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Infection Microbiology: Antimicrobial Resistance and Molecular Typing
Provider: Faculty of Health and Medical Sciences

Activity no.: 3125-21-00-01There are 6 available seats 
Enrollment deadline: 01/10/2021
Date and time01.11.2021, at: 09:00 - 12.11.2021, at: 16:00
Regular seats16
Course fee14,520.00 kr.
LecturersLuca Guardabassi
ECTS credits6.00
Contact personCarmen Espinosa Gongora    E-mail address: ceg@sund.ku.dk
Enrolment Handling/Course OrganiserPhD administration     E-mail address: fak-phdkursus@sund.ku.dk

Aim and content
This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at graduate schools in the other Nordic countries. 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 Nordic countries. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.

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 interpret correctly data on antimicrobial susceptibility testing.
• Evaluate the different tools available for typing antimicrobial-resistant bacteria and for studying the occurrence of AMR genes or the effects of antimicrobial therapy in complex bacterial communities.

• Perform and interpret data generated by current methods for AMR detection and antimicrobial susceptibility testing.
• Analyze data generated by different bacterial typing methods, including whole genome sequencing.
• Analyze data generated by 16S rRNA gene sequencing and shotgun metagenomics.

• 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, the impact of antimicrobials on the gut microbiome, 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 AMR gene profiling through shotgun metagenomics sequencing. 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 the results of their team work by a poster 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 programmes
The course is relevant to PhD students from the following graduate programmes 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
Luca Guardabassi, lg@sund.ku.dk, Department of Veterinary and Animal Sciences/Section for Veterinary Clinical Microbiology

Responsible teacher: Carmen Espinosa Gongora, ceg@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

1 - 12 November 2021

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

Please register before 1 October 2021 – contact Carmen (ceg@sund.ku.dk) after deadline for registration if seats are available

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.

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