Attribute values fall within expected ranges. "NA", "ND", and "NT" indicate that no data were collected for an attribute in a particular sample. See attribute definitions for specific meaning of these codes.
Methodology:
Methodology_Type: Field
Methodology_Description:
Gull fecal samples were collected by inserting a sterile swab into recently deposited fecal material. Swabs were subsequently placed into vials with bacterial transport media, and kept cool on ice packs, for approximately 4–48 hours until frozen at -80 degrees Celsius.
Methodology:
Methodology_Type: Lab
Methodology_Description:
Samples were inoculated, using a sterile cotton swab, into a vial containing 2 ml brain heart infusion broth (BHI-broth; Becton, Dickinson, USA), supplemented with vancomycin (16 mg/L, ICN Biomedicals Inc., USA) and incubated for 18-24 hours at 36 degrees Celsius for enrichment.
Methodology:
Methodology_Type: Lab
Methodology_Description:
Selective screen: 10 µl incubated turbid BHI-broth was inoculated onto CHROMagar C3GR plates (CHROMagar, France) to screen for E. coli. All plates were incubated in aerobic conditions for 18–24 hours at 36 degrees Celsius. One randomly selected pure E. coli colony, confirmed by MALDI-TOF, was chosen from each plate displaying evidence for E. coli growth and tested for antibiotic susceptibility. Antimicrobial susceptibility testing was performed equivalently on all E. coli isolates resulting from selective screening approaches in accordance with the European Committee on Antibiotic Susceptibility (EUCAST) disc diffusion method (Matuschek et al. 2014) using the following set of antibiotic discs (obtained through Oxoid Ltd, Basingstoke, Hampshire, England): ampicillin (10 µg), cefadroxil (30 µg), chloramphenicol (30 µg), ciprofloxacin (5 µg), gentamicin (10 µg), mecillinam (10 µg), meropenem (10 µg), nalidixic acid (30 µg), nitrofurantoin (100 µg), piperacillin-tazobactam (36 µg), tetracycline (30 µg), trimethoprim (5 µg), trimethoprim-sulfamethoxazole (25 µg), amoxicillin/clavulanic acid (30/1 μg), cefotaxime (5 μg), ceftazidime (10 μg), cefepime (30 μg), and cefoxitin (30 μg). Inhibition zone diameters were interpreted according to EUCAST breakpoints (Matuschek et al. 2014). There are currently no defined clinical breakpoints for chloramphenicol, nalidixic acid, and tetracycline for E. coli isolates, therefore the inhibition zone diameters were interpreted by breakpoints defined by the Normalized Resistance Interpretation method (Kronval et al. 2003).
Methodology:
Methodology_Type: Lab
Methodology_Description:
Non-selective screen: Ten µl from all turbid BHI-broth samples were inoculated on Uriselect agar plates (Bio-Rad Laboratories, France) to identify E. coli isolates. All plates were incubated in aerobic conditions for 18–24 hours at 36 degrees Celsius. One randomly selected pure E. coli colony, confirmed by MALDI-TOF, was chosen from each plate displaying evidence for E. coli growth and tested for antibiotic susceptibility. Antimicrobial susceptibility testing was performed equivalently on all E. coli isolates resulting from selective screening approaches in accordance with the European Committee on Antibiotic Susceptibility (EUCAST) disc diffusion method (Matuschek et al. 2014) using the following set of antibiotic discs (obtained through Oxoid Ltd, Basingstoke, Hampshire, England): ampicillin (10 µg), cefadroxil (30 µg), chloramphenicol (30 µg), ciprofloxacin (5 µg), gentamicin (10 µg), mecillinam (10 µg), meropenem (10 µg), nalidixic acid (30 µg), nitrofurantoin (100 µg), piperacillin-tazobactam (36 µg), tetracycline (30 µg), trimethoprim (5 µg), and trimethoprim-sulfamethoxazole (25 µg). Inhibition zone diameters were interpreted according to EUCAST breakpoints (Matuschek et al. 2014). There are currently no defined clinical breakpoints for chloramphenicol, nalidixic acid, and tetracycline for E. coli isolates, therefore the inhibition zone diameters were interpreted by breakpoints defined by the Normalized Resistance Interpretation method (Kronval et al. 2003).
Methodology:
Methodology_Type: Lab
Methodology_Description:
DNA was extracted from all antimicrobial resistant E. coli isolates using the MagnaPure compact nucleic acid isolation kit (Roche, Mannheim, Germany). Multiplexed DNA libraries were prepared for whole genome sequencing using the Nextera DNA Flex library preparation kit (Illumina, San Diego, USA) according to manufacturer’s instructions. Paired-end sequencing was performed using the MiSeq or HiSeq 4000 platform (Illumina, San Diego, USA) using either 150, 250, or 300 base pair read lengths.
Source_Information:
Source_Citation:
Citation_Information:
Originator: National Center for Biotechnology Information (NCBI)
Publication_Date: Unknown
Title: BioSample
Geospatial_Data_Presentation_Form: database
Online_Linkage: https://www.ncbi.nlm.nih.gov/biosample
Type_of_Source_Media: digital database file
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2020
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: NCBI BioSample
Source_Contribution:
Sequences obtained in this study were submitted to the NCBI BioSample publicly available genetic sequence data database.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Kronvall, G.
Originator: Kahlmeter, G.
Originator: Myhre, E.
Originator: Galas, M.F.
Publication_Date: 2003
Title:
A new method for normalized interpretation of antimicrobial resistance from disk test results for comparative purposes
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Clinical Microbiology and Infection
Issue_Identification: 9(2):120-132
Publication_Information:
Publication_Place: online
Publisher: Elsevier
Other_Citation_Details:
Kronvall, G., Kahlmeter, G., Myhre. E., Galas, M.F. 2003. A new method for normalized interpretation of antimicrobial resistance from disk test results for comparative purposes. Clinical microbiology and infection 9(2):120-132 doi:10.1046/j.1469-0691.2003.00546.x
Online_Linkage: https://doi.org/10.1046/j.1469-0691.2003.00546.x
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2003
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Kronval et al 2003
Source_Contribution:
Lab Technique: describes the Normalized Resistance Interpretation method to determine inhibition zone diameters breakpoints.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Matuschek, E.
Originator: Brown, D.f.J.
Originator: Kahlmeter, G.
Publication_Date: 2014
Title:
Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories.
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Clinical Microbiology and Infection
Issue_Identification: 20(4):0255-0266
Publication_Information:
Publication_Place: online
Publisher: Elsevier
Other_Citation_Details:
Matuschek, E., Brown, D.F.J., Kahlmeter, G. 2014. Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories. Clinical Microbiology and Infection 20:0255-0266 doi:10.1111/1469-0691.12373
Online_Linkage: https://doi.org/10.1111/1469-0691.12373
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2014
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Matuschek et al. 2014
Source_Contribution:
Lab Technique: describes the techniques used in non-selective screen
Process_Step:
Process_Description:
Data were transcribed from field data collections sheets. Antimicrobial susceptibility measurements were obtained from J. Bonnedahl and colleagues at Kalmar County Hospital, in Kalmar Sweden and categorized as resistant, intermediate, or susceptible according to breakpoints described in methods.
Process_Date: Unknown