Molecular Epidemiology of Infectious and Parasitic Diseases


At the end of this course students should be able to:
1. Identify what molecular epidemiology is.
2. Choose and interpret molecular typing methods.
3. Use and interpret molecular analysis methods such as phylogenetics and population genetics.
4. Analyze geographic studies of infectious and parasitic agents and generate hypotheses.
5. Criticize methodologies used in transmission studies.
6. Assess evidence of a causal link between the presence of a pathogenic organism and a disease or pathology.
7. Discuss current issues of molecular epidemiology in different groups of pathogenic organisms and in clinical practice.
8. Produce and evaluate written scientific presentations on molecular epidemiology.

General characterization





Responsible teacher

Isabel Maurício


Weekly - 13,5

Total - 40

Teaching language



Attendance of 2/3 of classes is mandatory


• Molecular Epidemiology of Infectious Diseases. Principles and Practices. 2004 Ed Lee Riley. ASM Press.
• Molecular Epidemiology: practical approach. Ed. Carrington and Hoelzel. 2001 Oxford University Press.
• Tenover FC, Arbeit RD, Goering RV. How to select and interpret molecular strain typing methods for epidemiological studies of bacterial infections: a review for healthcare epidemiologists. Molecular Typing Working Group of the Society for Healthcare Epidemiology of America. Infect Control Hosp Epidemiol. 1997 Jun;18(6):426-39.
• Paustenbach D, Galbraith D. Biomonitoring and biomarkers: exposure assessment will never be the same. Environ Health Perspect. 2006 Aug;114(8):1143-9.

Teaching method

Classroom teaching: Theoretical classes and Theoretical-practical classes. Learning will be supported by formative assessment and feedback, in practical classes, in-class discussions and based on the initial version of the written analysis of three articles, with comments from faculty and other students.

Evaluation method

The summative assessment will be based in a final version of the written assay.

Subject matter

I. Introduction to UC. What is molecular epidemiology.
II. Genotyping methodologies and development. Genotyping errors.
III. Review of epidemiology concepts.
IV. Geographic associations.
V. Direct transmission studies.
VI. Vector (indirect) transmission studies.
VII. Pathogenicity studies.
VIII. Biomarkers. Concepts and integration in epidemiological studies.
IX. Biobanks and their relevance in the management of biological samples: the case study of Biotropical Resources.
X. Bioinformatics and databases for molecular epidemiology.
XI. Molecular epidemiology of malaria, drugs and vaccines.
XII. Population biology: basic concepts and application in molecular epidemiology.
XIII. Phylogenetics: basic concepts and application in molecular epidemiology.
XIV. Examples: epidemics and virus transmission.
XV. Examples: control of bacterial infections.
XVI. Examples: studies of the relationship between helminths and diseases considered non-communicable.
XVII. Mycoses and examples of application of genotyping in medical mycology.
XVIII. Molecular epidemiology of leishmaniasis - practical applications.
XIX. The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs.
XX. Metagenomics in Molecular Epidemiology: project.
XXI. Clinical: Molecular Pathological Epidemiology.


Programs where the course is taught: