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Questions and Answers
What method is considered the mainstay for diagnosing bacterial infections?
What method is considered the mainstay for diagnosing bacterial infections?
Which of the following bacteria can be diagnosed through antigen detection?
Which of the following bacteria can be diagnosed through antigen detection?
Which technique provides increased sensitivity compared to microscopy in bacterial diagnosis?
Which technique provides increased sensitivity compared to microscopy in bacterial diagnosis?
For which of the following conditions is nucleic acid amplification - PCR standard of care?
For which of the following conditions is nucleic acid amplification - PCR standard of care?
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In diagnostic testing, which method is noted to have limited value when analyzing sputum samples?
In diagnostic testing, which method is noted to have limited value when analyzing sputum samples?
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Which of the following host factors can increase the risk of exposure and infection?
Which of the following host factors can increase the risk of exposure and infection?
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What is one potential direct effect of viral infection on the body?
What is one potential direct effect of viral infection on the body?
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How do viral mutations affect the transmission of viruses?
How do viral mutations affect the transmission of viruses?
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Which of the following factors is considered an environmental factor that can affect infection risk?
Which of the following factors is considered an environmental factor that can affect infection risk?
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Which factor is NOT a behavioral aspect that affects exposure to infection?
Which factor is NOT a behavioral aspect that affects exposure to infection?
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What is the primary purpose of culture media in microbiological testing?
What is the primary purpose of culture media in microbiological testing?
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What does the appearance of bacterial colonies indicate in microbiology?
What does the appearance of bacterial colonies indicate in microbiology?
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Which factor is NOT a disadvantage of antigen detection methods?
Which factor is NOT a disadvantage of antigen detection methods?
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How are bacterial sensitivities to antibiotics typically tested?
How are bacterial sensitivities to antibiotics typically tested?
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What is the correct incubation temperature for performing antibiotic sensitivity tests?
What is the correct incubation temperature for performing antibiotic sensitivity tests?
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Which of the following is true regarding antigens?
Which of the following is true regarding antigens?
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What is NOT a characteristic of cultures used for diagnosis?
What is NOT a characteristic of cultures used for diagnosis?
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Which statement best describes the role of antibiotics in the context of bacterial cultures?
Which statement best describes the role of antibiotics in the context of bacterial cultures?
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Which viral surface protein is associated with the binding of HIV to its cell receptor?
Which viral surface protein is associated with the binding of HIV to its cell receptor?
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What is the replication site for Hepatitis C, which has a negative sense SS RNA genome?
What is the replication site for Hepatitis C, which has a negative sense SS RNA genome?
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Which receptor does the Spike protein of SARS-COV-2 bind to during viral entry?
Which receptor does the Spike protein of SARS-COV-2 bind to during viral entry?
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What is the genome type of Herpes simplex, and where does it replicate?
What is the genome type of Herpes simplex, and where does it replicate?
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What kind of viruses are encompassed by the Baltimore classification system?
What kind of viruses are encompassed by the Baltimore classification system?
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Which viral entry mechanism is associated with the influenza virus?
Which viral entry mechanism is associated with the influenza virus?
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Which of the following statements about viral proteins is INCORRECT?
Which of the following statements about viral proteins is INCORRECT?
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What is the role of CD21 in the entry of Epstein Barr Virus into cells?
What is the role of CD21 in the entry of Epstein Barr Virus into cells?
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What is Cyclophilin A primarily associated with?
What is Cyclophilin A primarily associated with?
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Which of the following correctly defines apoptosis?
Which of the following correctly defines apoptosis?
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What characterizes the type of infections associated with fungi?
What characterizes the type of infections associated with fungi?
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What is the primary effect of hypoxia on cells?
What is the primary effect of hypoxia on cells?
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Which type of cells are classified as neurons?
Which type of cells are classified as neurons?
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Which of the following statements is true regarding microvascular thrombus?
Which of the following statements is true regarding microvascular thrombus?
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What is a characteristic of free-living fungi?
What is a characteristic of free-living fungi?
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Which type of receptor is particularly expressed in the lung?
Which type of receptor is particularly expressed in the lung?
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What roles do cytokines and chemokines play in the innate immune response to fungi?
What roles do cytokines and chemokines play in the innate immune response to fungi?
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Which type of receptors is involved in recognizing glucans in the innate immune response to fungi?
Which type of receptors is involved in recognizing glucans in the innate immune response to fungi?
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Which soluble elements contribute to the innate immune response to fungi?
Which soluble elements contribute to the innate immune response to fungi?
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What is the primary function of pattern recognition receptors (PRRs) in the immune system?
What is the primary function of pattern recognition receptors (PRRs) in the immune system?
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Which of the following is NOT an example of a pattern recognition receptor involved in fungal detection?
Which of the following is NOT an example of a pattern recognition receptor involved in fungal detection?
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What type of immune cells are primarily activated from the release of cytokines during a fungal infection?
What type of immune cells are primarily activated from the release of cytokines during a fungal infection?
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How do intracellular influenza receptors contribute to the immune response to fungi?
How do intracellular influenza receptors contribute to the immune response to fungi?
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What happens after the recognition of fungal PAMPS by pattern recognition receptors?
What happens after the recognition of fungal PAMPS by pattern recognition receptors?
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Study Notes
Learning Outcomes
- Recall the types of diagnostic tests available to identify organisms causing infection.
- Recall the key features of viruses and examples of viral replication cycles.
- Explain how viruses cause disease by overcoming local, innate, and adaptive immunity and what outcomes may follow infection.
- Identify how viruses are classified and what classes of viruses are associated with human infection.
- Explain how the structure of fungi differs from other organisms and what fungi are associated with human disease.
- Describe the immune response to medically important fungi.
- Describe the differences between protozoa, amoebae, and helminths.
- Describe the key features of parasites and vectors with examples of parasite lifecycles, including malaria.
- Describe the immune response to parasites, including the role of eosinophils in helminthic infections.
Diagnostic tests in infectious diseases
- Diagnostic tests complement clinical skills and are vital for targeting appropriate therapy.
- Include tests for bacteria, viruses, fungi, and parasites.
- Use clinical examples to illustrate the use of tests.
Examples of samples that can be taken easily
- Urine
- Sputum
- Stool
- Blood
- Swabs (wounds, skin, throat, urethra)
- Pus draining from an abscess
Examples of invasive samples
- Lung samples via bronchoscopy
- Cerebrospinal fluid (CSF) via lumbar puncture
- Bone marrow
- Deep tissue or abscess samples via image-guided aspiration or biopsy
Types of tests that can be done
- Microscopy
- Direct visualisation of microorganisms
- Culture
- Grow microorganisms in the laboratory
- Immunological tests
- Measure the immune response to specific antigens
- Antigen detection
- Identify antigens specific to organisms
- Nucleic acid detection
- Amplify and identify sequences of RNA or DNA specific to individual organisms
Light Microscopy
- Direct visualisation of microorganisms
- Use of stained or unstained preparations for identification
- Limited sensitivity and specificity, particularly for non-pathogenic microorganisms from non-sterile body sites.
Electron Microscopy
- Visualise viruses
- Expensive and requires specialized interpretation
- Not routinely used in clinical practice
Immunostaining
- Used in specialized settings
- Technique utilizing antibodies against specific antigens to identify pathogens in cellular samples.
- Used to confirm herpes simplex virus type 2 infection.
Culture overview
- Culture can be used on any fresh clinical specimen
- Added to culture media designed to encourage growth in vitro
- Appearance of bacterial colonies can be useful for identification
- More detailed diagnostic tests identify organisms based on metabolic and biochemical phenotype
- Antimicrobial sensitivity testing is possible
Culture - antibiotic sensitivity testing
- Bacteria from a positive culture are spread over agar
- Paper discs containing antibiotics are added and incubated
- Sensitivity to antibiotics can be determined by observing zones of inhibition around the discs
Antigen detection advantages and disadvantages
- Advantages: Rapid, specific immunoassay, easy to perform, point-of-care tests available, not affected by antibiotics
- Disadvantages: Only detects one organism per test, lower sensitivity compared to molecular techniques, no antimicrobial sensitivity data
Antigen detection example - COVID-19
- A nasal/pharyngeal swab is placed in fluid that solubilizes viral antigens
- The fluid is added to the testing chamber
- Antigens are captured by specific antibodies
- A color change visualizes the result
- Sensitivity 70–75%, Specificity 98–99%
Serological tests in infection
- Measure immunoglobulins (IgM, IgG, IgA, and IgE)
- Evidence that an individual has mounted an immune response
- Does not necessarily indicate active infection
- Can be negative early in infection before antibody is detectable ('window period')
- May be difficult to interpret due to cross-reacting antibodies or distinguishing active infection from previous infection or immunization.
Dynamics of antibody response
- Shows IgM and IgG levels over time for various infection statuses.
- IgM is a sign of early infection, IgG reflects longer-term or past infection.
Nucleic acid detection - the way forward
- Direct hybridization of RNA or DNA lacks sensitivity
- PCR amplification is the most common technique
- Practicalities: Used with many biological specimens, detects multiple pathogens from the same specimen, high specificity and sensitivity, technology improving, and becoming more cost-effective
- Uses: Rapid accurate diagnosis, detection of antimicrobial resistance, improved clinical decision-making, identification of new and emerging pathogens, and providing genomic information,
Viruses study guide
- Microscopy and Culture: Viruses are not visible in microscopy, must be grown inside cells.
- No longer in routine use.
- Serology: Diagnoses some acute viral infections, screens for chronic infections (HIV, viral hepatitis), confirms immunity from past infections or immunizations.
- Antigen detection: Diagnoses acute infections (COVID-19), detects early infections, distinguishes active from past infection.
- Nucleic acid amplification (PCR): diagnoses respiratory viruses, dengue, cytomegalovirus (CMV) in immunocompromised individuals monitoring response to therapy, detects antiviral resistance.
Bacteria study guide
- Microscopy: Urine, CSF, and pus samples are useful for bacterial identification.
- Culture: The mainstay of bacterial diagnosis, identification, and antimicrobial sensitivity testing.
- Serology: Diagnosis of bacterial infections (e.g., syphilis).
- Antigen detection: used in some bacterial infections (e.g., Streptococcus pneumoniae, Legionnaires disease, ).
- Nucleic acid amplification(PCR): Standard care in tuberculosis, and sensitivity compared to microscopy.
Fungi study guide
- Microscopy: Used to recognize fungal elements (yeasts, molds) from clinical specimens.
- Culture: Is the main tool for diagnosis and identification.
- Serology: Diagnosis for some fungal infections.
- Antigen detection: detection of some fungal antigens is helpful in certain invasive fungal infections (eg:, galactomannan in aspergillosis).
- Nucleic acid amplification (PCR): used to detect multiple fungal types in immunocompromised patients.
Parasites study guide
- Microscopy: Key for diagnosis by visual identification of blood, urine, and stool samples.
- Culture: Parasites cannot be cultured in-vitro.
- Serology: Helps make diagnoses in parasitic infections, hard to interpret sometimes.
- Antigen detection: Useful for malaria diagnosis.
- Nucleic acid amplification(PCR): Not widely available, but increasing use in specialist centres
Summary
- Many infections are clinically diagnosed and treated empirically.
- Microscopy, culture, serology, antigen detection, and nucleic acid amplification are tests that identify organisms and their antibiotic sensitivity.
Glossary (virals, fungal, and parasitic infections)
- Includes definitions of various terms relevant to the study of viruses, fungi, and parasites, and their associated diseases.
Viral replication steps
- Attachment to cellular receptors
- Cell entry by membrane fusion or receptor-mediated endocytosis
- Uncoating with release of genome
- Replication of the genome
- Transcription of mRNA
- Translation of non-structural and structural proteins
- Incorporation of new genomes into new viral particles during assembly
- Release of virions from the cell by budding, cell lysis, or cell-to-cell spread
Minimal virus structure
- Genome (nucleic acid core - RNA or DNA)
- Capsid (protein shell of repeating subunits known as capsomeres), with geometrical symmetry
Complex virus structure
- Envelope/membrane (Lipid bilayer, derived from host cell, damaged by detergents, alcohol, etc.; transmembrane glycoprotein spikes; host cell receptor attachment; mediates viral entry; modifies host immune responses)
- Capsid/shell (Protein subunits : capsomeres; protects the genome; icosahedral or helical shapes)
- Enzymes (involved in viral replication)
- Matrix protein (involved in viral assembly)
- Transport Channels: Needed by some viruses, e.g., Influenza
Viral Morphology
- Different shapes and structures of viruses such as smallpox, herpes simplex, parvovirus, SARS-CoV-2, and Ebola.
Viral Replication Cycle - overview
- Contains the most important steps in brief form for viral replication.
Baltimore Virus Classification
- Classification scheme is based on the nature of the viral genome and its method of replication.
Viral entry through cellular receptors
- Includes examples of viruses and their corresponding cellular receptors.
Examples of Viral Replication Cycles: Hepatitis C and Herpes Simplex
- Hepatitis C replication occurs in the cytoplasm with negative sense RNA.
- Herpes Simplex replication occurs in the nucleus with double stranded DNA.
HIV related terms in glossary and protozoan and helminthic infections
- Definitions for terms dealing with HIV and infectious diseases relevant to Protozoan and helminthic infections.
Steps in viral replication
- Attachment to cellular receptors
- Cell entry
- Uncoating
- Replication of the genome
- Assembly/maturation of new viral particles
- Release
How Viruses Cause Disease
- Viral effects on cells, causing direct organ infection, severe illness and even death. Also, discusses inflammatory response, viral mutations, and immune evasion responses.
Viral mutations and transmission
- Viral mutations can increase viral replication, shedding, and transmission.
Viral evasion of innate immunity
- Explains how viruses avoid the innate immune response by mechanisms like preventing recognition by pattern recognition receptors
- Also describes how viruses inhibit activation of complement pathways and avoid NK cells.
Viral evasion of adaptive immunity- strategies for success
- Shows strategies parasites use to avoid immune responses, including hiding in sequestered sites, changing surface antigens.
Innate immune response to parasites (protozoa)
- Discusses the immune recognition of pathogens associated molecular patterns (PAMPs), through pattern recognition receptors (PRRs) on epithelial cells or phagocytes
- The resulting release of cytokines, chemokines and pro-inflammatory mediators. This results in the activation of immune responses to the pathogens.
Cellular innate immune response (protozoa)
- Phagocytosis and killing of protozoa by macrophages and neutrophils resulting in the release of mediators—cytokines and chemokines.
- Dendritic cells also engulf, process, and present protozoan antigens to T-cells including T helper cells, which in turn produce cytokines, thus contributing to adaptive immune responses.
- Natural killer cells (NK cells) recognize and kill infected host cells; a crucial role in activating macrophages and initiating TH-1 adaptive immune response.
Adaptive immune response to Protozoa
- Humoral and cellular immune responses against Protozoa
- The roles of IgM and IgA in host-parasite interactions.
Example: Immune response to malaria
- Innate and adaptive immune responses against malaria
- Innate immunity role in phagocytosis
- Adaptive immune role in controlling malaria with antibody production.
How does malaria avoid the immune response?
- Antigenic variation (Changing surface antigens to evade antibodies)
- Hiding within cells (Entering vacuoles in hepatocytes or erythrocytes)
- Sequestration (Hides from immune system by entering the vascular endothelium, leading to the clumping of red blood cells)
Immune response to helminths
-
Epithelial defences
-
Mechanisms involving immunoglobulin type E, mast cells, and eosinophils
-
Th2 immune responses
-
Mechanisms by which parasites evade.
-
Molecular Mimicry.
-
Antigen Shedding and Surface Variation
-
Hiding - sequestering away
Summary (Parasites)
- Protozoa and helminths cause various diseases, with varied transmission and life cycle.
Glossary (Parasites)
- Definitions of terms used for the discussion about parasites.
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Description
Test your knowledge on the key methods and techniques used in diagnosing bacterial and viral infections. This quiz covers crucial concepts such as PCR, antigen detection, and various host factors. Dive into the world of microbiology and enhance your understanding of infectious diseases.
