2010-2011 academic year
Microbiology (20548)
Qualification/course: bachelor's degree in Medicine
Year: third
Term: second
Number of ECTS credits: 7 credits
Student commitment: 175 hours
Teaching language or languages:
Teaching staff: teaching will be coordinated by Juana Díez at UPF and by Margarita Salvadó at the UAB.
1. Introduction to the subject
The subject of Microbiology is a basic training subject within the bachelor's degree in Medicine and the bachelor's degree in Human Biology. It is taught in the second term of the third year.
2. Competences to be acquired
Theoretical competences
a) Knowledge of the impact of microorganisms on human history.
b) Knowledge of the benefits of microorganisms for human health and daily life.
c) Knowledge of the core aspects of the structure, biology and life cycle of the four groups of microorganisms important in human health: bacteria, virus, fungi and parasites.
d) Knowledge of the the main human pathogens.
e) Knowledge of the pathogenicity mechanisms in the various groups of microorganisms, transfer mechanisms and the associated clinical profiles.
f) Knowledge and interpretation of the main diagnostic tests for infectious diseases.
g) Knowledge of the basic principles of immunotherapy and the associated problems.
h) Knowledge of the basic principles of antimicrobial therapy and the problems of resistance to treatments.
Practical competences
a) Use of disinfection and sterilization techniques.
b) Work under asepsis conditions, obtaining pure cultures, estimating the number of feasible bacteria, and undertaking bacterial staining.
c) Diagnosis of urine cultures by means of microbiological and biochemical techniques and performing an antibiogram.
d) Performing diagnostic tests based on the presence of antigens.
e) Produce viral cultures and estimate the number of feasible viruses.
f) Culture and diagnosis of fungi. Observation of parasites.
General objectives
The teaching project presented here aims to avoid microbiology being studied in terms of an exhaustive list of infectious agents. On the contrary, it emphasises the main concepts of microbiology in order that students learn about the various aspects of the process of infection and the main infectious agents and their problems in a critical way. For example, if students learn the definition of bacterial conjugation, it could be the "mechanism by which a plasmid is transferred from one bacterium to another." However, if students learn about the concept of bacterial conjugation they will ask questions such as what is its biological significance? How widespread is it? How does it affect us? Learning about the concept of bacterial conjugation is active learning in which the students develop critical thought, and includes definitions and concepts from other subjects. Once learnt, it will not be forgotten, and it will in turn facilitate the learning of new concepts.
Students will be taught: i) the basic characteristics of microorganisms important to human health, ii) the biological foundations for the pathogeny and the diagnosis, treatment and prevention of the main infectious agents. These agents have been selected due to their importance to human health or their special biological characteristics. From our point of view, it would be very effective for learning if the detailed diagnosis and treatment of each of the infectious diseases was part of a future subject of Medical Pathology which included an Infectology module. This module, which is included in all medicine courses, studies the various infectious syndromes, and the infectious syndrome is thereby integrated with the approriate diagnosis and treatment.
Specific objectives
Students will have specific objectives for each topic and practical session throughout the teaching process.
3. Contents
Theory programme
As mentioned above, approximately ten topics are taught in seminar format.
I. GENERAL PRINCIPLES
The general and fundamental concepts of the microbial world are presented, as well as their classification and microbiological diagnosis.
1. Introduction to the world of microorganisms. Classification.
2. Microorganisms in human health: microflora.
3. How infectious diseases are established.
4. Diagnostic principles of infectious diseases.
II. BACTERIOLOGY
Bacterial morphology, structure, metabolism, reproduction, genetics and pathogenicity will be discussed. The main groups of pathogens will also be presented, and the pathogeny, clinical profile, epidemiology, diagnosis, treatment and prophylaxis will be described for each.
5. Bacterial morphology and structure.
6. Bacterial genetics.
7. Bacterial metabolism and growth.
8. Bacterial pathogenicity mechanisms.
9. Control of microbial growth: antimicrobial drugs, prophylaxis.
10. The genus Staphylococcus: abscesses and toxin-mediated diseases.
11. The genera Streptococcus and Enterococcus.
12. The Enterobacteriaceae family: Salmonella, Shigella and Yersinia.
13. The genus Pseudomonas and other opportunist gram-negative bacilli.
14. The genera Bordetella, Haemophilus and Legionella.
15. Anaerobic microorganisms. The genera Clostridium and Bacteroides.
16. The genera Helicobacter, Vibrio and Campylobacter.
17. The genus Mycobacterium: tuberculosis and leprosy.
18. The genus Neisseria: N. meningitidis and N. gonorrhoeae. Treponema pallidum and syphilis.
19. The genera Chlamydia and Mycoplasma: special pathogens.
20. The genus Rickettsia: the importance of Q fever.
III. VIRUSES
An introduction to the general characteristics of viruses, their classification and the main virus groups in terms of their impact on health. The pathogeny, clinical profile, epidemiology, diagnosis, treatment and prophylaxis for the main groups are considered.
21. What is a virus? The origin and development of viruses.
22. The viral multiplication cycle.
23. How viruses cause harm. The main human pathogens.
24. Viral hepatitis: the hepatitis A, B and C virus.
25. The influenza virus and other respiratory viruses.
26. Rotaviruses: diarrhoea caused by viruses.
27. Retroviruses: HIV.
28. Herpesviruses: latent infections.
29. Human papillomavirus: viral oncogenesis.
30. Treatment and prevention of viral diseases.
31. Prions.
IV. FUNGI AND PARASITES
The general characteristics of fungi and parasites will be explained, as well as their classification and the main groups that cause disease in man. The pathogeny, clinical profile, epidemiology, diagnostic, treatment and prophylaxis of these groups will be described.
32. General characteristics of fungi. Pathogeny and chemotherapy.
33. Fungi causing surface and subcutaneous mycosis.
34. Fungi causing opportunist mycoses.
35. Fungi causing systemic mycoses.
36. Introduction to pathogenic parasites: pathogenesis and chemotherapy.
37. Intestinal and urogenital protozoa.
38. Titration and systemic protozoa.
39. Nematodes. Cestodes and trematodes.
V. APPENDIX
40. Nosocomial diseases and opportunist infections.
41. Zoonosis. New and emerging diseases.
42. Infections in patients with immunosuppression.
43. Infections during pregnancy.
44. Use microorganisms for curative or palliative ends.
Practical programme
1. Microbial diversity
Objective: to learn the basic techniques of bacteriology.
Bacteria will be seeded, isolated and observed microscopically. Estimation of the number of units forming colonies. Simple and differential staining.
2. Urine analysis
Objective: to perform a microbiological analysis to detect a possible infection, identify the microorganism causing it and determine its sensitivity to antibiotics.
Urine samples will be observed. Seeding. Biochemical tests and antibiogram.
3. Diagnostic tests based on using antibodies (taught jointly with Immunology)
Objective: to carry out diagnostic tests based on using antibodies.
Various diagnostic techniques will be used, including an ELISA.
4. Virus propagation
Objective: to learn the basic techniques of virology.
An infection and titration with the VSV virus will be performed. The effect of interferon and the neutralising antibodies on the viral infection will also be measured.
5. Identification and growth of fungi. Identification of parasites
Objective: to learn the basic techniques of micology. Observe fungi and parasites.
Various fungi will be seeded, stained and observed. Various parasites will be observed.
4. Assessment
a) Assessment methods
The assessment method applied will be part of the unified assessment methodologies established by the educational authorities. We will also include a continuing assessment system. In our experience, continuing assessment fosters active learning and participation among students.
b) Types and number of assessments
There will be three types of assessment:
1. Formative evaluation: this takes place halfway through the term, is not compulsory and if passed, the student will obtain a small positive impact on the final mark. The format used will be the same as in the final assessment.
2. The following will be assessed continuously during the course:
-Practical sessions: the achievement of the objectives set will be assessed at the end of each practical session. This will involve practical tests and theoretical questions.
-Seminar and blog sessions: students' participation and where appropriate, the quality of their oral or written presentation, will be assessed.
3. Final assessment: this begins at the end of the teaching process and will include a multiple choice test (MPT) and an essay test on all the theoretical content.
c) Impact of the various types of assessment on the final mark
Final assessment: 6.5 (60% MPT, 40% essay)
Practical sessions: 1.5
Seminar sessions: 1.5
Blog: 0.5
Passing the formative evaluation entails an improvement on the final accrediting mark (a maximum of 0.5 points).
d) Pass and grading criteria
To pass the subject, students must: i) participate in the scheduled activities; ii) obtain a minimum mark of 4 out of 10 in the final theoretical assessment, and iii) obtain a minimum mark of 4 out of 10 in the continuing assessment of practical sessions.
Final considerations
As a whole, according to the planned programme, each student must write a piece of work (for the blog) and a PowerPoint presentation (for the scientific mini-seminar). Students work in groups for both activities. They must also read some scientific articles for seminar sessions and at least five of the studies uploaded to the blog. To avoid an overload of work that has a negative impact on learning, coordination between the three subjects is essential, so that if necessary, the number of activities can be adjusted and overlapping prevented.
5. Bibliography and teaching resources
5.1. Basic bibliography
We recommend two books that contain all the basic content for the subject and other more specific books for each group of microorganisms. The two basic books are:
Mechanisms of Microbial disease. 2007. N. Cary Engleberg, Victor DiRita, Terence S. Dermody. Fourth Edition. Lippincott Williams & Williams.
Sherris - Microbiología médica. 2004. 4th ed. Kenneth Ryan. McGraw-Hill Interamericana.
Microbiología clínica. 2006. Prof. G. Prats. Editorial Médica Panamericana.
Bacterial Pathogenesis: A Molecular Approach. 2001.2nd ed. Abigail A. Salyers and Dixie D. Whitt. American Society for Microbiology Press.
Microbiología médica by Jawetz, Melnick and Adelberg. 2005. 18th ed. Manual Moderno.
6. Methodology
The teaching methodology used focuses on stimulating curiosity, interest and participation in the class of students. This is essential to ensure the learning of concepts and to foster life-long learning, which are the basis of the ideas contained in the Bologna declaration in the European Higher Education Area (EHEA).
The teaching activities are based on those successfully applied by our teaching team, and are as follows:
6.1. Lectures
A graphic aid consisting of PowerPoint presentations will be used. All the presentations will be made available to students in the Virtual Classroom before the classes. This is vital if students are to take full advantage of their time and not spend class time "copying" without understanding what is being explained to them.
It is very important that lectures are designed to foster students' interest and attendance. To that end, the following activities will take place in some classes:
(i) Participation of medical professionals. The teaching of some subjects will be completed with contribution from doctors from the Hospital del Mar in order to emphasise the fact that the concepts discussed have real consequences for human health. For example, the practical consequence of the ability of bacteria to form bacterial biofilms is the contamination of catheters and prostheses, a very common cause of sepsis.
(ii) Active learning exercises. In order to foster student participation, there will be short active learning exercises involving questions with an answer that can be deduced from the content that has just been explained or questions on its social or scientific impact. For example, regarding tuberculosis, they may be asked whether immigrants should be tested for tuberculin before being admitted to Spain and why. The exercise takes about five minutes.
(iii) Microbiology news. Once a week, there will be five-minute section with the presentation of a news item related to microbiology published that week in Nature or other leading journals. This activity is very useful for showing students the wide variety of biomedical research fields in which microbiology is important.
6.2. Seminars
Approximately 20% of the syllabus will be taught in seminars. These will have various formats to avoid monotony and therefore retain the students' interest. These formats include:
a) Discussion of scientific articles.
b) Discussion of clinical cases.
c) A biofilm session.
d) A scientific miniseminar in which the students, in groups of five (a total of six groups) will present various aspects of a subject related to microbiology currently being debated. Examples of subjects to be discussed are: zoonosis and new diseases, the use microorganisms in human health (gene therapy, oncolytic viruses, prebiotics) and vaccination and the reasons behind its rejection by part of the population.
These seminars will be subject to continuous assessment.
6.3. Practical classes
Practical classes will be coordinated with the theoretical information and will complement some aspects of it; specifically, the subject of diagnosis is represented in two of the practical sessions (see programme).
The subject of Microbiology is taught with Pharmacology and Immunology, as they are closely related areas. This gives us the opportunity to coordinate these three subjects in order to promote synergies, as well as to avoid repetition of concepts. As a first step in this direction, we have established collaboration with the subject coordinators of Immunology for teaching a joint practical session on diagnostic tests based on the use of antibodies.
6.4. Online activities
Blogs are a new and very frequently used vehicle for communication and debate. Using a blog to discuss topics related to microbiology has been very highly rated by our Biology students, and we are adapting it to this new programme as a result. The objective of this activity is: (i) to foster interest, interaction and debate among students, (ii) to work on written communication by the presentation and discussion of a scientific opinion essay.
The mechanics of the activity are as follows: students are divided into groups of 5 or 6 (a total of 20 groups) and the order in which the articles are to be presented will be determined during the first week. Four subjects complementing those in the theory classes will be proposed every two weeks. Possible examples of these subjects are: "Do enterobacteriaceae provide protection from colorectal cancer?", "the relationship between circumcision and the incidence of HIV" and "tuberculosis in Barcelona." Students will have a week to prepare a well-argued article based on good bibliographical sources of at most 1,000 words in length. Two of the four articles will be selected for uploading to the blog and opened up for discussion. A total of ten articles will be subject to debate.
7. Programme of activities