Here you will find the presentations and materials from the simulated exercises conducted in the EURGen-RefLabCap project.
1st virtual multidisciplinary training workshop to resolve a CCRE outbreak scenario using simulation exercises (September/October 2022)
Multidisciplinary training workshop engaging a mix of national microbiology experts and health care epidemiology experts.
The training included exercises on WGS data analysis, including sequence quality control, in silico typing and detection of antimicrobial resistance genes as well as cluster analysis. The training was organised as virtual outbreak exercise to practice and test the capability to use WGS-data in outbreak investigations and interpreting these in relation to the epidemiological investigations.
The first workshop was divided into two online sessions of approximately two hours. The first session introduced the scenario, introduce phylogenetic analysis and explain the exercise dataset and setup. After the first session, sequences and exercise material will be shared with the participants and they will have approximately two weeks to work with the exercise. During the second session, a walk-through of the exercise will be presented, and participants can ask questions, show their own results and participate in discussion with other participants and exercise coordinators.
Exercise overview
Intro and CSIPhylogeny by Jette Sejer Kjeldgaard, DTU
SNP vs cgMLST by Henrik Hasman, SSI
MinION typing by Henrik Hasman, SSI
Exercise guidelines
Exercise questions
Exercise metadata
2nd Virtual multidisciplinary training workshop to resolve a carbapenem resistant Klebsiella pneumoniae outbreak scenario using a simulation exercise (May 2023).
The training workshop continued along the lines of the first workshop in September/October 2022. In this workshop, participants were trained in using WGS and other epidemiological data to investigate an outbreak situation caused by a carbapenem-resistant Klebsiella pneumoniae. The workshop included exercises on WGS data analysis, including sequence quality control, in silico typing and detection of antimicrobial resistance genes as well as cluster analysis.
The workshop was divided in two sessions, and the release of data injects between these sessions.
Invitation
Session 1(May 02, 2023): Online seminar to introduce outbreak scenario and methods to be used to investigate the outbreak
Session 2 (May 12, 2023): Online seminar to evaluate the results and the introduction of additional tools for WGS analysis of Klebsiella spp.
Exercise Materials
3rd Virtual multidisciplinary training workshop to resolve a carbapenem-resistant Pseudomonas aeruginosa outbreak scenario using simulation exercises (September 2023).
Multidisciplinary training workshop engaging a mix of national microbiology experts and health care epidemiology experts.
The training included exercises on WGS data analysis, including sequence quality control, in silico typing and detection of antimicrobial resistance genes, plasmid typing, as well as cluster analysis. The training was organized as virtual outbreak exercise to practice and test the capability to use WGS-data in outbreak investigations and interpreting these in relation to the epidemiological investigations.
Invitation
Session 1 (September 14, 2023): Online seminar to introduce outbreak scenario and methods to be used to investigate the outbreak
Session 2 (September 22, 2023): Online seminar to evaluate the results and the introduction of additional tools for plasmid typing using WGS data
Exercise Materials
4th virtual multidisciplinary training workshop to resolve a carbapenem-resistant and/or colistin-resistant Acinetobacter baumannii outbreak using simulation exercises (January, 2024)
This training workshop was held as a simulation exercise based on a fictitious outbreak scenario, with data release over time (22nd January to 06th February). The aim was to investigate a possible multi-hospital outbreak situation with the help of data injects (epidemiological and genomic data) from different hospitals. The publicly available Illumina sequence data was used for the simulation exercise.
The participants were familiarized with the methods of visualization of epidemiological data to be able to decide the existence of an outbreak. The participants also learnt about principles and methodologies for subtyping and cluster analysis to be able to detect CRAb outbreaks by using WGS-based methods.
Invitation
Session 1 (January 22, 2024): Online seminar to introduce the scenario and the tools to be used in the exercise
Session 2: (February 06, 2024: Online seminar to evaluate and discuss the results
Exercise Materials
5th virtual multidisciplinary training workshop to resolve a CCRE outbreak scenario using simulation exercises (October 2024)
The training workshop will continue along the lines of the previous workshops in the EURGen-RefLabCap project, and will include exercises on WGS data analysis, including sequence quality control, in silico typing and detection of antimicrobial resistance genes as well as cluster analysis. The exercise will focus on E. coli and K. pneumoniae and will be organized as virtual exercise to practice and test the capability to use WGS-data in outbreak investigations and interpreting these in relation to the epidemiological investigations.
The workshop will start on October 31, 2024 and will conclude on November 11, 2024. The invitation was sent out in September 2024.
Invitation
Online Session 1:Thursday 31 October, 2024
Online Session 2: Monday 11 November, 2024
Exercise Materials