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Questions and Answers
What are the four most abundant phyla in the human microbiome?
What are the four most abundant phyla in the human microbiome?
What is the difference between microbiota and microbiome?
What is the difference between microbiota and microbiome?
Microbiota refers to the organisms that comprise the microbial community, while microbiome refers to the collective genomes of the microbes.
The microbiota is now considered to be a human organ with its own functions.
The microbiota is now considered to be a human organ with its own functions.
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What are the most important sites for the normal microbiota of the skin?
What are the most important sites for the normal microbiota of the skin?
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The diversity of our skin microbiome is less extensive than the diversity of our DNA.
The diversity of our skin microbiome is less extensive than the diversity of our DNA.
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What is the ratio of bacterial cells to human cells in our bodies?
What is the ratio of bacterial cells to human cells in our bodies?
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What are the three developmental changes in humans that affect the composition of the normal flora?
What are the three developmental changes in humans that affect the composition of the normal flora?
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What are the five factors that affect the normal flora?
What are the five factors that affect the normal flora?
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Antibiotic usage has no impact on the human gut microbiota.
Antibiotic usage has no impact on the human gut microbiota.
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What is fecal bacteriotherapy?
What is fecal bacteriotherapy?
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What are the four criteria designed to establish a causative relationship between a microbe and a disease, often referred to as Koch's postulates?
What are the four criteria designed to establish a causative relationship between a microbe and a disease, often referred to as Koch's postulates?
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What are the two main types of toxins produced by bacteria?
What are the two main types of toxins produced by bacteria?
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What are the six main portals of entry of infection?
What are the six main portals of entry of infection?
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What are the two main types of vectors that can transmit human pathogens?
What are the two main types of vectors that can transmit human pathogens?
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What are the two main categories of parasites based on their location within a host?
What are the two main categories of parasites based on their location within a host?
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What term refers to the organisms that are found in the microbial community?
What term refers to the organisms that are found in the microbial community?
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The human microbiota is now considered to be a human organ.
The human microbiota is now considered to be a human organ.
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What is the term for host-bacteria interactions that are essential for human health?
What is the term for host-bacteria interactions that are essential for human health?
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Which of these is NOT one of the four most abundant phyla in the human microbiome?
Which of these is NOT one of the four most abundant phyla in the human microbiome?
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Which of the following species is NOT typically found in the oral cavity?
Which of the following species is NOT typically found in the oral cavity?
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What is the name of the bacteria that is often found in autistic children with gastrointestinal dysfunction and is absent in non-autistic children with the same condition?
What is the name of the bacteria that is often found in autistic children with gastrointestinal dysfunction and is absent in non-autistic children with the same condition?
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Which of the following is NOT a factor that can influence the composition of the normal flora?
Which of the following is NOT a factor that can influence the composition of the normal flora?
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What is the term for the process of establishing a site of reproduction for microbes on a person without causing tissue invasion or damage?
What is the term for the process of establishing a site of reproduction for microbes on a person without causing tissue invasion or damage?
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What is the name of the medical treatment that involves restoring colon homeostasis by introducing normal bacterial flora from a healthy donor?
What is the name of the medical treatment that involves restoring colon homeostasis by introducing normal bacterial flora from a healthy donor?
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The number of microbes required to cause disease in 50% of inoculated test animals is known as the infectious dose (ID50).
The number of microbes required to cause disease in 50% of inoculated test animals is known as the infectious dose (ID50).
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Which of the following is NOT a mechanism by which bacteria can overcome host defense?
Which of the following is NOT a mechanism by which bacteria can overcome host defense?
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Which of these is a characteristic of exotoxins?
Which of these is a characteristic of exotoxins?
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Endotoxins are typically released from bacterial cells during active growth.
Endotoxins are typically released from bacterial cells during active growth.
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Which of these is NOT an example of a cytotoxin?
Which of these is NOT an example of a cytotoxin?
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Toxoids are inactivated forms of exotoxins that can no longer cause disease but can stimulate the production of antitoxins.
Toxoids are inactivated forms of exotoxins that can no longer cause disease but can stimulate the production of antitoxins.
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Match the following bacterial virulence factors with their effect:
Match the following bacterial virulence factors with their effect:
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Study Notes
Lecture 4: Microbiology: Bacterial Infection & Pathogenesis
- The lecture covers bacterial infection and pathogenesis.
- Content includes normal human microbiota, virulence of bacteria, bacterial virulence factors (exotoxin, endotoxin), and pathogenesis.
- Pathogenesis covers types of bacterial infections, transmission, adherence, invasiveness, toxin production, infection process (development), and outcomes.
The Human Microbiome
- Bacteria, fungi, and viruses outnumber human cells in the body, by a factor of 10 to 1
- Microbes synthesize nutrients, fend off pathogens and impact development up to brain development.
- The Human Microbiome Project does a census of the microbes, sequencing the genomes of many species.
- Over 1,000 different species live in and on the body.
- 25 species in the stomach include Helicobacter pylori and Streptococcus thermophilus
- 500-1,000 species in the intestines, including Lactobacillus casei, Lactobacillus reuteri, Lactobacillus gasseri, Escherichia coli, Bacteroides fragilis, Bacteroides thetaiotaomicron, Lactobacillus rhamnosus, and Clostridium difficile.
- Several species like Streptococcus viridans, Neisseria sicca, Candida albicans, Streptococcus salivarius are found in mouth, pharynx and respiratory system
- 1,000 species are found on the skin, including Pityrosporum ovale, Staphylococcus epidermidis, Corynebacterium jeikeium,Trichosporon, and Staphylococcus haemolyticus
- 60 species are found in the urogenital tract, including Ureaplasma parvum and Corynebacterium aurimucosum
Microbiota and Microbiome
- Microbiota refers to the organisms that comprise the microbial community.
- Microbiome refers to the collective genomes of the microbes (bacteria, bacteriophages, fungi, protozoa, and viruses).
- Microbiota is now considered a human organ, with its own functions.
- Modulates expression of genes involved in mucosal barrier fortification, angiogenesis, and postnatal intestinal maturation.
- Vast majority of microbial species in microbiota give rise to symbiotic host-bacteria interactions fundamental for human health.
A Map of Diversity in the Human Microbiome
- Lactobacillus species (L. gasseri, L. jensenii, L. crispatus, L. iners) are predominant in vagina.
- Streptococcus dominates the oral cavity
- Staphylococcus epidermidis colonize external body sites.
- 4 most abundant phyla present are Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria
- Most observed species present in healthy human microbiomes and corresponding locations in the body
Relationships of Microbiota with Humans
- Symbiotic - benefits the host
- Commensal - neutral to the host
- Parasitic - injures the host
- Residents strains with established niche, indefinite occupancy
- Transients acquired from environment, excluded by competition or defense mechanisms
- The term 'carrier state' is used to describe potentially pathogenic organisms, although their risk implication is not always justified.
Normal Human Microbiota
- Typical human body contains about 10^12-10^13 eukaryotic cells.
- Humans house about 10^13-10^14 microbial cells (10x more than eukaryotic).
- Almost every epithelial surface has a complex microbial community (skin, mouth, vagina, gastrointestinal tract).
- Microbes even live in the acidic stomach (pH=2).
- Hundreds & thousands of microbes, not just individual species.
- Majority are bacteria; also archaea, fungi, eukaryotic microorganisms, and viruses.
- Total weight of human microbiota varies from 1 to 3 kg (approximately 1%-3% of total weight).
Functions of Microbiota
- Essential for health and happiness.
- Gut microbiota participates in host energy metabolism by processing dietary complex polysaccharides.
- Protects from pathogen invasion.
- Produces vitamins that cannot be made.
- Benefits the body by competing with or inhibiting pathogen growth.
- Modulates the development and functioning of the immune system, transforms/excretes toxic substances, and maintains epithelial homeostasis.
- Dysbiosis: perturbation of normal microbial profile, linked to multiple diseases (dental plaque, bacterial vaginosis, psoriasis, atopic dermatitis, and cystic fibrosis).
A Healthy Microbiome is a Healthy You
- Microbiome plays extremely important role in human bodily function.
- Helps digest food, protects against toxins, boosts the immune system, promotes skin health, and influences mental health.
Colonization vs Infection
- Colonization: establishment of a site of reproduction without tissue invasion or damage.
- Infection: growth and multiplication with or without disease production.
- Outcomes: transient colonization, permanent colonization, disease, normal flora, and pathogenesis.
Microbiota at Different Sites
- Blood, body fluids, and tissues are sterile.
- Sterile sites include sinuses, middle ear, brain, lower respiratory tract (trachea, bronchiole, lungs), bladder, cervix, and uterus.
- Sites that may be colonized include outer ear, nasopharynx, eye, oral cavity, skin, oropharynx, gastrointestinal tract (esophagus, stomach, small intestine, large intestine), genitourinary system (vagina, urethra, penis).
Oral Cavity
- Researchers have identified about 700 microbial species in the human mouth.
- Common oral bacteria include Streptococcus viridans, Lactobacilli, Staphylococci (S. aureus and S. epidermidis), Corynebacterium sp., Bacteroides sp., Streptococcus sanguis, Streptococcus mutans, and Actinomyces sp.
- Accumulating evidence suggests the structure of the oral microbiome is hierarchical, not haphazard.
Oral Microbiota
- Oral bacteria implicated in cardiovascular disease, pancreatic cancer, colorectal cancer, rheumatoid arthritis, and preterm birth.
- Bacteria in subgingival plaque, supragingival plaque, hard palate, tongue dorsum, saliva, buccal mucosa, and tonsils.
Nares and Nasopharynx
- Nares are inhibited by Staphylococcus sp., Corynebacterium sp., Peptostreptococcus sp., and Fusobacterium sp.
- Nasopharynx has predominance of Streptococcus spp such as Streptococcus salivarius, Streptococcus parasanguinis, and Streptococcus pneumoniae, along with several Gram-negative coccobacilli.
Normal Microbiota of Upper and Lower Respiratory Tract
- Upper respiratory tract: Staphylococcus epidermidis, Corynebacterium, Staphylococcus aureus, Neisseria sp., and Haemophilus sp., Streptococcus pneumoniae.
- Lower respiratory tract generally sterile.
- Susceptibility to infection by pathogens descending from the nasopharynx, example are H. influenzae and S. pneumonia .
Lung Microbiota
- Constant flow of aspirated bacteria from the mouth.
- Cleansing mechanisms create dynamic community.
- Much less dense than oral and gut microbiome.
- Lungs lack microbe-friendly mucosal lining, instead containing surfactant and cilia.
Skin Microbiota
- Common skin microbiota includes Propionobacterium, Corynebacterium (diphtheroides), and Staphylococcus (coagulase-negative).
- Important sites are axilla, groin, and areas between toes.
Non-health Related Applications of Microbiome
- Skin microbiome highly diverse between individuals.
- Can uniquely fingerprint individuals, helpful in forensics, identifying individuals at crime scenes since this microbiome is unique to a person.
Skin Microbiota
- Helocococcus kunzii is a recently identified bacterium, non-pathogenic member of skin flora .
- Report isolation from infected cyst on a 57-year-old immunocompromised woman.
- Opportunistic role both immunocompromised and healthy people.
Intestinal Microbiota
- Stomach: Lactobacillus, Candida, Streptococcus, Helicobacter pylori, and Peptostreptococcus
- Duodenum: Streptococcus and Lactobacillus
- Distal ileum: Clostridium, Bacteroides, and Actinomycinae
- Jejunum: Streptococcus and Lactobacillus
- Proximal ileum: Streptococcus and Lactobacillus
- Colon: Bacteroides, Clostridium, Bifidobacterium, and Enterobacteriaceae.
The Body's Microbiomes give us information about the sex of the person:
- Mouth: Diverse communities.
- Lungs: 1000 times less dense compared to oral microbiome.
- Skin: Diverse and diverse types of habitats. Oil/sebaceous, Moist, Dry.
- Vaginal Micro biome: Dominated by lactobacillus (ferment carbohydrates to lactic acid).
- Mother and Child: Diversity in newborns. Exposed from mother’s mouth and breast milk during and after birth.
- Penis: Low microbiome density compared to others. Contains lactobacilli and streptococci species, while others have more anaerobes.
Genitourinary Tract Microbiota
- In Women: Lactobacillus species (iners, crispatus, gasseri, or jensenii).
- Role of these species in lowering pH.
- Composition differs by age and ethnicity.
- In Men: Lactobacillus, Streptococcus, Prevotella, and Fusobacterium.
When do We Get Colonized with Normal Microbiota?
- Colonization happens during birth.
- Fetus is sterile in the uterus, colonization of surfaces begin when water breaks,
- Handling and feeding of infants after birth, flora are established on skin, oral cavity, and intestinal tract after about 48 hours
Development of Microbiota
- Intestine initially thought to be sterile; changing views.
- When present in the uterine compartment, Some bacteria such as Ureaplasma and Fusobacterium spp appear most significantly associated with negative outcomes such as prematurity.
Development of Microbiota - delivery
- Delivery introduces microbes from mothers gut and vaginal microbes
- Infant's gut highly influenced by mothers vaginal and fecal bacterial.
- Includes facultative anaerobes such as streptococci and enterobacteriaceae.
- First important phase is when the newborn fetus passes through the birth canal and ingests vaginal and colonic microorganisms
Vaginal Delivery vs Cesarean Delivery
- Vaginal delivery introduces lactobacillus, normal gut microbiome development, and immune system development with cytokine production for proper development and functioning.
- Cesarean delivery introduces staphylococcus, disrupted intestinal microbial colonization, higher risk of asthma, allergic rhinitis, celiac disease, and delayed onset of lactation due to little breast milk support for gut flora.
Development of Microbiome
- Natural birth exposed to microbes from a variety of sources (maternal vaginal, fecal, and skin).
- Initial gut colonization highly influenced by mothers vaginal and fecal microbial communities; include facultative anaerobes.
- First colonization occurs during birth canal passage and ingestion of maternal vaginal and colonic microorganisms.
Development of Microbiota(differences between cesarean vs vaginal)
- Babies delivered by Cesarean section have fewer bacteria compared to vaginally delivered babies
- Vaginally delivered babies mirror mother's vaginal/intestinal microbiota.
- Bacteria found in vaginal babies include Lactobacillus, Prevotella, Escherichia, Bacteroides, and Bifidobacterium.
- Colonization by bifidobacteria can be delayed in Cesarean section babies up to 6 months.
Role of Microbiota in Defense
- Intestinal mucosal barrier function is the capacity of the intestine to host commensal bacteria and molecules, while preserving nutrient absorption and preventing host intrusion.
- Dense bacterial communities separated from tissues by a monolayer of epithelial cells.
- Intestinal barrier assembly initiation in fetal development and continues in early postnatal life.
- Collectively, gut microbiota influences tissue regeneration, permeability of the epithelium, vascularization of the gut, and tissue homeostasis.
Factors Disrupting Microbiota
- Epidemiological studies have shown an association between mode of delivery (cesarean section), antibiotic use and the occurence of health disorders.
- Increased use of cesarean section delivery in recent decades, reaching 50.1% in Brazil in 2009.
- Concern about increased rates of short-term and long-term deleterious effects on children.
- Increased risk of allergies, asthma, and type 1 diabetes in children delivered via cesarean section.
Factors Influencing Microbiota
- Factors like genetics, age, sex, stress, nutrition and diet of the individual.
- Developmental changes (weaning, eruption of teeth, onset/cessation of ovarian function) affect normal flora in intestinal tract, oral cavity, and vagina.
- Within limits of fluctuations, bacterial flora constant enough for generl description of situations.
Factors Affecting Normal Flora
- Local environment (pH, temperature, redox potential, O2, H2O, nutrient levels)
- Diet
- Age
- Health conditions (immune activity)
- Antibiotics usage
Factors Disrupting Microbiota
- Antibiotic usage changes gut microbiota greatly
- Significant reduction in Bacteroides and concurrent increase in Firmicutes.
- Understanding mechanisms behind functional changes in the microbiome is still limited.
- Response depends on types of antibiotics, dosing length, and baseline microbiome.
Fecal Bacteriotherapy
- Officially known as fecal microbiota transplantation (FMT)/ fecal microbiota therapy/ fecal transfusion/ stool transplant/ fecal enema/ human probiotic infusion (HPI).
- For patients with pseudomembranous colitis due to Clostridium difficile, or ulcerative colitis.
- Involves reintroducing normal bacterial flora by obtaining a healthy donor stool sample, mixing it with salt water, filtering, and administering through colonoscopy, enema, or nasogastric tube
Fecal Transplantation
- Similar to organ transplants, fecal transplantation needs a donor (often a family member).
- Fresh stool samples (200-300 grams) mixed with salt water in a blender, filtered.
- Administered to the recipient through colonoscopy, enema, or naso-gastric route if the inflamed area is in the colon.
Microbes and Humans
- Very few microbes are always pathogenic.
- Many microbes are potentially pathogenic.
- Most microbes are never pathogenic.
Robert Koch's Postulates
- Germ should be discoverable in every instance of the disease
- The germ must be extracted from the body, grown in a pure culture, and maintainable over generations.
- The germ must be able to produce disease in experimental animals.
- The germ must be able to be retrieved from the inoculated animal and cultured
Pathogenicity
- Pathogen: microorganism that causes disease in plants, animals, or insects.
- Pathogenicity: ability to produce disease, step-by-step capability.
- Virulence: degree of pathogenicity.
- Determinants of virulence: genetic, biochemical, or structural features that let a pathogen cause disease in a host.
Mechanisms of Bacterial Pathogenicity
- Invasiveness: ability to invade tissues encompassing mechanisms for colonization (adherence and initial multiplication), production of extracellular substances, facilitating invasion (invasins), bypassing/overcoming host defense mechanism.
Prokaryotic and Eukaryotic Interactions
- Control of virulence factors include pilin, capsule, invasins, toxins, etc.
- Adherence blockers can inhibit adhesion.
Number of Invading Microbes
- LD50: Lethal dose of a microbe/toxin that kills 50% of inoculated animals within a timeframe
- ID50: Infectious dose needed to cause disease in 50% of inoculated animals.
How Bacteria Overcome Host Defense
- Adherence: Ability to attach, often with adhesins/ligands, to host bind sites
- Capsules
- Enzymes (Leukocidins, Hemolysins, Coagulase ,Kinases, Hyaluronidase, Collagenase, Necrotizing factor)
Bacterial Virulence Factors
- Various factors like exotoxins, adhesion pili, capsules, iron binding proteins, virulence plasmids, toxin producing phages, flagella, virulent enzymes, surface proteins etc.
Adherence
- Surface molecules (adhesins/ligands) on a pathogen that specifically bind to complementary receptors on host tissue cells.
Capsule: Prevents phagocytosis
- Examples includes Streptococcus pneumoniae, Klebsiella pneumoniae, Haemophilus influenzae, Bacillus anthracis, Streptococcus mutans, Yersinia pestis, and Klebsiella pneumoniae
Enzymes
- A. Leukocidins: Attack WBCs, preventing phagocytosis and lysis of lysosomes causing more tissue damage.
- B. Hemolysins: Damage and lyse RBCs (incomplete or complete). Alpha hemolytic vs beta hemolytic.
- C. Coagulase: Causes blood to coagulate, protecting bacteria from phagocytosis.
- D. Kinases: Dissolve blood clots (streptokinase for streptococci, staphylokinase for staphylococci).
- E. Hyaluronidase: Breaks down hyaluronic acid, allowing bacteria to spread. Often mixed with a drug to spread to connective tissues.
- F. Collagenase: Breaks down collagen in connective tissues allowing spreading. Used in cosmetics to fight cellulitis and contracture
- G. Necrotizing Factor: Causes death (necrosis) to tissue cells, used by bacteria commonly
Bacterial Toxins
- Toxins are poisonous substances produced by microorganisms.
- Primary factor in pathogenicity.
- Examples include various exotoxins and endotoxins.
- 220 known bacterial toxins, approximately 40% of cause disease from damaging the eukaryotic cell membrane causing toxemia.
Toxins
- Toxigenesis: Capacity to produce toxins.
- Bacteria produce two main types of toxins: exotoxins and endotoxins.
- Exotoxins released from bacterial cells, may act at tissue sites distant from bacterial growth
- Endotoxins associated with bacterial cells (classic sense), lipopolysaccharide components of Gram-negative bacterial outer membranes.
Toxins
- Toxins: Endotoxins released from growing/lysed bacterial cells from host immune response or antibiotics, cause cytotoxic effects through blood and lymph.
- Some bacterial toxins act at colonization sites impacting invasion.
Toxins
- Exotoxins: kill
- shigella (kills cells)
- vibrio (interfere with normal nerve impulses)
- botulinum; tetanus (affect cells lining GI tract)
- E.coli, Salmonella (affect cells lining GI tract)
- Response to exotoxins: Antibodies (antitoxins) can be generated.
- Inactivated exotoxins (heat/chemical treatment) as toxoids, stimulating antitoxin production for immunity.
Microbial Mechanisms of Pathogenic
- Portals of entry (mucous membranes, respiratory tract, GI tract, genitourinary tract, conjunctiva, skin, parenteral routes)
- Number of invading microbes
- Penetration/evasion of host defense (capsules, cell components, enzymes, etc.), damage to host cells (siderophores, toxins, lysogenic conversion, cytopathic effects), portals of exit.
Portals of Entry of Infection
- Ingestion (fecal-oral)
- Inhalation (respiratory)
- Trauma (e.g., burns)
- Arthropod bites (zoonoses)
- Sexual transmission
- Iatrogenic (needle stick, blood transfusion)
- Maternal-neonatal
Modes of Infectious Disease Transmission
- Ingestion (Salmonella, Shigella, Vibrio, Clostridium)
- Inhalation (Mycobacterium, Mycoplasma, Chlamydia)
- Trauma (Clostridium tetani)
- Arthropod bites (Rickettsia, Yersinia pestis)
- Sexual transmission (Neisseria gonorrhoeae, HIV, etc.)
- Needle stick (Staphylococcus, HIV, HBV)
- Maternal-neonatal transmission) (HIV, HBV, Neisseria)
Modes of Infectious Disease Transmission
- Contact transmission (person-to-person)
- Indirect contact (formites)
- Droplet transmission
- Vehicle transmission
- Airborne transmission
- Waterborne transmission
- Foodborne transmission
- Vector transmission
Extracellular versus Intracellular Parasitism
- Extracellular parasites are destroyed when phagocytosed, damaging tissues as they remain outside cells, inducing opsonizing antibodies; acute short-duration diseases.
- Intracellular parasites can multiply within phagocytes, and frequently cause chronic diseases.
Reading
- Chapters 9: Pathogenesis of bacterial infection, 10: Normal human microbiota (in provided manual)
11. Normal Microbial Flora of the Human Body
- Role of resident flora, Normal flora of the skin, Normal flora of the mouth & upper respiratory tract, Normal flora of the intestinal tract, Normal flora of urethra, Normal flora of vagina, Normal flora of conjuctiva.
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Description
This quiz covers key concepts from Lecture 4 on microbiology, focusing on bacterial infection and the mechanisms of pathogenesis. Topics include normal human microbiota, virulence factors, types of infections, and the impact of microbes on human health. Test your understanding of how bacteria interact with the human body and the significance of the human microbiome.