PAC548 Microbiology LOs

Describe the microbial composition of the human microbiome.

Mainly consists of bacteria and fungi that are permanent residents (commensals); viruses and parasites are not considered normal flora, but can be found in asymptomatic individuals.

List the sites of the human body that are typically colonized with microorganisms.

Major sites include the skin, oropharynx, colon, and vagina.

List the sites of the human body that are typically sterile.

CNS, blood, lower bronchi/alveoli, liver, spleen, kidneys, and bladder are normally sterile.

Discuss the importance of being a carrier of pathogenic organisms in regards to public health.

Carriers harbor pathogenic organisms without symptoms and can be reservoirs for others, spreading infection despite being asymptomatic; e.g., Typhoid Mary with Salmonella typhi.

Explain the functions and importance of normal flora that benefit human hosts.

They provide colonization resistance by occupying attachment sites, produce antimicrobial compounds (bacteriocins, lactic acids), regulate mucosal immunity (IgA, GALT, T helper cells), help in nutrition (produce B vitamins, vitamin K, absorb iron, digest fibers).

Discuss how alterations in our commensal flora can lead to disease.

Antibiotic suppression allows pathogens to grow (e.g., C. diff); can cause vitamin deficiencies, contribute to obesity, and become pathogenic in immunocompromised individuals or if relocated in the body.

Identify the most common commensal microorganisms on the skin.

Staphylococcus epidermidis, Staphylococcus aureus, Propionibacterium acnes, Peptococcus, Candida albicans, and Demodex mites.

Identify the most common commensals in nose and nasopharynx/throat.

S. aureus and S. epidermidis in the nose; Corynebacterium, Haemophilus, Neisseria, Moraxella catarrhalis, Viridans streptococci, Strep. pneumoniae in the nasopharynx.

Identify the most common commensals in the mouth.

Candida albicans, Lactobacillus, Neisseria, Viridans streptococci (e.g., Strep. mutans, Strep. sanguinis), Eikenella corrodens, anaerobes like Bacteroides, Prevotella, Fusobacterium, Clostridium, Peptostreptococcus, Actinomyces.

Identify the most common commensals in the colon.

Bacteriodetes, Firmicutes, Bifidobacterium, Eubacterium, coliforms (E. coli), Enterococcus faecalis, Lactobacillus, Candida albicans; 90% are anaerobes.

Identify the most common commensals in the vagina.

Lactobacillus spp., E. coli, Enterobacter, Gardnerella vaginalis, Corynebacterium, S. epidermidis, Group B Strep, S. aureus.

Identify the most common commensals in the distal urethra.

Staph. epidermidis, coliforms, diphtheroids, nonhemolytic streptococci; also Mycobacterium smegmatis and Staph. saprophyticus on skin.

Identify the most common pathogens of integumentary infections.

S. aureus, S. pyogenes, Propionibacterium acnes, Candida albicans.

Identify the most common pathogens of oral and dental infections.

Strep. mutans (caries), Strep. sanguinis (endocarditis), Actinomyces israelii (abscesses), Eikenella corrodens (bites), anaerobes causing periodontal disease.

Identify the most common pathogens of upper respiratory infections.

S. pneumoniae, H. influenzae, Moraxella catarrhalis, S. aureus, Group A Strep, Corynebacterium diphtheriae.

Identify the most common pathogens of gastrointestinal infections.

E. coli, Salmonella, Shigella, Campylobacter, C. difficile, B. cereus, V. cholerae, H. pylori, B. fragilis.

Identify the most common pathogens of genitourinary infections.

E. coli, Enterococcus faecalis, Candida albicans, N. gonorrhoeae, Chlamydia trachomatis, Gardnerella vaginalis, Group B Strep.

Discuss where biofilms form.

On foreign bodies like prosthetic joints/heart valves, IV/urethral catheters, native heart valves, teeth; also in chronic wounds, lungs (e.g., Pseudomonas in CF).

How do biofilms contribute to human disease?

They protect bacteria from antibiotics and immune defenses, slow wound healing, allow persistent infections, and form dental plaque.

How is virulence of a microbe determined using LD50 and ID50?

LD50 is the dose that kills 50% of hosts, ID50 infects 50%; lower LD50/ID50 means higher virulence (e.g., Shigella <100, Salmonella 100,000).

How do mutations and horizontal gene transfer contribute to pathogenicity?

Mutations can increase resistance and virulence; horizontal transfer spreads virulence genes via conjugation, transduction (bacteriophages), or transposons.

How do extracellular structures contribute to pathogenicity?

Spores resist environment, capsules inhibit phagocytosis, glycocalyx helps biofilm adherence, flagella aid movement, pili help attachment to cells.

How do endotoxins contribute to pathogenicity?

LPS in Gram-neg bacteria causes fever, shock, DIC; stimulates immune system excessively leading to tissue damage even after bacterial death.

How do exotoxins and secretion systems contribute to pathogenicity?

Exotoxins (Gram pos/neg) cause cell damage; Type III secretion systems (injectosome) inject toxins directly into host cells avoiding antibodies.

List types of microscopic analysis for diagnosing bacterial infections.

Gram stain (Gram pos/neg), acid-fast stain (Mycobacteria), dark field (Treponema), Giemsa (intracellular like Chlamydia).

List culture-based methods for diagnosing bacterial infections.

Cultures from various sites grown on specific media, tested for metabolic use and antibiotic sensitivity via disk diffusion (zone of inhibition).

List molecular methods for diagnosing bacterial infections.

RADT (enzyme immunoassays), NAAT/PCR for DNA/RNA; detect antigens or toxins (e.g., Strep, H. pylori, Shiga toxin).

List serologic methods for diagnosing bacterial infections.

Antibody tests like Western blot (Lyme), ASO (Strep), VDRL/RPR (Syphilis), FTA-ABS (Treponemal).

List general antibiotic targets in bacterial treatment.

Antibiotics may inhibit cell wall synthesis, disrupt membranes, inhibit nucleic acid or protein synthesis.

What type of bacteria is Streptococcus pyogenes and what diseases does it cause?

Gram positive cocci in chains, β-hemolytic; causes strep throat, rheumatic fever, and necrotizing fasciitis.

What are the major virulence factors of Streptococcus pyogenes?

M protein (antiphagocytic, cross-reactive with cardiac myosin), capsule, glycocalyx, enzymes (streptolysins), and exotoxins (superantigens).

How is Streptococcus pyogenes transmitted?

Person-to-person via respiratory droplets or skin contact; it is part of the normal flora of the oropharynx and skin.

What type of bacteria is Staphylococcus aureus and what infections can it cause?

Gram positive cocci in clusters; causes skin infections, pneumonia, osteomyelitis, food poisoning, TSS, and scalded skin syndrome.

What are the key virulence factors of Staphylococcus aureus?

Protein A (binds IgG), capsule, coagulase, hemolysins, leukocidins, exfoliative toxin, enterotoxins, and TSST-1.

How is Staphylococcus aureus transmitted?

Colonizes skin and nares; spreads via direct contact, fomites, or respiratory droplets.

What type of bacteria is Clostridium tetani and how does it cause disease?

Gram positive spore-forming anaerobic bacilli; produces tetanospasmin toxin which inhibits inhibitory neurons → spastic paralysis.

What are the key features of Clostridium botulinum?

Gram positive anaerobe; produces botulinum toxin which blocks ACh release → flaccid paralysis; found in canned foods and honey (infant botulism).

What is the mode of transmission for Clostridium botulinum?

Ingestion of preformed toxin in improperly canned food or spores in honey (infants).

What diseases are caused by Clostridium perfringens and what is the main virulence factor?

Gas gangrene (myonecrosis) and food poisoning; α-toxin (lecithinase) causes tissue necrosis and hemolysis.

How does Clostridium difficile cause disease and what triggers it?

Antibiotic use suppresses normal flora → overgrowth; produces toxins A and B → pseudomembranous colitis with diarrhea.

What are key traits of Bacillus anthracis and its virulence factors?

Gram positive spore-forming rod; capsule made of D-glutamate, lethal toxin and edema toxin; causes cutaneous, inhalational, and GI anthrax.

How is Bacillus cereus transmitted and what does it cause?

Found in rice; produces emetic toxin (preformed) → vomiting and diarrheal enterotoxin → watery diarrhea.

What kind of organism is Gardnerella vaginalis and what condition does it cause?

Gram variable facultative anaerobic bacillus; causes bacterial vaginosis; associated with clue cells and fishy odor.

What type of organism is Chlamydia trachomatis and how is it transmitted?

Obligate intracellular Gram negative-like organism; transmitted sexually or perinatally.

What diseases are caused by Chlamydia trachomatis?

Urethritis, cervicitis, PID, neonatal conjunctivitis, pneumonia, LGV (L1-3), and trachoma (A-C).

What are the key virulence traits of Neisseria gonorrhoeae?

Gram negative diplococcus with pili, opacity proteins; evades immunity by antigenic variation; no capsule.

What diseases are caused by Neisseria meningitidis?

Meningitis and meningococcemia; petechial rash, shock, DIC; has polysaccharide capsule.

What are transmission modes for Neisseria meningitidis?

Respiratory droplets, close contact; vaccine available targeting capsule polysaccharides.

What organism causes syphilis and what is its bacterial classification?

Treponema pallidum; spirochete seen by dark field microscopy or serologic testing.

What are the stages of syphilis and symptoms?

Primary: painless chancre; secondary: rash on palms/soles, condyloma lata; tertiary: gummas, aortitis, neurosyphilis.

What causes chancroid and what are its symptoms?

Haemophilus ducreyi; Gram negative coccobacillus; causes painful genital ulcers with lymphadenopathy.

What type of organism is Corynebacterium diphtheriae and how is it transmitted?

Gram positive bacilli; transmitted by airborne droplets; infects upper respiratory tract and broken skin.

What are the virulence factors of Corynebacterium diphtheriae?

Diphtheria toxin (from bacteriophage) causes cell death and pseudomembrane formation in throat and heart; thick, adherent, grayish exudates on mucosa.

What diseases are caused by Corynebacterium diphtheriae?

Diphtheria: gray pseudomembrane in throat, fever, pharyngitis, cervical lymphadenopathy, myocarditis, endocarditis, nerve palsies, peripheral neuritis.

What is Haemophilus influenzae and how is it transmitted?

Gram negative bacilli; airborne droplet transmission; colonizes respiratory tract and can spread to meninges.

What are the virulence factors of Haemophilus influenzae?

Polysaccharide capsule (resists phagocytosis), IgA protease, LPS endotoxin.

What diseases does Haemophilus influenzae cause?

URIs, meningitis, sepsis in children, epiglottitis (most common cause), pneumonia in adults with lung disease (e.g., COPD).

Describe Bordetella pertussis and its mode of transmission.

Gram negative coccobacilli; airborne droplet transmission; infects upper respiratory tract.

What are the virulence factors of Bordetella pertussis?

Capsule, pili for adhesion, pertussis toxin (causes mucosal edema), tracheal cytotoxin (damages ciliated cells), LPS endotoxin.

What disease does Bordetella pertussis cause?

Whooping cough (acute tracheobronchitis); paroxysmal cough with inspiratory whoop and possible post-tussive emesis.

What organism is Legionella pneumophila and how is it spread?

Gram negative motile bacilli with flagella; inhalation of aerosolized contaminated water (air conditioners, hot tubs, cooling towers).

What are Legionella’s virulence factors?

LPS endotoxin, catalase (resists phagolysosome destruction), biofilm formation, β-lactamase.

What diseases are caused by Legionella pneumophila?

Legionnaire’s disease (atypical pneumonia, diarrhea, confusion, AKI); Pontiac fever (flu-like, no pneumonia).

Describe Streptococcus pneumoniae and its transmission.

Gram positive diplococci/short chains, α-hemolytic; transmitted from normal flora of oropharynx into respiratory tract.

What are the virulence factors of Streptococcus pneumoniae?

Capsule (evasion), lipoteichoic acid (LTA → septic shock), IgA protease, pneumolysin (α-hemolysis), PBP mutations (resistance).

What infections does Streptococcus pneumoniae cause?

Most common cause of community-acquired pneumonia (rusty sputum), otitis media, sinusitis, mastoiditis, meningitis, bacteremia in asplenic patients.

Describe Pseudomonas aeruginosa and its transmission.

Gram negative bacilli, blue-green pigment, fruity odor; lives in soil, water, and medical equipment; can colonize intestines.

What are Pseudomonas virulence factors?

Glycocalyx biofilm, LPS endotoxin, Type III secretion system (exotoxins), Exotoxin A, elastase/proteases, antibiotic and disinfectant resistance.

What diseases are caused by Pseudomonas aeruginosa?

Sepsis, pneumonia (especially in CF), chronic wounds, UTIs, malignant otitis externa (DM), hot tub folliculitis, corneal infections, ecthyma gangrenosum.

What type of bacteria is Klebsiella pneumoniae and how is it spread?

Gram negative facultative anaerobic bacilli; part of normal colon flora, also found in water/soil and some respiratory tracts.

What are the virulence factors of Klebsiella pneumoniae?

Capsule (evades phagocytosis), LPS endotoxin, extended-spectrum β-lactamases (resistance).

What infections are caused by Klebsiella pneumoniae?

UTIs, pneumonia (currant jelly sputum), abscesses, necrosis, and can spread to bloodstream, meninges, and liver.

What is Listeria monocytogenes and how is it transmitted?

Gram positive motile bacilli; intracellular; from contaminated food (unpasteurized milk, deli meat, raw veggies), can be transplacental.

What are the virulence traits of Listeria monocytogenes?

Beta hemolysis, internalin (invades tissue), listeriolysin (evades phagosomes), actin rockets (cell-to-cell spread), cold enhancement.

What diseases are caused by Listeria monocytogenes?

Gastroenteritis, meningitis, sepsis in neonates, pregnant women, immunocompromised; can cause miscarriage, stillbirth, and neonatal infection.

What is the classification and transmission route of Salmonella typhi and S. enterica?

Gram negative flagellated facultative anaerobic bacilli; transmitted via fecal-oral route through contaminated food or water (e.g., poultry, eggs); S. typhi has only a human reservoir.

What are the virulence factors of Salmonella?

Vi capsular antigen (prevents phagocytosis), curli (tissue adhesion), typhoid toxin (cell death), and Type III secretion system (injects toxins into cells, evading antibodies).

What diseases are caused by Salmonella?

S. enterica: enterocolitis with diarrhea (bloody/non-bloody); S. typhi: typhoid fever with high fever, delirium, rose spots, constipation, and Reiter's syndrome; more severe in immunocompromised.

How is Shigella dysenteriae transmitted and what are its traits?

Gram negative facultative anaerobe; fecal-oral transmission through contaminated water or food; human-only reservoir; very low ID50 (<100 organisms).

What are the virulence factors of Shigella?

Shiga toxin (kills intestinal cells → bloody diarrhea), Type III secretion system, antibiotic resistance; toxin encoded by bacteriophage.

What disease does Shigella cause?

Enterocolitis with invasion of distal ileum and colon → ulceration, fever, abdominal cramps, and bloody diarrhea; can cause Reiter’s syndrome.

What is Vibrio cholerae and how is it transmitted?

Gram negative curved vibrio (comma-shaped); fecal-oral transmission via contaminated water or seafood (e.g., oysters, shrimp); limited vaccine effectiveness.

What are Vibrio cholerae's virulence factors?

Cholera toxin (causes Cl⁻ and water secretion → watery diarrhea), mucinase (degrades protective mucus), toxin encoded by bacteriophage.

What disease is caused by Vibrio cholerae?

Cholera: profuse rice-water stools without abdominal pain, leading to dehydration and hypovolemic shock.

What type of organism is Helicobacter pylori and how is it transmitted?

Gram negative urease-positive bacilli; transmitted person-to-person by ingestion; not found in food, stool, or water.

What are the virulence factors of H. pylori?

Urease (produces ammonia → neutralizes acid), damages mucosa; resistant to metronidazole.

What disease is caused by Helicobacter pylori?

Gastritis and peptic ulcers; upper abdominal pain and GI bleeding; long-term infection can cause gastric carcinoma.

What type of bacteria is Campylobacter jejuni and how is it transmitted?

Gram negative microaerophilic bacillus; fecal-oral transmission via contaminated food (poultry, meat, milk), water, or contact with animal feces.

What disease is caused by Campylobacter jejuni?

Enterocolitis in children (watery then bloody diarrhea), fever, abdominal pain; can cause Guillain-Barré, reactive arthritis, and Reiter’s syndrome.

What is Escherichia coli and how is it transmitted?

Flagellated Gram negative facultative anaerobe that ferments lactose; transmitted fecal-orally via contaminated water/food or cattle (O157:H7); no vaccine.

What are the virulence factors of E. coli?

Capsule (antiphagocytic), pili (attachment), flagella (mobility), LPS endotoxin (shock), enterotoxins (watery diarrhea), Shiga toxin (bloody diarrhea), Type III secretion system.

What diseases are caused by E. coli?

Traveler’s diarrhea, dysentery, hemolytic uremic syndrome (HUS), UTIs (cystitis, pyelonephritis), sepsis; cranberry juice can prevent binding in UTIs.

What type of organism is Yersinia pestis and how is it transmitted?

Gram negative bacillus; zoonotic transmission via fleas from infected rodents; pneumonic form transmitted via respiratory droplets; vaccine offers partial protection.

What are the virulence factors of Yersinia pestis?

F1 capsule (evades phagocytosis), LPS endotoxin (DIC), Yersinia Outer Proteins (Yops via T3SS), extremely low ID50 (1–10 organisms).

What diseases are caused by Yersinia pestis?

Bubonic plague (fever, painful lymphadenopathy or buboes, abscesses); pneumonic plague (airborne, often fatal); septic shock.

Describe Pasteurella multocida and its transmission.

Gram negative bacillus; zoonotic via cat or dog bites; part of normal oral flora of pets; no vaccine.

What are Pasteurella’s virulence factors and diseases?

Capsule, LPS endotoxin; causes rapidly spreading cellulitis or osteomyelitis after bites, especially cat bites; avoid suturing these wounds.

What type of organism is Bartonella henselae and how is it transmitted?

Gram negative bacillus; zoonotic via cat scratches or bites (especially kittens); possibly fleas; no vaccine.

What are Bartonella's virulence traits and diseases?

Induces angiogenesis; causes cat scratch disease (fever, lymphadenopathy), resolves spontaneously; bacillary angiomatosis in immunocompromised (angiomas in skin/organs).

What type of organism is Mycobacterium tuberculosis and how is it transmitted?

Acid-fast bacilli; inhalation of aerosolized droplets; infects upper lung lobes; resides in macrophages.