Genomics in Medical Microbiology


The main objective of this course is to provide the fundamental concepts needed to understand the role of the emerging area of Genomics in the field of Medical Microbiology. It is also intended that students will become familiar with specific aspects related to relevant cases in which Genomics has made important contributions to the elucidation of pertinent questions in the field of Medical Microbiology.

After attending this course students should master the fundamental concepts underlying Microbial Genomics. They should also be able to critically appreciate the importance of genomics in the study of various subjects in the field of medical microbiology.

The skills to be acquired during the course are the ability to analyze and interpret genomics data, including skills in manipulating computer tools and analyzing data obtained from them. Students should also be able to study and critically discuss issues of Medical Microbiology studied with genomic approaches.

General characterization





Responsible teacher

José Paulo Nunes de Sousa Sampaio


Weekly - 4

Total - 48

Teaching language



Basic knowledge of General Biology, Microbiology, Molecular Biology and Molecular Genetics


Padmanabhan R, Mishra A K, Raoult D, Fournier P-E. Genomics and metagenomics in medical microbiology, 2013, Journal of Microbiological Methods 95: 415-424

Didelot X, Bowden R, Wilson DJ, Peto T, Crook WDW. 2012. Transforming clinical microbiology with bacterial genome sequencing. Nature Reviews Genetics 13: 601–612. 

Fournier P-E, Raoult D. 2011. Prospects for the future using genomics and proteomics in clinical microbiology. Annual Review of Microbiology 65: 169-188.


Teaching method

Available soon

Evaluation method

Available soon

Subject matter

The fundamental aspects driving the implementation of genomics in microbiology will be presented, as well as the currently most relevant laboratory techniques and the approaches underlying basic bioinformatic analyses. Procedures leading to genome mapping and annotation will be discussed. The topic of genome organization will be addressed by comparing bacteria and fungi and key concepts such as pan / core-genome, islands of pathogenicity, HGT (horizontal gene transfer) and pseudogenes, among other. The potentialities of comparative genomics and functional genomics will be analyzed. The role of the study of the human microbiome in health and disease will be analyzed. Case studies will be presented to understand the emerging role of genomics in advancing the field of medical microbiology, using both bacterial and fungal models.


Programs where the course is taught: