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14 protocols using bacteriological agar

1

Cultivating and Maintaining EHEC Strains

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EHEC EDL-933 and TUV93–0 was a gift of Tobi Doerr (Cornell University) and John Leong (Tufts University), respectively. C. rodentium DBS100 was obtained from Gregory Sonnenberg (Weill Cornell Medicine). Difco MacConkey agar was purchased from BD Biosciences. Bacteriological agar was purchased from VWR, yeast extract and tryptone were purchased from IBI Scientific, and sodium chloride was purchased from Fisher Scientific.
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2

Characterization of S. aureus PJI Strains

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Bacterial strains, plasmids, and oligonucleotides used in this work are listed in Table 1 and Table 2. The forty-three PJI S. aureus strains used in this study were isolated from patients admitted at Sahlgrenska University Hospital (Mölndal, Sweden) with PJI of the hip or knee [32 (link),33 ]. On the other hand, twenty-six strains from wound swabs, isolated between 1966 and 2010, were obtained from the Culture Collection University of Gothenburg (CCGU).
Escherichia coli and S. aureus strains were routinely grown in Luria-Bertani medium (LB; Conda-Pronadisa, Madrid, Spain) and Trypticase soy broth (TSB; Conda-Pronadisa, Madrid, Spain), respectively, at 37 °C. When required, media were supplemented with appropriate antibiotics at the following concentrations: erythromycin (Ery), 10 µg/mL or 2.5 µg/mL; ampicillin (Amp), 100 µg/mL. Bacteriological agar was used as a gelling agent (VWR, Radnor, PA, USA).
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3

Bacterial and Phage Culture Protocols

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For P. aeruginosa and K. pneumoniae bacterial and phage culture, Lysogeny Broth (LB) (Lennox, L3022-1KG; Sigma-Aldrich, Burlington, MA, USA) and Tryptic Soy Broth (TSB) No. 2 (Millipore, Molsheim, France, 51228-500G-F) were used, respectively, with or without the addition of bacteriological agar (VWR Chemicals, Suwanee, GA, USA, # 9002-18-0).
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4

Culturing Bacterial Strains and Plasmids

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Bacterial strains, plasmids, and oligonucleotides used in this work are listed in Tables S1, S2 and S3, respectively. Escherichia coli and S. aureus strains were routinely grown in Luria-Bertani medium (Conda-Pronadisa), Trypticase soy broth (TSB; Conda-Pronadisa), or Mueller Hinton broth (MHB; Conda-Pronadisa) at 37°C. When required, media were supplemented with appropriate antibiotics at the following concentrations: erythromycin, 10 µg mL−1; ampicillin, 100 µg mL−1; and chloramphenicol, 20 µg mL−1. Bacteriological agar was used as gelling agent (VWR International).
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5

Cultivation of Foodborne Pathogens

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Listeria monocytogenes LMG 23775 (isolated from sausages) and S. Typhimurium LMG 14933 (isolated from bovine liver) were used within this study. These strains were both acquired from the Belgian Co-ordinated Collections of Micro-organisms/Laboratory of Microbiology (BCCM/LMG) of Ghent University in Belgium. Stock-cultures were stored at −80°C in Brain Heart Infusion broth (BHI, VWR International, Belgium) and Tryptic Soy Broth (TSB, Becton Dickinson, United States), respectively, which were both supplemented with 20% (v/v) glycerol (VWR International, Belgium).
For every experiment, a purity plate was prepared by spreading a loopful of stock-culture onto an agar plate [Lennox LB broth (Becton Dickinson, United States) supplemented with 14 g/L bacteriological agar (VWR Chemicals, Belgium) and 5 g/L NaCl (Sigma-Aldrich, United States)]. Agar plates were incubated for 24 h at 30 (L. monocytogenes) or 37°C (S. Typhimurium), which are the optimal growth temperatures for these microorganisms (BCCM, 2017 ). Pre-cultures were prepared by transferring one colony from the incubated purity plate into an Erlenmeyer flask containing 20 mL of broth (Lennox LB broth supplemented with 5 g/L NaCl). Pre-cultures were again incubated for 24 h at previously mentioned optimal growth temperatures to obtain stationary phase cultures with a cell density of approximately 109 CFU/mL.
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6

Bacterial Cultivation and Strain Storage

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Bacterial strains used in this study are listed in Table S2 in the supplemental material. Pseudomonas strains were grown in Casamino Acids medium, King’s B medium, or tryptic soy broth (TSB), and Escherichia coli was grown in 2.5% LB (media were from BD Bacto and MP Biomedicals). E. coli and P. aeruginosa were grown at 37°C, and other Pseudomonas strains were grown at 30°C with shaking at 200 rpm. Plasmids were propagated in E. coli TOP10F′ (Invitrogen), and E. coli Rosetta (DE3)pLysS (Novagen) was used for production of recombinant proteins. Growth media were supplemented with filter-sterilized antibiotics when needed: ampicillin (100 µg/ml; Sigma-Aldrich), chloramphenicol (15 µg/ml; Sigma-Aldrich), kanamycin (50 µg/ml; Sigma-Aldrich), and tetracycline (12.5 µg/ml; Sigma-Aldrich). Media were solidified with bacteriological agar (1.5%; VWR). Bacterial strain stocks were stored at −80°C in 25% (vol/vol) glycerol.
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7

Yeast Cultivation and Isolation Protocol

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Acetonitrile and HPLC-grade water were purchased from J.T. Baker,
Deventer, Netherlands. Formic acid and powdered, premixed yeast extract
peptone dextrose (YPD) broth were purchased from Sigma-Aldrich, Gillingham,
UK. Bacteriological agar was purchased from VWR International, Leuven,
Belgium. Donor plates of Saccharomyces cerevisiae BY4741 were provided by Dr Saverio Brogna at the University of Birmingham,
UK. Donor plates of Candida glabrata (in-house strain)
and Cryptococcus neoformans H99 were sourced from
the Institute of Microbiology and Infection, University of Birmingham,
UK.
Colonies of the three yeast species were inoculated from
overnight liquid YPD cultures onto YPD agar plates (60 mm diameter)
and incubated at 30 °C until the colonies reached a size suitable
for sampling (approximately 5 mm diameter).
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8

Culturing Bacterial Strains and Plasmids

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Bacterial strains, plasmids, and oligonucleotides used in this work are listed in Tables S1, S2 and S3, respectively. Escherichia coli and S. aureus strains were routinely grown in Luria-Bertani medium (Conda-Pronadisa), Trypticase soy broth (TSB; Conda-Pronadisa), or Mueller Hinton broth (MHB; Conda-Pronadisa) at 37°C. When required, media were supplemented with appropriate antibiotics at the following concentrations: erythromycin, 10 µg mL−1; ampicillin, 100 µg mL−1; and chloramphenicol, 20 µg mL−1. Bacteriological agar was used as gelling agent (VWR International).
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9

Antimicrobial Disk Diffusion Assay Protocol

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Pseudomonas aeruginosa ATCC27853, Escherichia coli ATCC25922, and Staphylococcus aureus indicator strains were used in this study. Lysogeny broth (LB) was prepared in distilled water with 10 g/L NaCl (VWR International Co., Mississauga, ON, Canada), 5 g/L yeast extract (EMD Chemicals Inc., Darmstadt, Germany), and 10 g/L tryptone (VWR Chemicals LLC, Solon, OH, USA). The agar medium for the disk diffusion assays was obtained by adding 15 g/L bacteriological agar (VWR International LLC, Solon, OH, USA) to the above-mentioned LB. Frozen cultures were revived on LB agar plates overnight at 37 °C. Colonies were transferred to liquid LB using a sterile cotton swab and incubated for 16 h at 37 °C and 150 rpm shaking, and this saturated culture was then used for the inoculant for the disk diffusion assay.
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10

Isolation and Cultivation of Bacterial Strains

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Bacterial strains, plasmids, and oligonucleotides are listed in Supplementary tables S1, S2 and S3. The forty-five PJI S. aureus strains were previously isolated at Sahlgrenska Hospital (Sweden) from PJI of the hip or knee [27 (link),28 (link)]. Twenty-six strains from wound infections, isolated between 1966 and 2010, were obtained from the Culture Collection University of Gothenburg (CCUG) [29 (link),30 (link)]. Escherichia coli and S. aureus were grown in Luria-Bertani medium (LB; Conda-Pronadisa, Madrid, Spain) and Trypticase soy broth (TSB; Conda-Pronadisa, Madrid, Spain) at 37 °C. Bacteriological agar was used as a gelling agent (VWR, Radnor, PA, USA). When required, growth media were supplemented with antibiotics at the following concentrations: erythromycin (Ery), 10 μg/mL or 2.5 μg/mL; ampicillin (Amp), 100 μg/mL.
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