Ten microliters of each uncentrifuged urine sample was cultured on UriSelect chromogenic agar (Bio-Rad, Berkeley, CA, USA), blood agar (bioMérieux, Marcy-l’Étoile, Lyon, France) and eosin-methylene blue agar (EMB; Bio-Rad, Berkeley, CA, USA) plates with a calibrated loop, according to the manufacturer’s instructions; the plates were incubated at 37 °C for 24–48 h, aerobically [39 (link)]. In the first part of the study period (2008–2012), presumptive, biochemical reaction-based methods and VITEK 2 Compact ID/AST (bioMérieux, Marcy-l’Étoile, France) were used for bacterial identification. Starting from 2013, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was introduced to the workflow of the Institute of Clinical Microbiology. Mass spectrometry was performed by the microFlex LT MALDI Biotyper (Bruker Daltonics, Bremen, Germany) instrument, using the MALDI Biotyper RTC 3.1 software (Bruker Daltonics, Bremen, Germany) and MALDI Biotyper Library 3.1 for the spectrum analysis. The sample preparation procedure, methodology, and the technical details of the MALDI-TOF MS measurements were described elsewhere [39 (link)].
Blood agar
Manufactured by bioMérieux
Sourced in France, United States, Germany
Blood agar is a growth medium used in microbiology laboratories to cultivate and identify certain types of bacteria. It consists of a nutrient agar base supplemented with defibrinated blood, typically from sheep or horse. The blood agar supports the growth of a wide range of bacteria and allows for the observation of hemolytic reactions, which can be used to differentiate and identify bacterial species.
Automatically generated - may contain errors
Lab products found in correlation
Chocolate agar, by bioMérieux (4 mentions)
Vitek 2 compact id ast, by bioMérieux (3 mentions)
Maldi biotyper rtc 3, by Bruker (3 mentions)
Maldi biotyper library 3, by Bruker (3 mentions)
Uriselect chromogenic agar, by Bio-Rad (3 mentions)
Maldi tof ms, by Bruker (3 mentions)
Vitek 2 compact, by bioMérieux (2 mentions)
Maldi tof mass spectrometry, by bioMérieux (2 mentions)
Macconkey agar, by bioMérieux (2 mentions)
Microflex maldi biotyper, by Bruker (2 mentions)
Maldi biotyper microflex lt, by Bruker (1 mentions)
Blood agar, by Carl Roth (1 mentions)
Sabouraud dextrose agar, by Thermo Fisher Scientific (1 mentions)
Vitek 2 compact bacterial identification system, by bioMérieux (1 mentions)
Vitek 2 automated system, by bioMérieux (1 mentions)
Egg yolk tellurite emulsion, by Merck Group (1 mentions)
Staph, by bioMérieux (1 mentions)
Trypticase soy broth (tsb), by BD (1 mentions)
Chapman agar, by bioMérieux (1 mentions)
Api id32 staph test, by bioMérieux (1 mentions)
27 protocols using blood agar
1
Urine Bacterial Culture and Identification
2
Extraction and Analysis of Hawthorn Seed Compounds
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Certified standards of furfural, 2-methoxyphenol, and catechol were purchased from Aladdin Industrial Corporation (Shanghai Aladdin Bio-Chem Technology Co. LTD, Shanghai, China). High-performance liquid chromatography (HPLC) grade methanol was purchased from Honeywell B&J (Ulsan, Korea).
The dried hawthorn seed was held for more than 30 min at 150 °C in a distillation kettle to remove the moisture and the volatile oils. Then, fractions were collected for every 20 °C until the temperature rose to 270 °C. The mix sample was collected from 150 to 270 °C, relatively (Table 4 ). All extracts used in this study were provided by Shandong Buchang Shenzhou Pharmaceutical Co. LTD (Heze, China).
The standard strains (Escherichia coli ATCC25922, Staphylococcus aureus ATCC25923, Pseudomonas aeruginosa ATCC27853) were provided by The First Affiliated Hospital of Sun Yat-sen University (Guangzhou, China). The other strains (Gardnerella vaginalis BNCC337545 and Candida albicans BNCC186382) were purchased from Bena culture collection (Suzhou Bena Chuanglian Biotechnology Co. LTD, Suzhou, China). The blood agar and the Sabauraud agar used for the passage of stains were purchased from BioMérieux (Lyon, France). Meanwhile, the Muller Hinton Broth and Sabouraud medium for test were procured from Hopebiol Corporation (Qingdao Hopebiol Biotechnology Co. LTD, Qingdao, China).
The dried hawthorn seed was held for more than 30 min at 150 °C in a distillation kettle to remove the moisture and the volatile oils. Then, fractions were collected for every 20 °C until the temperature rose to 270 °C. The mix sample was collected from 150 to 270 °C, relatively (
The standard strains (Escherichia coli ATCC25922, Staphylococcus aureus ATCC25923, Pseudomonas aeruginosa ATCC27853) were provided by The First Affiliated Hospital of Sun Yat-sen University (Guangzhou, China). The other strains (Gardnerella vaginalis BNCC337545 and Candida albicans BNCC186382) were purchased from Bena culture collection (Suzhou Bena Chuanglian Biotechnology Co. LTD, Suzhou, China). The blood agar and the Sabauraud agar used for the passage of stains were purchased from BioMérieux (Lyon, France). Meanwhile, the Muller Hinton Broth and Sabouraud medium for test were procured from Hopebiol Corporation (Qingdao Hopebiol Biotechnology Co. LTD, Qingdao, China).
3
Rabbit Skin Infection Examination
4
Characterization of Acinetobacter baumannii Phage
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Acinetobacter baumannii clinical isolate (PUM45202) identified by VITEK®2 compact (bioMérieux Inc., Durham, NC, USA) was used in this study. The bacterial strain was stored at −80 °C before use and was grown on blood agar (bioMérieux Inc., Durham, NC, USA) for 18–24 h at 37 °C to revitalize. This strain was described before by Grygorcewicz et al. (2022) [26 (link)]. CFU of Acinetobacter baumannii was analyzed with standard plating methods on LB medium. The bacteriophage vB_AbaP_AGC01 was used in this study. Used bacteriophage was previously characterized by Grygorcewicz et al. (2020) [8 (link)]. Bacteriophage was propagated as described before using LB medium (Miller modification, Merck KgaA, Darmstadt, Germany) at 37 °C with shacking 160 rpm for 4 h. After that, phage lysate was centrifuged and filtered through a 0.22 μm polyethersulfone membrane syringe filter. The standard double-layer agar method assessed phage viable particles as described before [27 (link)].
5
Anaerobic Culture of Bt (DSM 2079)
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Bt (DSM 2079) was purchased by DSMZ (Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures) and cultured on blood agar (Biomerieux, Marcy l’Etoile, France) at 37°C under anaerobic conditions with GENbox and GENbox anaer systems (Biomeriux, Marcy l’Etoile, France).
6
Isolation and Characterization of Clinical Microbes
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Clinical isolates of Candida spp. were maintained on Sabouraud dextrose agar (Oxoid, Wesel, Germany) and incubated at 37 ⁰C for 24 h. Lactobacillus spp. were maintained on de Man Rogosa Sharpe (MRS) agar (Oxoid) and blood agar (Carl Roth GmbH, Karlsruhe, Germany), followed by incubation at 37 ⁰C, 5% CO2 for 24–48 h. Gram-negative bacteria, particularly Escherichia coli were maintained on blood agar and incubated at 37 ⁰C for 24 h. Subsequently, species level identification was done using the Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (bioMérieux, Marcy I’Etoile, France). All identified microbes were stored at -80°C in a preservative Cryobank tubes (CRYOBANKTM Mast Group Ltd., Merseyside, UK) according to the manufacturer’s instruction. All strains were isolated from clinical specimens.
7
Antibiotic Resistance Profiling of Acinetobacter baumannii
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Acinetobacter baumannii (ATCC®16909™) was obtained from ATCC (Manassas, VA, USA). In addition, 185 MDRAB strains isolated from clinical specimens were accessed at the Pomeranian Medical University in Szczecin (Szczecin, Poland). Strains were characterized using a VITEK®2 Compact Bacterial Identification System (bioMérieux, Warsaw, Poland) and validated by MALDI-TOF mass spectrometry. Antibiotic susceptibility was assessed according to CLSI guidance. Bacterial strains were stored at −80 °C before use. Bacterial strains were grown on blood agar (bioMérieux, Warsaw, Poland) for 24 h at 37 °C to revitalize prior to further application.
8
Campylobacter Isolation from Turkey Samples
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Campylobacter isolates were recovered in 2014 (n = 170; 133 C. coli and 37 C. jejuni) from turkey samples obtained in the framework of the European Antimicrobial Resistance Surveillance program (DC 652/2013) in Spain (European Comission, 2013 ). Samples were collected at the largest turkey slaughterhouses in Spain located in different regions within the country. Each Campylobacter isolate represented a single farm and they were obtained by culturing pooled feces from turkeys (117 pooled samples: 10 animals per pool, 1170 individual fecal samples analyzed). Each pooled sample was cultured on Campylobacter blood-free selective medium (CCDA) (Oxoid). Inoculated media were incubated at 42°C for 48 h under microaerobic conditions with a commercial gas-generating system (atmosphere generator system, Oxoid). Suspected colonies were subcultured onto blood agar (BioMérieux) at 37°C for 48 h. All strains were identified by conventional multiplex PCR of the genus Campylobacter that allows the differentiation between C. coli and C. jejuni with specific primers, as described previously (Ugarte-Ruiz et al., 2012 (link)).
9
Endotracheal Tube Microbiome Analysis
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ETTs were removed (extubation) by medical staff, immediately placed in 500 mL sterile glass bottles (Schott, Germany), and processed at the Microbiology Laboratory of the University Hospital Fundación Santa Fe. 10 cm from the distal part of each tube were cut and placed in 0.85% NaCl. Associated bacteria were dislodged using three vortex cycles (30 s) followed by sonication (60 s).
The suspension obtained from each ETT was used to recover microorganisms on blood agar (bioMérieux, France), MacConkey agar (bioMérieux, France) and Chocolate agar (bioMérieux, France), incubating at 37 °C for 18–24 h [14 ]. Bacterial identification was carried out employing the VITEK® 2 automated system (bioMérieux, France). All samples were handled by the same person, stored at 4 °C for 2–4 h prior to further analyses, taking care to minimize variability associated with sample handling.
The suspension obtained from each ETT was used to recover microorganisms on blood agar (bioMérieux, France), MacConkey agar (bioMérieux, France) and Chocolate agar (bioMérieux, France), incubating at 37 °C for 18–24 h [14 ]. Bacterial identification was carried out employing the VITEK® 2 automated system (bioMérieux, France). All samples were handled by the same person, stored at 4 °C for 2–4 h prior to further analyses, taking care to minimize variability associated with sample handling.
10
Isolation and Identification of Staphylococcus aureus
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The reference strain S. aureus American type culture collection (ATCC) 25923, obtained from the collection of L.A. Tarasevich State Research Institute for Standardization and Control of Medical Biological Preparations (Moscow, Russia) was used in this study [28 ]. Microorganism cultures were freeze-dried in 0.5% semi-liquid meat-peptone agar at 4°C ± 1°C. Microorganisms were cultured at 37 ± 1°C for 24 or 48 h on Blood Agar (Biomerieux, Marcy l’Etoile, France), Nutrient Broth and Baird–Parker Agar (HiMedia™ Laboratories Pvt. Ltd., Mumbai, India)) with 50 mL egg yolk tellurite emulsion (Merck, Darmstadt, Germany). Identification of S. aureus was confirmed using API (analytical profile index) Staph (Biomerieux).
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