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Infectious Diseases Summary - Medical Biology - Radboud University
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A summary of the Medical Biology Bachelor course 'Infectious Diseases' (Radboud University, 2023/2024)
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SummaryInfectious Diseases
Radboud University
2023-2024
, Chapters
1. Viruses – Background, classification and principles p. 3
2. Flaviviruses/+strand RNA viruses/Arboviruses p. 6
3. Respiratory viruses p. 8
3.1. SARS-Cov2 p. 8
3.2. Respiratory syncytial virus p. 8
3.3. Influenza A p. 9
4. Mucosal immunity p. 10
5. Principles of vaccination p. 12
6. Herpesviruses: Antiviral immunity, latency and reactivation p. 14
7. Immunity to viral infections p. 17
8. Clinical presentation and treatment of HIV/AIDS p. 19
9. Bacterial respiratory infections p. 22
9.1. Tuberculosis p. 22
9.2. Haemophilus influenzae p. 22
9.3. Neisseria meningitidis p. 24
10. Pneumococcal infections p. 25
11. Gastro-intestinal tract infections p. 28
12. Sexually transmitted infections p. 30
12.1. Bacterial infections p. 30
12.2. Viral infections p. 31
13. Scabies infections p. 32
14. Bacterial skin infections p. 33
15. Bacterial sepsis p. 35
16. Fungal infections p. 37
17. Zoonoses p. 41
18. Climate change and infectious diseases p. 42
19. Malaria treatment and resistance p. 43
20. Tropical parasitic infections p. 45
21. Self-study week 1: Virus replication (+) RNA virus (poliovirus) p. 46
22. Self-study week 2: RSV vaccines p. 47
23. Self-study week 3: HIV-1 cure p. 48
24. Self-study week 4: Whooping cough/Gastro-intestinal tract infections p. 49
25. Self-study week 5: SSTIs p. 50
2
,Chapter 1
Viruses – Background, classification and principles
Infectious diseases are caused by pathogenic microorganisms such as viruses, bacteria, fungi and parasites, the
diseases can be spread, directly or indirectly from one person to another. Zoonoses are infectious diseases of
animals that can cause disease when transmitted to humans.
A virus is a small, obligatory intracellular, infectious agent
possessing its own genome. It ONLY replicates in the host, not
in a medium. It’s fully dependent on this host for energy
metabolism, lipid biogenesis, and protein synthesis. Virus
particles themselves do not grow or divide. Instead, they are
produced de novo from the assembly of pre-formed
components. While viruses within a family are not transmitted
the same way and do not cause the same diseases and
symptoms, viruses infect ALL living organisms.
RNA virus classification DNA virus classification
3
, Diagnostics general principles
Diagnostics support the differential diagnosis: The process of weighing the probability of one disease versus that
of other diseases. General principles:
• sensitivity = probability that a truly infected individual will test positive.
• specificity = probability that a truly uninfected individual will test negative.
• positive predicted value (PPV) = probability that those testing positive are truly infected.
• negative predicted value (NPV) = probability that those testing negative are truly uninfected.
Gram staining
Gram staining is a bacterial classification technique that divides bacteria into two groups: Gram-positive and
Gram-negative, based on cell wall composition. Gram-positive bacteria retain the violet stain, appearing purple,
due to their thick peptidoglycan layer, while Gram-negative bacteria appear red or pink, having a thinner
peptidoglycan layer and an outer membrane. This staining method is crucial for bacterial identification, aiding in
antibiotic selection and understanding bacterial pathogenicity. Gram staining results guide additional laboratory
tests and influence medical decisions in the treatment of bacterial infections.
Determining the bacterium/virus type
Identification of bacteria relies on colony morphology, while detecting viruses is challenging as it requires host
cells. Cytopathic Effect (CPE) refers to observable changes in host cells due to viral infection during cell culture
studies. Lack of CPE suggests no cytopathic virus. Some viruses cause cell lysis, releasing new viral particles and
visibly altering cell morphology.
Plaque assays quantify virus infectivity by forming
localized areas of cell damage or death, known as
plaques, originating from individual virus infection
events. These assays are valuable for assessing
viral characteristics in laboratory settings.
Qualitative PCR is employed to determine the presence or absence of specific DNA or RNA sequences, aiding in
the identification of bacteria or viruses. For example, in the context of viral infections, qualitative PCR can confirm
the presence of viral genetic material in a patient sample.
Quantitative PCR (qPCR), on the other hand, goes beyond mere detection and provides information about the
amount of DNA or RNA present in a sample. This is crucial for assessing the severity of an infection, monitoring
treatment effectiveness, or determining the viral load in a patient.
Fluorescently labeled antibodies are commonly used in immunofluorescence assays. These antibodies specifically
bind to target antigens on pathogens, allowing for their visualization under a fluorescent microscope. In the context
of viral infections, this method can identify and locate viruses within host cells, providing valuable information
about the infection's progress.
Metagenomics involves analyzing the collective genetic material (DNA or RNA) from a microbial community in a
specific environment. This culture-independent technique utilizes multiplexed whole-genome sequencing to
determine the presence and genomic content of microorganisms across all domains of life. The primary goal is
understanding microbial community structure and function in different ecosystems, including diversity,
interactions, and contributions to processes like nutrient cycling and disease. Metagenomics allows the
reconstruction of whole genomes, facilitating the discovery of new viruses and bacteria. Key methods include
shotgun sequencing, which sequences random fragments for species and functional gene identification, and 16S
rRNA sequencing, targeting a specific gene to characterize microbial diversity.
Serology involves studying serum and body fluids, particularly blood, to examine the antibody response to
infections. The initial immune response is mediated by IgM antibodies, rapidly present but declining after a few
weeks. Measurement of IgM antibodies aids in diagnosing recent infections, indicating recent exposure to a
pathogen. After a few weeks, the response shifts to IgG antibodies, which can persist for months or years,
sometimes providing lifelong immunity. This temporal shift from IgM to IgG serves as a classical approach to host-
based diagnostics, offering insights into infection timing and potential immunity duration.
4
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