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.
The course contributes to the Sustainable Development Goals (SDGs) of the 2030 Agenda, particularly to SDGs 3, 4, 9, 10, 12, and 17, through the promotion of health and well-being (SDG 3), the guarantee of quality education (SDG 4), the encouragement of scientific and technological innovation (SDG 9), the reduction of inequalities through equitable access to knowledge (SDG 10), the promotion of responsible use of resources in the biomedical field (SDG 12), and the strengthening of scientific and academic partnerships for social progress (SDG 17).
Pre-course requirements
It is regarded as essential to have taken the Microbiology course (first year). It is important to review and reinforce the general concepts learned, as they may be assessed throughout the course. General knowledge of cell biology and molecular biology, anatomy, histology and physiology
Objectives
1. Explain the morphological, physiological, and biological cycle characteristics of the main microorganisms responsible for diseases in humans, distinguishing pathogens from commensals and describing normal microbiota and its physiological functions.
2. Describe the reservoirs of microorganisms and explain their transmission routes.
3. Analyze the pathogenicity mechanisms and virulence factors that contribute to the pathogenic capacity of microorganisms.
4. Present the pathophysiology of infection by explaining the pathogen-host relationship, teaching host defense mechanisms, and defining the concept of opportunism.
5. Introduce the main clinical syndromes associated with different etiological agents.
6. Teach the different microbiological techniques for etiological diagnosis of infectious diseases, transmitting knowledge about the use and processing of clinical samples and the study of antibiotic susceptibility.
7. Provide the basic measures for the prevention and control of infections, describing the different antimicrobials, explaining the concepts of resistance, and defining nosocomial infection as well as the techniques for outbreak investigation.
Competences/Learning outcomes of the degree programme
- CN11 - Identify the impact of microbiology, genetics and biochemistry on human health, as well as the diagnostic tools used in each of the different healthcare fields.
- CP02 - Apply scientific methodology to interpret practical or theoretical data by evaluating situations and results from a critical and constructive point of view.
- CP05 - Apply biological foundations in the search for practical solutions to health problems, following ethical standards and scientific rigour and respecting fundamental equal rights between men and women, and the promotion of human rights and the values inherent in a peaceful society of democratic values that includes inclusive, non-discriminatory language without stereotypes.
- HB05 - Recognise how the essential medicines work and their ability to modify biological activity.
- HB06 - Calculate the frequency and distribution of diseases, their causes and determining factors, as well as the necessary treatments to maintain or restore good health.
Learning outcomes of the subject
Upon completing the course, students should be able to:
● Identify the pathogenic mechanisms and clinical presentations associated with major human pathogens.
● Describe the main diagnostic tests for infectious diseases and select appropriate microbiological techniques for each clinical context.
● Identify reservoirs and transmission routes of medically relevant microorganisms, and understand basic measures for infection prevention and control.
● Analyse the structure, life cycle, and mechanisms of action of clinically relevant bacteria, viruses, fungi, and parasites, relating them to their pathological manifestations.
● Relate different microorganism groups to the infectious syndromes they cause, considering host factors, the microorganism, and epidemiological context.
● Recognise the role of the human microbiota in health and disease, distinguishing between commensal, pathogenic, and opportunistic flora.
Syllabus
The syllabus covers the core areas of Clinical Microbiology (Bacteriology, Mycology, Virology, Parasitology). Clinical syndromes (Block VI) will be taught transversally and expanded upon in the case methods.
Block I. Introduction
Clinical Microbiology. Human microbiota. Microorganisms with pathogenic potential for humans. Reservoirs and routes of transmission. Host–parasite relationship. Mechanisms of microbial pathogenicity and defence mechanisms. Microbiological diagnosis of infectious diseases. Prevention and control measures.
Block II. Bacteriology
Clinical bacteriology. Basic concepts. Pathogenesis and virulence factors. Microbiological diagnosis. Antibiotics.
Gram-positive cocci in clusters. Staphylococcus aureus. Coagulase-negative staphylococci.
Gram-positive cocci in chains. Streptococcus pyogenes. Streptococcus agalactiae, Streptococcus pneumoniae, viridans group streptococci. Enterococcus.
Gram-negative cocci. Neisseria.
Gram-negative bacilli (part 1). Enterobacterales: primary and opportunistic pathogenic enterobacteria.
Gram-negative bacilli (part 2). Pseudomonas aeruginosa and other non-fermenting Gram-negative bacilli. Curved Gram-negative bacilli (Campylobacter, Helicobacter and Vibrio). Fastidious Gram-negative bacilli (Legionella, Brucella, Bordetella, Haemophilus).
Gram-positive bacilli. Coryneform bacteria. Corynebacterium diphtheriae. Listeria monocytogenes. Lactobacillus. Spore-forming Gram-positive bacilli (Bacillus).
Anaerobic bacteria. General characteristics. Non-spore-forming anaerobes. Spore-forming anaerobes (Clostridium/Clostridioides).
Special bacteria. Acid–fast bacilli (Mycobacterium), spirochetes (Treponema, Borrelia, and Leptospira), mycoplasmas, chlamydiae, and rickettsiae.
Block III. Mycology
Clinical mycology. Basic concepts. Pathogenesis. Classification of mycoses. Microbiological diagnosis. Antifungals.
Yeasts causing opportunistic infections. Candida, Cryptococcus, and others.
Filamentous fungi causing opportunistic infections. Upper filamentous fungi (Aspergillus) and lower filamentous fungi (zygomycetes).
Cutaneous and subcutaneous mycoses. Dermatophytes. Sporothrix schenckii, and others.
Systemic mycoses by dimorphic fungi. Histoplasma capsulatum and others.
Block IV. Virology
Clinical virology. Basic concepts. Transmission. Pathogenic action. Viral infections and syndromic grouping. Microbiological diagnosis. Antivirals.
Non-enveloped RNA viruses. Picornaviruses (Enterovirus and others). RNA viruses causing enteritis (rotavirus, norovirus, and others).
Non-enveloped DNA viruses. Adenoviruses. Papillomaviruses. Parvovirus.
Enveloped DNA viruses. Herpesviruses. Other enveloped DNA viruses.
Enveloped RNA viruses. Families Orthomyxoviridae and Paramyxoviridae. Other enveloped RNA viruses.
Hepatitis viruses. Characteristics of the different hepatitis viruses.
Other viruses of interest. Retroviruses (human immunodeficiency virus). Arboviruses and others.
Block V. Parasitology
Clinical parasitology. Basic concepts. Classification: protozoa (amoebae, flagellates, ciliates, apicomplexa) and helminths (platyhelminths, nematodes). Life cycles. Pathogenesis. Microbiological diagnosis. Prevention and control.
Protozooses. 1) Intestinal protozoa (Entamoeba histolytica, Giardia, Cryptosporidium); 2) genital protozoa (Trichomonas); 3) systemic protozoa (Trypanosoma, Leishmania, Plasmodium, Toxoplasma).
Helminthiases. 1) Platyhelmints (tapeworms, schistosomes, and others); 2) Intestinal nematodes (Ascaris, Strongyloides, and pinworms); 3) Blood and tissue nematodes (filariae and Trichinella).
Block VI. Microbiological diagnosis of infectious syndromes
Bacteremia, fungemia, sepsis. Skin and soft tissue infections. Central nervous system infections. Urinary tract infections. Enteritis. Respiratory infections. Sexually transmitted infections. Osteoarticular infections. Polymicrobial infections. Acquired immunodeficiency syndrome. Hepatitis.
Case Methods
- Antimicrobial susceptibility testing (antibiogram). Major multidrug-resistant bacteria. Nosocomial infection control. Outbreak investigation.
- Bacteraemia and sepsis.
- Enteritis.
- Integrated recap session.
Teaching and learning activities
In person
The methodology and teaching resources that we will use in this subject are the following:
Master classes (MC) (20 hours): 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) (8 hours) : 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 kept and maintained according to its original percentages. However, students may attend the various methodologies again and obtain a new grade whenever they wish.
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 33% 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. The written questions are optional and will only be used in two special cases: if the final score is between 4.7 and 5, allowing the student to pass the exam, or at the student's discretion for those seeking honors.
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).
10) All parts of the course except for the final exam will be considered as continuous assessment.
Bibliography and resources
Bibliography
Prats G. Microbiología y Parasitología médicas. 2ª ed. Madrid. Editorial Médica Panamericana.
2023. Panamericana. 2006.
Additional bibliography
Murray PR, Rossental KS, Pfaller MA. Microbiología médica. 9ª ed, Elsevier. 2021.
Mandell GL, Bennet JE, Dolin R. Enfermedades infecciosas: principios y práctica: Mandell,
Douglas y Bennett. 7ª ed. Elsevier. 2012.
Engleberg NC, DiRita VJ, Dermody TS. Schaechter's Mechanisms of Microbial Disease. 6th
ed., Wolters Kluwer Health. 2021.
Interesting links
Centers for disease control and prevention (www.cdc.gov)
American Society for Microbiology (www.asm.org)
Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (https://seimc.org/ )
Evaluation period
- E1 14/01/2026 A08 14:00h
- E2 22/06/2026 A16 14:00h