. acnes standard strain ATCC 6919 was obtained from the American Type Culture Collection (ATCC) (Manassas, VA, USA), while S. epidermidis DSM 28319 (equivalent to ATCC 35984) was obtained from the German Collection of Microorganisms (Braunschweig, Germany). C. acnes was cultured anaerobically on RCM agar (Oxoid Limited, Basingstoke, United Kingdom (UK) and incubated for 48 h at 37 °C under ~5% CO2 using an anaerobic jar and anaerobic atmosphere generation bags (Sigma–Aldrich, St. Louis, MO, USA). Isolated colonies of C. acnes were sub-cultured in an RCM broth for 48 h at 37 °C under anaerobic conditions. For S. epidermidis, the bacteria were cultured aerobically on brain heart infusion (BHI) agar (LAB M limited, Lancashire, UK) and incubated at 37 °C for 18 h. Isolated colonies of S. epidermidis were sub-cultured in BHI broth and incubated at 37 °C for 18 h aerobically. Glycerol stock of each bacterial strain were prepared using their appropriate media supplemented with 25% glycerol and stored in a −70 °C freezer (Thermo Fisher Scientific, Waltham, MA, USA).
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8

Cryogenic Preservation of Listeria Strains

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All strains (Table 1) were stored in 2 ml cryovials with a 7% dimethyl sulfoxide (DMSO) at -80 o C. L. monocytogenes 10403S and EGD-e were cultured onto Brain Heart Infusion (BHI) agar (LABM, Lancashire UK) and L. monocytogenes LO28 onto Tryptic Soy Broth (Oxoid, UK) supplemented with 5% yeast extract (TSBY; Oxoid, UK) and incubated at 37 o C overnight.
Three colonies from each plate were transferred, with an inoculation loop, into BHI and TSBY broth respectively in 10 ml Sterilin polystyrene tubes and incubated at 37 o C with shaking (150 rpm) for 18 h. These overnight cultures were used to inoculate 20 ml cultures of the corresponding media (1% inoculum) in 250 ml conical flasks which then were subsequently incubated overnight at 37 o C with shaking at (150 rpm) for 18 h.
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9

Culturing Propionibacterium acnes and Staphylococcus epidermidis

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Propionibacterium acnes ATCC 6919 and Staphylococcus epidermidis ATCC 28319 were kindly provided by Dr. Mayri A. Diaz, Manchester University, UK. S. epidermidis was cultured aerobically on brain heart infusion (BHI) agar (LAB M limited, Lancashire, UK) and incubated at 37 °C for 18 h. We sub-cultured isolated colonies of S. epidermidis in BHI broth and incubated at 37 °C for 18 h aerobically. For P. acnes, we cultured the bacteria anaerobically on reinforced clostridial medium (RCM) agar (Oxoid Limited, Basingstoke, UK) for 48 h at 37 °C and ~5% CO2 using anaerobic jar and anaerobic atmosphere generation bags (Sigma-Aldrich, St. Louis, MO, USA). We sub-cultured isolated colonies of P. acnes in RCM broth for 48 h at 37 °C under anaerobic conditions.
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