Login for PhD students at UCPH      Login for others
Infection Microbiology: Antimicrobial Resistance and Molecular Typing
Provider: Faculty of Health and Medical Sciences

Activity no.: 3125-24-00-01 
Enrollment deadline: 08/03/2024
Date and time08.04.2024, at: 09:00 - 19.04.2024, at: 15:00
Regular seats16
Course fee15,600.00 kr.
LecturersRikke Heidemann Olsen
ECTS credits6.00
Contact personMattia Pirolo    E-mail address: mapi@sund.ku.dk
Enrolment Handling/Course OrganiserPhD administration     E-mail address: phdkursus@sund.ku.dk

Aim and content

Seats for this course are reserved for PhD students at the Graduate School of Health and Medical Sciences at UCPH.

Anyone can apply for the course, but if you are not a PhD student at the Graduate School, you will be placed on the waiting list until enrollment deadline. After the enrolment deadline, available seats will be allocated to the waiting list.

The course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at NorDoc member faculties. All other participants must pay the course fee.

Learning objectives

The objective of the course is to give the students a thorough understanding of antimicrobial resistance (AMR). What is AMR? How can we measure it? How does it develop and spread? What is the public health impact? What are the molecular typing methods and approaches currently available for studying transmission of AMR between different individuals and reservoirs? These are some examples of the specific questions that will be addressed by the course.

A student who has attended and completed the assignments of the course will be able to:

• Describe resistance genes, mechanisms and epidemiological features of clinically relevant AMR
phenotypes and genotypes in key Gram-positive and Gram-negative pathogens.
• Understand the theory and the definitions that are necessary to correctly interpret data on antimicrobial susceptibility testing.
• Evaluate the different tools available for typing antimicrobial-resistant bacteria and for studying the occurrence and location of their AMR genes.

• Perform and interpret data generated by current methods for AMR detection and antimicrobial susceptibility testing.
• Gain practical skills on DNA extraction and whole genome sequencing.
• Analyze data generated by different bacterial typing methods, including whole genome sequencing.

• Design and carry out research on AMR.
• Operate open-source software for sequence analysis.
• Collaboration with fellow students when performing and evaluating laboratory experiments.
• Critical analysis and interpretation of results.


The course has a duration of 2 weeks and employs a problem-based learning approach in which real clinical cases and epidemiological scenarios are used to promote student learning of concepts and principles that are relevant to AMR research. The proportion of theory and laboratory work is approximately 50:50. The theoretical part includes lectures, exercises and group discussions on different subjects related to AMR and molecular typing, including common methodological pitfalls in AMR studies. The first part of the course provides basic definitions and concepts for understanding and measuring AMR. The significance and impact of AMR on human and animal health, and the relative contribution of veterinary antimicrobial use on AMR problems in human medicine are also covered by this introduction, which is followed by more advanced lectures addressing the latest trends and cutting-edge methodologies in AMR research.

The laboratory work focuses on state-of-the-art methods for rapid detection of clinically relevant AMR phenotypes (e.g., methicillin-resistant Staphylococcus aureus and ESBL-producing Escherichia coli), antimicrobial susceptibility testing (e.g., disc diffusion, E-test, broth microdilution and AMR gene profiling by whole genome sequencing), bacterial typing, as well as prediction of AMR gene location. The laboratory exercises are linked to 2-3 real cases, and each case is assigned to a group of students. At the end of the course, every group is supposed to summarize and discuss results of their work by an oral presentation. This group assignment is conceived to enhance student’s motivation and performance as well as a tool to evaluate student’s understanding of the topics and methods covered by the laboratory exercises.


PhD students are required to have basic knowledge and skills in microbiology.

Relevance to graduate programs

The course is relevant to PhD students from the following graduate programs at the Graduate School of Health and Medical Sciences, UCPH:

- Molecular Bacteriology and Infection
- Pharmaceutical Science
- Clinical Research
- Veterinary and Animal Sciences
- Public Health and Epidemiology
- Biostatistics and Bioinformatics




Lectures, laboratory work, group discussions, journal club, poster presentations

Course director

Rikke Heidemann, cava@sund.ku.dk, Department of Veterinary and Animal Sciences/Section for Veterinary Clinical Microbiology


Responsible teacher: Mattia Pirolo, mapi@sund.ku.dk, 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


8 - 19 April 2024

Course location

Department of Veterinary and Animal Sciences, Stigbøjlen 4, 1870 Frederiksberg C


Please register before 8 March 2024

Contact Mattia Pirolo (mapi@sund.ku.dk) after deadline for registration if seats are available.

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.

Click the search button to search Courses.

Course calendar
See which courses you can attend and when

New courses
Courses are published regularly. High demand courses are announced in spring and autumn.

Learn which courses are announced on fixed dates