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5 protocols using trypto casein soy agar

1

Antimicrobial Compound Screening Media

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In the experiments described herein, the culture media used were the following: cation-adjusted Mueller–Hinton broth (MHB II; Sigma-Aldrich, St. Louis, MO, USA and Biokar Diagnostics, Allone, Beauvais, France), Luria–Bertani broth (LB-B; Sigma, St. Louis, MO, USA), Tryptic Soy broth (TSB; Scharlau Chemie S. A., Barcelona, Spain), and Trypto-Casein Soy agar (TSA; Biokar Diagnostics, Allone, Beauvais, France). For the QS inhibition assays, the agar medium used was Luria–Bertani with a few modifications (LB*-A) and was prepared in house. The composition was as follows: 1.0 g yeast extract (Merck, Darmstadt, Germany), 10.0 g tryptone (Biolab, Budapest, Hungary), 10.0 g NaCl (Molar Chemicals, Halásztelek, Hungary), 1.0 g K2HPO4 (Biolab, Budapest, Hungary), 0.3 g MgSO4·7 H2O (Reanal, Budapest, Hungary), 5 mL Fe-EDTA stock solution and 20.0 g of bacteriological agar (Molar Chemicals, Halásztelek, Hungary) per liter of media.
The chemicals used—DMSO, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), sodium dodecyl sulfate (SDS), phosphate-buffered saline (PBS; pH 7.4), ethidium bromide (EB), reserpine, carbonyl cyanide 3-chlorophenylhydrazone (CCCP), PMZ, PAβN, and CV—were bought from Sigma-Aldrich Chemie GmbH (Steinheim, Germany), and doxorubicin (2 mg/mL) was purchased from Teva Pharmaceuticals, Budapest, Hungary.
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2

Culturing and Characterizing Microorganisms

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The culture media used in the experiments were the following: cation-adjusted Mueller-Hinton broth (MHB II; Sigma-Aldrich, St- Louis, MO, USA and Biokar Diagnostics, Allone, Beauvais, France), Tryptic Soy broth (TSB; Scharlau Chemie S. A., Barcelona, Spain), and Trypto-Casein Soy agar (TSA; Biokar Diagnostics) were purchased. Sabouraud Dextrose Agar (SDA) was purchased from Bio-Mérieux (Marcy L’Etoile, France), RPMI-1640 broth medium from Biochrom AG (Berlin, Germany), which was buffered with 3-(N-morpholino) propanesulfonic acid (MOPS), purchased from Sigma-Aldrich, to pH 7.0.
Dimethyl sulfoxide (DMSO), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), sodium dodecyl sulfate (SDS), phosphate-buffered saline (PBS; pH 7.4), ethidium bromide (EB), reserpine, and crystal violet (CV) were purchased from Sigma-Aldrich Chemie GmbH (Steinheim, Germany). Doxorubicin 2 mg/mL was purchased from Teva Pharmaceuticals, Budapest, Hungary. The antibiotics cefotaxime (CTX) was purchased from Duchefa Biochemie, Haarlem, The Netherlands, and vancomycin (VAN) from Oxoid, Basingstoke, England.
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3

Bacterial Growth Media Comparison

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Two general-purpose media were used to grow the 3 bacterial species, Brain-Hearth Infusion Broth and Trypto-Casein Soy Agar, both from BIOKAR Diagnostics©, Allonne, France.
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4

Antibiotic Susceptibility Profiling of Enterobacteriaceae

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The antibiotic susceptibility profile was evaluated for 44 isolates of Enterobacteriaceae (28 E. coli and 16 Klebsiella spp. isolates) using the disc diffusion method on Mueller–Hinton (MH) agar plates (Biokar Diagnostics, Beauvais, France) with antibiotic disc (Liofilchem, Roseto degli Abruzzi, Italy) according to the Clinical Laboratory Standards Institute (CLSI) [38 ]. Isolated colonies grown on Trypto–Casein–Soy agar (Biokar Diagnostics) for 22 ± 2 h at 37 °C were suspended in sterile saline until the turbidity was equivalent to the Mc Farlands 0.5 standard. The resulting bacterial suspensions were used to inoculate MH plates. After antibiotic disc deposition, the plates were incubated for 18 ± 2 h at 37 °C. Fifteen antibiotics were used: amoxicillin (AMX) 10 mg; amoxicillin/clavulanic acid (AMC) 30:10 mg; ceftazidime (CAZ) 30 mg; imipenem (IPM) 10 mg; cefpirome (CPO) 30 mg; aztreonam (ATM) 30 mg; cefoxitin (FOX) 30 mg; ampicillin (AMP) 10 mg; cefotaxime (CTX) 30 mg; chloramphenicol (CHL) 30 mg; tetracycline (TET) 30 mg; gentamycin (GEN) 10 mg; trimethoprim/sulfamethoxazole (SXT) 1:19 mg; azithromycin (AZM) 15 mg; ciprofloxacin (CIP) 5 mg. In each 90 mm plate, five different antibiotic discs were applied, and two replicates were used for each antibiotic. The ranges of the diameter of each antibiotic disc for analysis according to CLSI [38 ] are in Supplemental Table S1.
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5

Antibiotic Susceptibility Profiling of E. coli

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The antibiotic susceptibility profile was evaluated for 59 isolates of E. coli, using the disk diffusion method on Mueller-Hinton (MH) agar plates (Biokar Diagnostics, Beauvais, France) with antibiotic disks (Liofilchem, Roseto degli Abruzzi, Italy) according to the Clinical Laboratory Standards Institute (CLSI, 2021) [31] . Strain E. coli ATCC 25922 was used as a control. Briefly, isolated colonies grown on Trypto-Casein-Soy agar (Biokar Diagnostics) at 37 • C for 18 ± 2 h were suspended in sterile saline until the turbidity was equivalent to that of the McFarlands 0.5 standard (ca. 106 CFU/mL). The resulting bacterial suspensions were used to inoculate MH plates. After disk deposition (four per plate), plates were incubated for 18 ± 2 h at 37 • C. Fifteen antibiotics were used: amoxicillin (AMX) 10 µg, amoxicillin/clavulanic acid (AMC) 30:10 µg, ceftazidime (CAZ) 30 µg, imipenem (IPM) 10 µg, cefpirome (CPO) 30 µg, aztreonam (ATM) 30 µg, cefoxitin (FOX) 30 µg, ampicillin (AMP) 10 µg, cefotaxime (CTX) 30 µg, chloramphenicol (CHL) 30 µg, tetracycline (TET) 30 µg, gentamycin (GEN) 10 µg, trimethoprim/sulfamethoxazole (SXT) 1:19 µg, azithromycin (AZM) 15 µg, ciprofloxacin (CIP) 5 µg. The ranges of the diameters of the inhibition halos for each antibiotic used according to the CLSI 2021 [31] are listed in the Supplemental Table S1.
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