Universitat Internacional de Catalunya
Clinical Microbiology
Other languages of instruction: Catalan, English
Teaching staff
Questions will be resolved before or after class.
Course Instructor Contact Information:
Professor and Course Coordinator: Joan Marc Martínez Láinez (mlainez@uic.es)
Department of Biomedical Sciences / Microbiology Division
Lecturer: Nuria Prim (nprim@uic.es)
Seminar Instructor: Judith Lucena (jclucena@uic.es)
Introduction
Following the first-year introduction to the world of general microbiology, the clinical microbiology course aims to deepen the knowledge of the interactions between microorganisms and humans, microbiological techniques and infection control, all framed in a syndromic approach to infectious diseases.
Pre-course requirements
It is regarded as essential to have taken the Microbiology course (first year). General knowledge of cell biology and molecular biology, anatomy, histology and physiology
Objectives
Students will be provided with the knowledge of the microorganisms responsible for infectious diseases in humans. The basic concepts of the pathophysiology of microorganisms and their transmission routes will be described. The main associated clinical syndromes will be described, as well as their etiological diagnosis, treatment and prevention. Students will learn the applications of different microbiological techniques for the diagnosis and study of infectious diseases.
The training objectives are as follows:
1 Description of the main microorganisms that cause disease in humans. Learn about their most relevant characteristics, including morphology, physiology and biological cycles. Differentiate pathogenic microorganisms from commensal microorganisms. Description of the normal microbiota and its physiological functions.
2 Description of the reservoirs of microorganisms and their transmission routes.
3 Describe the pathogenicity mechanisms and virulence factors that contribute to the pathogenicity of microorganisms.
4 Describe the pathophysiology of infection: the relationship between pathogen and host. Learn about the defense mechanisms of the host. Define the concept of opportunism.
5 Learn about the main clinical syndromes associated with the different etiological agents.
6 Describe the different microbiological techniques for the etiological diagnosis of infectious diseases. Learn about the application of diagnostic tests, as well as the clinical samples that are required for the etiological diagnosis according to the source of infection, the procedures for obtaining them and their processing in the laboratory. Learn the techniques for the study of sensitivity to antibiotics.
7 Learn about the basic measures for the prevention and control of infections. Describe the different antimicrobials. Understand the concepts of intrinsic and acquired antibiotic resistance. Define the concept of nosocomial infection. Know the basic techniques to study an outbreak.
Competences/Learning outcomes of the degree programme
- CB01 - Students must demonstrate that they have and understand knowledge in an area of study that is based on general secondary education, and it tends to be found at a level that, although it is based on advanced textbooks, also includes some aspects that involve knowledge from the cutting-edge of their field of study.
- CB03 - Students must have the ability to bring together and interpret significant data (normally within their area of study) to issue judgements that include a reflection on significant issues of a social, scientific and ethical nature.
- CB04 - That students can transmit information, ideas, problems and solutions to specialist and non-specialist audiences.
- CE13 - To be aware of the impact of microbiology, genetics and biochemistry on human health, as well as the diagnostic tools used in each of the different healthcare fields.
- CG02 - To be aware of the aspects that govern pathological state and its implications at a clinical and diagnostic level.
- CG11 - To be aware of basic concepts from different fields connected to biomedical sciences.
- CT01 - To develop the organisational and planning skills that are suitable in each moment.
- CT02 - To develop the ability to resolve problems.
- CT03 - To develop analytical and summarising skills.
- CT04 - To interpret experimental results and identify consistent and inconsistent elements.
- CT05 - To use the internet as a means of communication and a source of information.
- CT06 - To know how to communicate, give presentations and write up scientific reports.
- CT07 - To be capable of working in a team.
- CT08 - To reason and evaluate situations and results from a critical and constructive point of view.
- CT09 - To have the ability to develop interpersonal skills.
- CT10 - To be capable of autonomous learning.
- CT11 - To apply theoretical knowledge to practice.
- CT12 - To apply scientific method.
- CT13 - To be aware of the general and specific aspects related to the field of nutrition and ageing.
- CT14 - To respect the fundamental rights of equality between men and women, and the promotion of human rights and the values that are specific to a culture of peace and democratic values.
Learning outcomes of the subject
At the end of the course, the student:
- Can identify the pathogenicity mechanisms and clinical pictures associated with the main human pathogens.
- Know the main diagnostic tests for infectious diseases, as well as the specific microbiological techniques which can be applied in each clinical setting.
- Can identify the reservoirs and routes of transmission of microorganisms of interest in medicine. Will know the basic measures for the prevention and control of infections.
Syllabus
The syllabus includes the basic topics in Clinical Microbiology (Bacteriology, Micology, Virology, Parasitology). Clinical syndromes are taught tranversally and they will be further covered during the case methods.
Part I. Introduction.
Introduction to Medical Microbiology. Microorganisms with pathogenic capacity for humans. Reservoir and transmission routes of pathogenic microorganisms. Human microbiota.
Pathogenesis of infections. Host-parasite relationships. Opportunistic infection. Microbial pathogenicity mechanisms and defense mechanisms.
Infectious diseases and clinical syndromes. Microbiological diagnosis and taking clinical samples. Direct and indirect diagnostic techniques. Antimicrobial sensitivity study. Prevention and control.
Part II. Bacteriology.
Introduction to bacteriology. Basic concepts: morphology and structure. Metabolism. Genetics. Main antibacterial drugs. Intrinsic resistance and acquired resistance to antibiotics.
Gram-positive cocci 1: Staphylococci. General characteristics. Staphylococcus aureus. Reservoir and pathogenic action. Other staphylococci with pathogenic capacity for humans.
Gram-positive cocci 2: Streptococci and enterococci. General characteristics, classification, reservoir and pathology. Streptococcus pyogenes. S.agalactiae, pneumococcus, viridans group streptococci. Genus Enterococcus.
Gram-negative cocci: Genus Neisseria. General characteristics, reservoir and pathology.
Gram-negative bacilli: Enterobacterales. General characteristics, reservoir and pathology. Primary and opportunistic pathogenic enterobacteria.
Non-fermenting gram-negative rods. General characteristics. Pseudomonas aeruginosa. Other non-fermenting gram-negative rods.
Curved gram-negative rods. Genera Campylobacter, Helicobacter and Vibrio.
Nutritionally demanding gram-negative rods. Genera Legionella, Brucella, Bordetella, Haemophilus, bacteria of the HACEK group.
Gram-positive bacilli. Corynebacterium diphteriae. Coryneform bacteria. Listeria monocytogenes. Genus Lactobacillus. Sporulated gram-positive bacilli (genus Bacillus).
Anaerobic bacteria. General characteristics. Non-sporulated anaerobic bacteria. Sporulated anaerobic bacteria (genus Clostridium).
Acid-fast bacilli. Genus Mycobacterium: Mycobacterium tuberculosis. M. leprae and environmental mycobacteria.
Spirochetes. Main genera Treponema, Borrelia and Leptospira. General characteristics, habitat and pathology.
Mycoplasmas, Chlamydia, and Rickettsiae. Bacteria of obligate intracellular life. General characteristics, habitat and pathology.
Part III. Mycology.
General mycology. Classification and morphology. Pathogenesis Classification of mycoses. Microbiological diagnosis. Antifungals.
Yeast fungi causing opportunistic infections. Candida and Cryptococcus. Pathology and diagnosis. Addendum: other opportunistic mycoses (Pneumocystis jirovecii).
Filamentous fungi causing opportunistic infections. Upper filamentous fungi (Aspergillus and others) and lower (zygomycetes). Pathology and diagnosis.
Cutaneous and subcutaneous mycoses. Dermatophytes. Sporothrix shenckii. Mycetoma and chromoblastomycosis agents.
Systemic mycoses caused by primary pathogens. Dimorphic fungi: Histoplasma capsulatum, Coccidioides immitis and others.
Part IV. Virology.
General virology. Basic concepts: morphology and structure. Replication of viruses. Classification. Transmission. Pathogenic action. Syndromic grouping of viral infections. Microbiological diagnosis. Antivirals.
Non-enveloped RNA virus. Picornavirus: Classification. Biological characteristics and pathology. RNA viruses causing enteritis: Rotavirus, Norovirus and other viruses. Biological characteristics and pathology.
Unenveloped DNA viruses. Adenovirus and papillomavirus. Biological characteristics and pathology. Papilloma and cancer. Parvovirus.
Enveloped DNA viruses. Herpesvirus. Classification. Biological characteristics. Pathology. Other enveloped DNA viruses
RNA enveloped viruses. Orthomyxoviridae and Paramyxoviridae families, and other respiratory viruses. Classification. Biological characteristics and pathology. Other enveloped RNA viruses.
Hepatitis viruses. Biological characteristics of the different hepatitis viruses. Epidemiology and transmission routes. Pathology, persistence, cirrhosis and cancer.
Retrovirus. HIV. Biological characteristics. Pathology, diagnosis and treatment.
Other viruses of interest in medicine: Arbovirus. Biological characteristics. Pathology
Part V. Parasitology.
General parasitology. Basic concepts. Classification: Protozoa (amoebae, flagellates, ciliates, apicomplexa) and Helminths (flatworms, nematodes). Life cycles. Pathogenesis Diagnosis. Prevention and control.
Intestinal and vaginal protozooses. Entamoeba histolytica, Giardia, and Trichomonas. Biological characteristics, reservoir and transmission, pathology and diagnosis.
Systemic protozooses. Trypanosoma. Leishmania. Plasmodium. Toxoplasma. Biological characteristics, life cycle, geographic distribution, pathology and diagnosis.
Flatworms. Tapeworms, flukes and schistosomes. Biological characteristics, life cycles, pathology and diagnosis.
Intestinal nematodes. Ascaris, Strongyloides and Enterobius vermicularis. Biological characteristics, life cycles, pathology and diagnosis.
Hemotissue nematodes. Filarias. Biological characteristics and classification, life cycles, pathology and diagnosis. Other nematodes: Trichinella spiralis.
Part VI. Microbiological diagnosis of the infectious syndromes.
Bacteraemia, fungemia and sepsis. Central nervous system infections. Respiratory tract infections and lung infections. Urinary tract infections. Sexually-transmitted infections. Enteritis. Skin and soft tissue infections. Bone and joint infections. Polymicrobial infections. Acquired-immunodeficiency syndrome. Hepatitis. Other infectious processes.
Nosocomial infection. The main multidrug-resistant bacteria. Measures for infection control. Outbreak surveillance.
Case Methods.
Teaching and learning activities
In person
The methodology and teaching resources that we will use in this subject are the following:
Master classes (MC): Presentation in two 50-minute blocks (separated by a 10-minute break). The lectures on the theoretical topic will be given by the teacher with audio-visual support. The student will have the content in advance through the internal computer network.
Clinical cases or case methods (CM): Approach to a real or imaginary situation in order to review and discuss with the students the basic principles of the etiological diagnosis of infectious diseases. Students work on the questions formulated in small groups or in interaction with the teacher and the answers are then discussed. The teacher intervenes actively and, if necessary, contributes new knowledge.
Virtual education (VE): Online material located on the Moodle platform that the student can consult from any computer, at any time, and it will contribute to self-learning of concepts related to the subject. The virtual material is part of the content of the subject and will be evaluated in the final exam.
The virtual education set includes both the subject's Forum and the aforementioned online material.
Evaluation systems and criteria
In person
Students in the first sitting: The final grade for the course will be calculated by adding the grades from:
- Midterm multiple choice exam 15%
- Final exam that will determine 55% of the total final grade.
- Note of clinical cases 20%.
- Participation in class: 5%.
- Group activity (recap): 5%
Students in second or subsequent sitting: the continuous assessment grade will be saved, although whenever they wish, students will be able to repeat their attendance at the different methodologies and obtain a new grade.
General points to keep in mind about the evaluation system:
1) In the final exam, a minimum grade of 5 must be obtained before calculating an average with the other marks. To pass the course it will be necessary to obtain an overall grade equal to or greater than 5 out of 10.
2) The final exam will be cumulative, so the whole course will be evaluated (including the materia evaluated in the midterm exam).
3) The exams will be multiple choice with 4 answer options of which only one will be correct. Unanswered questions will not count. Each question wrongly answered will subtract the equivalent of 25% from the value of one correctly answered.
4) The final exam will also include one or more short-answer questions a part from the multiple choice test.
5) Attendance at case methods is mandatory to qualify for 20%. Only one excuse for absence is permitted.
6) Attendance at theoretical classes is not compulsory. The attendees must be governed by the norms indicated by the professors. In the case of late arrival, they will enter in silence without disturbing or interrupting the class
7) For participation in class answers to the questions posed by the teacher will be taken into account. Part of the participation in the Lectures will be evaluated through a small questionnaire (via Moodle); a minimum score of 50% for the questionnaires will be required for the grade obtained in this evaluation to be considered in the overall mark.
8) The group activity is mandatory. This activity aims the students to recapitulate, deduce and integrate some concepts that will have been transversally worked during the course.
9) Students with active participation and a brilliant attitude can opt for + 10% excellence (out of 100% of the final grade).
Bibliography and resources
Specific bibliography
Prats G. Microbiología y Parasitología médicas. Madrid. 2nd Ed. Médica Panamericana. 2023.
Prats G. Microbiología clínica. Madrid. Ed. Médica Panamericana. 2005
Murray PR. Rossental KS. Pfaller MA. Medical Microbiology. 8th Ed. Philadelphia. Elsevier. 2016.
Engleberg NC, DiRita VJ, Dermody T. Schaechter's Mechanisms of Microbial Disease. 5th Ed. Wolters Kluwer Health/Lippincott Williams & Wilkins. 2013
Mandell GL. Bennet JE. Dolin R. Mandell, Douglas and Bennet 's - Principles and Practice of Infectious Diseases. 6th Ed. Philadelphia: Elsevier Churchill Livingstone. 2009.
Ausina V. Moreno Guillén S. Tratado SEIMC de Enfermedades Infecciosas y Microbiología Clínica. Madrid. Editorial Médica Panamericana. 2006.
Additional bibliography
Jameson JL, Fauci AS, Kasper DL, Hauser SL, Longo DL, Loscalzo J. Harrison's Principles of Internal Medicine, 20th Ed. McGraw-Hill Education. 2018.
Farreras-Rozman. Medicina Interna. 18a Ed. Elsevier España. 2016
Interesting links
Sociedad Española de Enfermedades Infecciosas y Microbiologia Clínica (www.seimc.org)
American Society for Microbiology (www.asm.org)
Centers for Disease Control and Prevention (www.cdc.gov)
Evaluation period
- E1 13/01/2025 A21 18:00h
- R1 30/01/2025 09:00h
- E2 19/06/2025 A08 16:00h