Title: Infectious Disease Diagnostics
Keywords: Tropical medicine
Technology
Pathogens
Laboratory science (incl.. quality assurance)
Health infrastructure
Country: Germany
Institution: Germany - Center for International Health at the Ludwig-Maximilian-Universität München
Course coordinator: Karsten Schacht
Date start: 2018-01-29
Date end: 2018-02-02
About duration and dates: One week with five full days (42 contact hours) on-campus, pre-reading (10 hours), seminar report submission after the course
Classification: advanced optional
Mode of delivery: Face to face
Course location:
Part 1: Department for Infectious Diseases and Tropical Medicine, Leopoldstr. 5, 80802 Munich, Germany
Part 2: Max von Pettenkofer- Institute, Marchioninistr. 17, 81377 Munich, Germany
Part 3: Institute of Medical Microbiology, Immunology and Hygiene, Trogerstr. 30, 81675 Munich, Germany
ECTS credit points: 2 ECTS credits
SIT: 60 Hours

Contact hours:
Part 1: Polymerase Chain Reaction (PCR) 12 hours
Part 2: Molecular Cloning Techniques 21.5 hours
Part 3: Parasite lifecycle based immunological and diagnostic methods (Schistosomiasis)8 hours
Self-Study: Pre-Reading Assignment, Parasite lifecycle 18 hours
Assessment: 0.5 hours
Language: English
Description:
At the end of the course, student will be able to:
• design laboratory settings for their own research projects
• apply the basics of molecular cloning as a specific breakout-technique of molecular diagnosis
• apply the value of basic microscopical and immunological research methods in an experimental animal model
• apply, analyze and evaluate up-to-date laboratory methods and techniques in the field of direct diagnosis of infectious diseases, such as mycobacterial DNA extractions, conventional PCR, dry-reagent-based PCR, quantitative real-time PCR as well as loop-mediated isothermal amplification procedures, and parasite isolation in the example of Schistosoma mansoni
• appraise requirements for working in a S2-laboratory
Assessment Procedures:
Written theoretical examination (multiple choice questions, 30 minutes) in the application and evaluation of molecular methods in diagnosis of tropical infectious diseases (PCR and cloning) on day 4. In case of failure, students will be subjected to an audio-visual oral online examination. Grading: A-D, F.

In addition, students will be assessed daily by the facilitators for their active participation on a pass/ fail basis. Day 5 will be assessed exclusively in this manner.
Content:
Polymerase Chain Reaction
• Application of different PCR formats and techniques for the diagnosis of mycobacterial infections (e.g. Buruli ulcer) in the context of various clinical questions (conventional, gel based PCR, dry-reagent-based PCR, quantitative real-time PCR, loop-mediated isothermal amplification procedures (LAMP))
• Trouble-shooting
• Parameters for validation of various PCR assays


Molecular Cloning Techniques
Learning and applying molecular cloning techniques. A target gene, encoding for the fluorescent mCherry protein, will be amplified and cloned into a standard plasmid vector. Competent E. coli bacteria will then be transformed with the newly generated transgene carrying plasmid. After culturing the bacteria in selective media, plasmids will be isolated and analyzed for the presence of the transgene. These techniques can for example be used to generate standards for Real Time PCR based quantification of pathogens.


Parasitology lifecycle based methods (Schistosomiasis)

• Familiarization of students through pre-course assignment with the etiology, clinical presentation and particularly the life cycle of schistosomiasis.
• On-campus familiarization with diagnostic parasitology laboratory facilities. Discussion of ethical aspects of animal models for basic immunological research questions in the field of host-parasite interaction (schistosome mouse model). Presentation of the different life cycle steps of schistosomiasis in two hosts (mouse and molluscs). Perform methods for qualitative and quantitative analysis of schistosome infestation. Demonstration of methods to assess the hosts immune responses at given infection timepoints.
Methods:
Day 1: PCR I, all-day
1) 45 minutes lecture to introduce the application of molecular methods for the diagnosis of tropical infectious diseases
2) 15 minutes laboratory safety instructions
3) 3 hours practical exercise:
• laboratory introduction
• laboratory practice
• DNA extraction
4) 1 hour lecture to introduce PCR and LAMP techniques
5) 3 hours practical exercise (different types of PCR)

Day 2: PCR II, morning session

1) 3 hours practical exercise (LAMP, analysis of PCR and LAMP results)
2) 1 hour presentation and discussion of results, wrap up

Day 2: Molecular Cloning techniques I, afternoon session

1) 1 hour instruction for working in a S2 laboratory
2) 30 minutes introduction of course contents and schedule
3) 1.5 hours lecture: Basic techniques in molecular cloning
4) 2 hours practical bench work (without incubation times):
• Amplification of target gene using PCR
• Analyses of PCR amplicons on agarose gels
• Ligation of amplicon and plasmid vector
• Transformation of competent E. coli bacteria
• Plating out bacteria on ampicillin agar plates

5) 15 minutes group discussion and first day summary

Day 3: Molecular Cloning techniques II, all-day

1) 1 hour lecture on molecular cloning for vaccine development
2) 5 hours practical bench work: Picking and growing transformed bacteria in selective media.
3) 2 hours lecture; restriction enzymes; expression of recombinant proteins; selection of resistant bacteria; eukaryotic expression systems
4) 15 minutes group discussion and second day summary

Day 4: Molecular Cloning techniques III, all-day

1) 5 hours of practical bench work:

• plasmid extraction
• molecular analyses of extracted plasmids for transgene insert using restriction enzyme digestion and via PCR analysis
1) 2 hours group working project
5) 30 minutes group discussion and final summary
6) 30 minutes multiple choice exam on contents of seminar days 1-4

Day 5: Parasitology lifecycle based methods (Schistosomiasis), all-day

1) 1 hour lecture on key aspects of schistosomiasis and schistosome life cycles
2) 30 minutes introduction of participants into laboratory facilities
3) 30 minutes introduction of participants into the different life cycle models
4) 5 hours of bench work with differentiation of schistosomes in its different developmental forms

5) 1 hour tutored microscopy of prepared histological samples in liver tissue for immunological granuloma assessment
Prerequisites:
• Basic laboratory skills
• Intermediate level training in infectious diseases;
• Proof of English fluency: tropEd students from an accredited tropEd home institution that have passed a core course in English language will be considered sufficiently fluent in English language. Also students that can provide proof of academic education passed entirely in English language will be considered sufficiently fluent. Applicants not being able to provide either of these criteria will be asked to proof fluency by a TOEFL (iBT score >= 79) or IELTS (score >=6.0)
Attendance:
Max. number of students 8
Up to 5 tropEd Master’s students are admitted
Selection:
Students are selected on a first-come, first-serve basis
Fees:
1000 Euro.
Scholarships:
None
tropEd accreditation:
Accredited in October 2015. This accreditation is valid until October 2020.
Remarks:
Upon completion of the one-week on-campus course, all participants are required to deliver a brief report on their personal reception and retained contents of the course, to be submitted within 14 days after the last on-campus course day. Reporting templates will be provided by CIH Office. The reports are mandatory but will not be graded
Email Address: froeschl@lrz.uni-muenchen.de
Date Of Record Creation: 2015-10-10 23:40:52 (W3C-DTF)
Date Of Record Release: 2015-10-11 03:52:14 (W3C-DTF)
Date Record Checked: 2017-10-24 (W3C-DTF)
Date Last Modified: 2017-10-25 15:12:18 (W3C-DTF)

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