Resources

E-learning

Find below links to e-learning courses on Antimicrobial Resistance, Whole Genome Sequencing and Metagenomics.

The course 'Antimicrobial resistance - theory and methods' prepared by the Technical University of Denmark, National Food Institute, is available as a massive open online course (MOOC) with on-demand features for anyone that wishes to know more about the basics of antimicrobial resistance.

In 16 short video-lectures, the course covers topics such as basic definitions and overview of antimicrobials and antimicrobial effects, antimicrobial mechanisms, selection and dissemination of antimicrobial resistance as well as module on antimicrobial susceptibility testing methods. Moreover, it includes the use of genomic tools for analysis of Whole Genome Sequencing data for detection of resistance genes (and other genes of interest).

We invite you to explore the MOOC via this link: https://www.coursera.org/learn/antimicrobial-resistance

An online course on 'Whole Genome Sequencing tools and applications in surveillance of pathogens' is available for access as a MOOC.

The course includes 12 short video lectures about bacterial subtyping and applications of next generation technology to perform research and monitoring, and also demonstrations and guided exercises on the use of online tools. The lectures provide a background for WGS analyses and present the Center for Genomic Epidemiology (CGE) tools which are available online and can be used widely and by non-bioinformaticians.

We invite you to explore the MOOC via this link: https://www.coursera.org/learn/wgs-bacteria

The course ‘Metagenomics applied to surveillance of pathogens and antimicrobial resistance’ is a third online course which is available for access as a MOOC.

The course includes 22 short video lectures about the potential of metagenomics for surveillance The lectures covers the steps from sampling to sequencing including the considerations in a metagenomics study, the basics of bioinformatics analysis of metagenomics data, and the interpretation of results and potential of metagenomics for surveillance.

We invite you to explore the course via this link: https://www.coursera.org/learn/metagenomics

Expert rules

European Committee on Antimicrobial Susceptibility Testing (EUCAST)

EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.

Link to EUCAST expert rules: http://www.eucast.org/expert_rules_and_intrinsic_resistance/

Clinical and Laboratory Standards Institute (CLSI)

Clinical and Laboratory Standards Institute (CLSI) documents are developed by experts working on document development committees, subcommittees or working groups under the direction and supervision of a consensus committee. Development of CLSI standards is a dynamic process with the current documents available for purchasing via the CLSI website: http://www.clsi.org

WGS for monitoring of AMR in bacteria

How to use whole genome sequencing for monitoring of antimicrobial resistance in bacteria

(PDF document, 250 KB)

Resources related to the protocols for detecting AmpC, ESBL and carbapenemase-producing E. coli

Validation of 96 hours storage of caecal samples

(PDF document 200 KB)

Survey on the practical application of the ESBL protocol in European laboratories

(PDF document 400 KB)

Stability report - mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, and variants

Stability report - mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, and variants

(PDF document 2 MB)

Literature overview of mcr genes

Literature overview of mcr genes (January 2024)

(Excel document 50 KB)

FASTA-file (mcr, all proteins and variants) (January 2024)

(text document 100 KB)

FASTA -file (mcr, all genes and variants) (January 2024)

(text document, 100 KB)

MIC-determination (broth microdilution)

EU Surveillance Thermo Scientific(TM) Sensititre(TM) System for Antimicrobial Susceptibility Testing (AST)

(Link to recorded webinar from November 2020)

Statement from TREK regarding reading of skips on a microtitre plate
(PDF document, 345 KB)

Statement from SVA (producer of VetMIC) regarding the use of Mueller Hinton broth supplemented with 2,5%-5% lysed blood when using VetMIC for antimicrobial susceptibility testing of Campylobacter

(PDF document, 31 KB)

Broth microdilution panels used by the EURL-AR

Broth microdilution panels used by the EURL-AR
(PDF document, 100 KB)

Confirmation of ESBL-production

Methods for confirmatory testing for ESBLs
(PDF document, 70 KB)

Using E-test for confirmation of ESBL-production, and description of interpretation of results (AB-Biodisk)
(PDF document, 580 KB)

Lysis of blood

Suggested procedure for lysis of blood
(PDF document, 25 KB)

Calculating cations

Calculating cations for cation adjusted Mueller Hinton broth
(PDF document, 25 KB)

Suggested procedure for handling of reference strains

EURL-AR reference strains

On the list of reference strains available for distribution for contacts in the EURL-AR network, it is registered when a strain is not avaliable for distribution from DTU Food. In such cases it is possible to send you the DNA for the use when performing PCR. Also, in case you should want to have the strain(s), and not only the boiling lysate you are welcome to contact the EURL and we can provide information regarding who can supply you with the strain(s).

EURL-AR reference strains
(PDF document, 90 KB)

EURL-AR primer list

List of primers for detection of antimicrobial resistance genes.

EURL-AR primer list
(PDF document, 140 KB)

Nagoya protocol

The Nagoya Protocol applied to Microbial Genetic Resources
(PDF document, 2 MB)

Find via this link a video of the presentation on 'The Nagoya Protocol applied to Microbial Genetic Resources' by Carolina dos Santos Ribeiro (RIVM, NL)

Resources​

E-learning​

Expert rules​