The threat from antimicrobial resistance
Overall Course Objectives
The course provides a multi-disciplinary approach combining the disciplines of conventional microbiology, whole genome sequencing and bioinformatics to characterize antimicrobial resistance in bacteria. Antibiotic resistance will be evaluated both through conventional phenotypic methods and through genotypic approaches. Bioinformatics software will be applied to further characterize bacterial genomes in relation to development and transmission of antimicrobial resistance, as well as for evaluation of genetic relatedness between bacterial isolates.
The student will upon completion of the course i) be able to perform phenotypic antimicrobial susceptibility testing, ii) be able to perform whole genome sequencing of DNA from bacteria, iii) be able to conduct bioinformatics analyses to determine the taxonomic identity, as well as presence of antimicrobial resistance and virulence genes, and iv) be able to interpret the analytic results with the purpose to explain concerns and actions.
See course description in Danish
Learning Objectives
- Describe the history and classification of different antimicrobial agents
- Describe the mode of actions of antimicrobials and the biological mechanisms of resistance
- Explain the threat of emerging antimicrobial resistance to critically important drugs, including in a One Health context
- Outline different surveillance and monitoring approaches for antimicrobial resistance
- Perform qualitative and quantitative antimicrobial susceptibility testing, including quality control measurements
- Perform library preparation and whole genome sequencing of bacterial isolates through current WGS technologies
- Perform bioinformatics analysis and characterization of single genomes including taxonomic and type identification, prediction of plasmid content, identification of genetic mechanisms of antimicrobial resistance, and cluster analysis
- Identify clusters and possible transmission routes of bacterial pathogens
- Utilize the knowledge acquired to elucidate the spread and potential impact of antimicrobial resistance and/or important bacterial clones
- Evaluate possibilities and actions to hamper or limit further transmission of antimicrobial resistance
Course Content
The course provides a multi-disciplinary approach to assess antimicrobial resistance in bacterial pathogens to understand this emerging global threat.
The course will focus on the theoretical background of development of antimicrobials, as well as their classification, modes of action and usage for treatment, and bacterial physiology, epidemiology, acquisition of resistance, presence and transmission of mobile elements, methodologies for phenotypic and genotypic antimicrobial susceptibility testing and interpretation of results.
The course provide hands-on laboratory experience in both conventional antimicrobial susceptibility testing and whole genome sequencing technologies of single bacterial isolates. Further, introduce bioinformatics analysis to determine antimicrobial resistance in bacteria, to elucidate genetic relatedness and to characterize bacterial genomes in a One Health context.
Recommended prerequisites
Teaching Method
Approx. 40% lectures (both traditional lecturing and e-learning), 30% hands on laboratory work (antimicrobial susceptibility testing and sequencing), 30% project based bioinformatic group work on case studies
Faculty
Remarks
It is mandatory to participate in the laboratory activities.
Limited number of seats
Minimum: 15, Maximum: 30.
Please be aware that this course has a minimum requirement for the number of participants needed, in order for it to be held. If these requirements are not met, then the course will not be held. Furthermore, there is a limited number of seats available. If there are too many applicants, a pool will be created for the remainder of the qualified applicants, and they will be selected at random. You will be informed 8 days before the start of the course, whether you have been allocated a spot.