Antimicrobial resistance: from susceptibility testing to resistome profiling
Graduate School of Health and Medical Sciences at University of Copenhagen
This is a specialised course. This means that 80% of the seats are reserved to PhD students enrolled at the Faculty of Health and Medical Sciences at UCPH and 20% of the seats are reserved to PhD students from other Danish Universities/faculties (except CBS).
The course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee.
Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.
Learning objectives
To equip PhD students with a comprehensive understanding of antimicrobial resistance (AMR), integrating both phenotypic and genotypic characterization of resistant bacteria with metagenomics and resistome-level analyses.
Knowledge:
• Explain the key mechanisms and epidemiology of AMR with focus on clinically relevant pathogens
• Understand the principles for antimicrobial susceptibility testing and results interpretation
• Evaluate genomic and metagenomic approaches for AMR surveillance and research
Skills:
• Perform and interpret antimicrobial susceptibility testing and basic molecular assays for AMR detection
• Prepare samples for whole genome sequencing and shotgun metagenomics
• Apply bioinformatics workflows to profile taxa and AMR genes from genomes and metagenomes
Competences:
• Operate open-source tools and databases for AMR gene detection and resistome profiling
• Critically evaluate methodological challenges in culture-based and metagenomic AMR studies
• Communicate findings and discuss their implications for AMR surveillance and research
Content
The course has a duration of 2 weeks and employs a problem-based learning approach, using real-life clinical and epidemiological scenarios to drive learning. The course integrates theory, laboratory work, and bioinformatics in an approximately 50:50 balance. The theoretical component consists of lectures, guided exercises, and group discussions covering AMR fundamentals, molecular epidemiology, One Health perspectives, and common methodological pitfalls in AMR research. The core practical theme is nasal colonization and AMR in staphylococci.
During the first week, students generate and analyze their own data from nasal swabs (voluntary participation), combining culture-based microbiology, molecular assays, and strain typing. Students will:
• Swab the anterior nares and perform culturomic plating on selective and non-selective media
• Isolate staphylococci for phenotypic and genotypic AMR testing (MIC, PCR and LAMP assays) and molecular typing (spa typing and MLST prediction)
• In parallel, students extract DNA from a second swab for shotgun metagenomic sequencing
During the second week, the bioinformatics module focuses on analysis of these metagenomic data, including:
• Community profiling using read-based approaches and MAG-based reconstruction
• Comparison of culture-based vs metagenomic findings
• Resistome profiling of nasal samples and critical interpretation of resistome outputs
• Extension activities using published datasets to explore epidemiological transmission of pathogens and resistome patterns across settings and reservoirs
Throughout the course, students work in groups on 2–3 case scenarios that link laboratory and bioinformatics outputs to epidemiological questions. At the end of the course, each group delivers an oral presentation summarizing methods, results, interpretation, and limitations, with emphasis on integrating phenotypic, typing, and resistome evidence.
Participants
PhD students are required to have basic knowledge and skills in microbiology.
Relevance to graduate programmes
The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH:
Veterinary, Animal Health and Microbiological Sciences
Immunology and Infectious Diseases
Biostatistics and Bioinformatics
Language
English
Form
Lectures, laboratory work, group discussions, journal club, poster presentations.
Course director
Luca Guardabassi (lg@sund.ku.dk) and Mattia Pirolo (mapi@sund.ku.dk), Department of Veterinary and Animal Sciences/Section for Veterinary Clinical Microbiology
Teachers
Responsible teacher: Mattia Pirolo, Department of Veterinary and Animal Sciences/Section for Veterinary Clinical Microbiology.
Other staff at the Department of Veterinary and Animal Sciences as well as invited lectures from other research institutions in Denmark and abroad.
Dates
21 September 2026 - 2 October 2026
Course location
Department of Veterinary and Animal Sciences, Stigbøjlen 4, 1870 Frederiksberg C
Registration
Please register before 21 August 2026
Expected frequency
The course is recurrent and held each year.
Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules.
Applications from other participants will be considered after the last day of enrolment.
Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.