Microbiology and Immunology Exam Notes

Pathogens and Microbes

• Pathogen: A microorganism that causes disease.
• Microbe: A microscopic organism, including bacteria, viruses, fungi, and protozoa.

Endemic, Epidemic, and Pandemic

• Endemic: Constantly present in a population.
• Epidemic: Sudden increase in disease cases in a region.
• Pandemic: An epidemic that spreads across countries or continents.

Infections

• Nosocomial infection: An infection acquired in a hospital setting.
• Latent infection: An infection that lies dormant in the body but can reactivate.

Protozoa Stages

• Trophozoite: Active, feeding stage of a protozoan.
• Cyst: Dormant, resistant stage of a protozoan.

Endospore

• Endospore: A tough, dormant form of certain bacteria used to survive harsh conditions.

Virulence Factors

• Virulence factors: Molecules that increase a microbe’s ability to cause disease.

Virus Components

• Capsid: Protein shell of a virus.
• Virion: Complete, infectious virus particle.
• Viroid: Infectious RNA molecule without a protein coat, affecting plants.

Bacteriophage

• Bacteriophage: A virus that infects bacteria.

Prion

• Prion: Infectious protein that causes neurodegenerative diseases.

Parasites

• Endoparasite: Lives inside the host (e.g., tapeworm).
• Ectoparasite: Lives on the host’s surface (e.g., lice).
• Intracellular parasite: Lives inside host cells (e.g., viruses).

Ribozymes

• Ribozymes: RNA molecules with enzymatic activity.

Genetically Modified Organisms (GMOs)

• Genetically modified organisms (GMOs): Organisms with altered DNA for desired traits.

Oxygen Requirements

• Aerobe: Requires oxygen.
• Capnophile: Thrives in high $CO_2$.
• Facultative anaerobe: Can survive with or without oxygen.
• Anaerobe: Grows without oxygen.

Symbiotic Relationships

• Mycorrhizae: Fungi that form symbiotic relationships with plant roots.
• Root nodules: Structures on plant roots housing nitrogen-fixing bacteria.

Nitrogen Fixation

• Nitrogen fixation: Conversion of nitrogen gas into ammonia by bacteria.

Disease Transmission

• Carrier: Infected person without symptoms.
• Vector: Transmits disease between hosts.
• Biological vector: Pathogen reproduces inside the vector (e.g., mosquito).
• Mechanical vector: Carries pathogen without being infected (e.g., fly).
• Reservoir: Natural host or environment where a pathogen lives.

Microbial Control

• Decontamination: Removing microbes to make something safe.
• Disinfection: Eliminating most pathogens.
• Sterilization: Killing all microbial life.
• Sanitization: Reducing microbes to safe levels.

Immunity

• Innate immunity: Immediate, nonspecific defense.
• Adaptive immunity: Specific, learned immune response.

Enteric vs. Nonenteric

• Enteric: Related to the intestines.
• Nonenteric: Not related to the intestines.

Bacterial Toxins

• Endotoxin: Part of gram-negative bacterial walls, released upon death.
• Exotoxin: Secreted by bacteria; often highly toxic.

Normal Flora

• Normal flora: Microorganisms normally living on/in the body without causing disease.

Hemoflagellate

• Hemoflagellate: Blood-dwelling protozoan with a flagellum (e.g., Trypanosoma).

Fungi

• Dermatophyte: Fungi infecting skin, hair, nails.
• Mycetoma: Chronic fungal infection causing swelling and discharge.
• Zygomycete: Fungi in the phylum Zygomycota.

Mycoplasmas

• Mycoplasmas: Bacteria without cell walls, often resistant to antibiotics.

More on Fungi

• Zygomycete: A group of fungi forming zygospores during reproduction.
• Dermatophyte: Fungi infecting skin, hair, nails.
• Dimorphic: Fungi with both yeast and mold forms depending on temperature.
• Mycetoma: Chronic infection with granules caused by fungi or bacteria.

Medical Terms

• Anaphylaxis: Severe, rapid allergic reaction.
• Prophylaxis: Measures taken to prevent disease.

Treatments

• Antibiotic: Substance that kills or inhibits bacteria.
• Probiotic: Live microbes that benefit health.
• Chemotherapy: Use of chemicals to treat disease (especially cancer or infections).

Sequelae

• Sequelae: Long-term consequences of an infection or disease.

Teratogenic

• Teratogenic: Capable of causing birth defects.

Cell Wall Composition

• Eukaryotes: Plants have cell walls made of cellulose; fungi have chitin; animals and protozoa lack cell walls.
• Prokaryotes: Bacteria have peptidoglycan (thick in Gram-positive, thin in Gram-negative); archaea may have pseudopeptidoglycan.

Sterilization Methods

• Autoclaving (moist heat), dry heat, filtration, radiation (UV or ionizing), and chemical sterilants (e.g., ethylene oxide).

Restriction Endonucleases

• Enzymes that cut DNA at specific sequences; used in genetic engineering and bacterial defense against phages.

Genetic Transfer in Bacteria

• Conjugation: Transfer of DNA via direct contact between bacteria (usually plasmids).
• Transformation: Uptake of free DNA from the environment.
• Transduction: Transfer of DNA via a bacteriophage.

Temperature Preferences of Microbes

• Psychrophile: Thrive in cold temperatures (below $15°C$).
• Mesophile: Prefer moderate temperatures ($20–45°C$); most human pathogens.
• Thermophile: Thrive at high temperatures (above $45°C$).

Antibiotic Mechanisms

• Penicillins: Inhibit bacterial cell wall synthesis.
• Aminoglycosides: Inhibit protein synthesis by binding to bacterial ribosomes.
• Sulfa drugs: Inhibit folic acid synthesis in bacteria.

Neisseria Species

• Virulence factors: Pili, endotoxin (LPS), capsule (in some strains), IgA protease.
• Treatment: Ceftriaxone is commonly used; prevention includes vaccines (e.g., for N. meningitidis).

E. coli Surface Antigens

• O antigen: Part of LPS, defines serogroup.
• H antigen: Flagellar protein.
• K antigen: Capsular antigen.

Lines of Immune Defense

• First line: Physical and chemical barriers (skin, mucous membranes, etc.).
• Second line: Innate immunity (phagocytes, inflammation, fever, complement).
• Third line: Adaptive immunity (B and T lymphocytes, antibodies).

B and T Cells

• B cells: Produce antibodies; responsible for humoral immunity.
• T cells: Helper T cells coordinate immune responses; cytotoxic T cells kill infected cells.

Types of Vaccines

• Live attenuated: Weakened pathogens (e.g., MMR).
• Inactivated: Killed pathogens (e.g., polio–IPV).
• Subunit/conjugate: Parts of the pathogen (e.g., HPV, Hib).
• mRNA: Encodes antigen (e.g., COVID-19 vaccines like Pfizer/Moderna).

Immunoglobulins

• IgG: Most abundant; crosses placenta; long-term immunity.
• IgA: Found in mucosal areas (saliva, tears, breast milk).
• IgM: First antibody produced in an immune response; pentamer structure.
• IgE: Involved in allergic reactions and parasitic infections.
• IgD: Functions mostly as a B cell receptor.

Immunity Types

• Natural: Acquired through infection or maternal antibodies.
• Artificial: Acquired through medical intervention (e.g., vaccines or immunoglobulin injections).
• Active: Your body makes antibodies (e.g., vaccines, infection).
• Passive: Antibodies are given (e.g., maternal, antitoxin injection).

Immune System Components

• Interferon: Antiviral proteins that interfere with viral replication.
• Complement: Group of proteins that assist in killing pathogens via membrane attack complex.
• Pyrogens: Substances (like IL-1) that induce fever.
• Cytokines: Signaling proteins that regulate immunity and inflammation.

Virulence Factors and Toxins

• Cord factor: Virulence factor in Mycobacterium tuberculosis; inhibits phagocytosis.
• Murine toxin: Toxin from Yersinia pestis (plague), affects vascular permeability.
• $mecA$ gene: Confers resistance to methicillin in MRSA.
• Tetanospasmin: Neurotoxin from Clostridium tetani; causes muscle rigidity/spasms.

Gram Stain

• Staphylococcus vs Streptococcus
  • Both are Gram-positive cocci.
  • Staph: Clusters; catalase-positive.
  • Strep: Chains/pairs; catalase-negative.

Infections/Diseases Caused By Specific Organisms

• Staph aureus: Skin infections, MRSA, toxic shock, food poisoning.
• Strep pneumoniae: Pneumonia, meningitis, otitis media.
• Strep pyogenes: Strep throat, scarlet fever, rheumatic fever, necrotizing fasciitis.
• Strep agalactiae: Neonatal sepsis, meningitis.
• Neisseria sp: N. gonorrhoeae (gonorrhea), N. meningitidis (meningitis).
• Mycobacterium avium complex: Lung disease in immunocompromised individuals.
• C. diff (Clostridioides difficile): Antibiotic-associated colitis.
• Clostridium sp (all): C. tetani (tetanus), C. botulinum (botulism), C. perfringens (gas gangrene).
• Pseudomonas aeruginosa: Opportunistic infections, especially in burns, cystic fibrosis.
• Haemophilus influenzae: Meningitis, pneumonia, epiglottitis.
• Haemophilus ducreyi: Chancroid (STD).
• Helicobacter pylori: Peptic ulcers, stomach cancer.
• Bordetella pertussis: Whooping cough (pertussis).
• Trichomonas vaginalis: Trichomoniasis (STD).
• Acanthamoeba sp: Eye infections (keratitis), brain infection (rare).
• Plasmodium sp: Malaria.
• Cryptosporidium sp: Diarrheal disease, especially in immunocompromised.
• Human papillomaviruses (HPV): Warts, cervical cancer.
• Adenoviruses: Conjunctivitis, respiratory infections.
• Polyomaviruses: JC virus (PML in AIDS), BK virus (kidney issues in transplant).
• Enteroviruses: Poliovirus, coxsackievirus, echovirus.
• Rhinoviruses: Common cold.
• Rotavirus, Norovirus: Viral gastroenteritis (rotavirus = infants; norovirus = outbreaks).
• CMV: Congenital infections, retinitis in HIV.
• HHVs: Herpesviruses, including HSV-1 (cold sores), HSV-2 (genital herpes).
• EBV: Mononucleosis, Burkitt’s lymphoma.
• VZV: Chickenpox (primary), shingles (reactivation).

Transmission of Specific Pathogens

• Necator americanus (hookworm):
  • Transmission: Larvae penetrate the skin, typically through bare feet from contaminated soil.
• Ascaris lumbricoides (giant roundworm):
  • Transmission: Ingestion of eggs in contaminated food or water (fecal-oral route).
• Enterobius vermicularis (pinworm):
  • Transmission: Ingestion or inhalation of eggs; eggs are often transferred via hands or contaminated surfaces.
• Sporothrix schenckii (causes sporotrichosis):
  • Transmission: Traumatic implantation (e.g., via thorns, splinters); known as “rose gardener’s disease.”
• Treponema pallidum pallidum (causative agent of syphilis):
  • Transmission: Sexual contact, transplacental (congenital syphilis), or via blood transfusion (rare).
• Francisella tularensis (causes tularemia):
  • Transmission: Contact with infected animals (especially rabbits), tick/deer fly bites, inhalation of aerosols, or ingestion of contaminated water/meat.
• Stachybotrys chartarum (black mold):
  • Transmission: Not person-to-person; exposure through inhalation of spores in water- damaged buildings.

Bacterial Structures

• Pili: Long, hair-like structures used for attachment and conjugation (DNA transfer).
• Fimbriae: Short, numerous bristle-like structures for adhesion of the surface.
• Cilia: Short, motile structures found only in eukaryotes for movement and fluid propulsion.
• Flagella: Long structures used for locomotion (bacterial movement).
• Periplasmic Flagella (Axial Filaments): Found in spirochetes; located between the inner and outer membranes for corkscrew-like movement.

Classification of Viruses

• By nucleic acid type: DNA vs RNA, single- vs double-stranded.
• Presence or absence of envelope.
• Shape: Helical, icosahedral, complex.
• Replication strategy (Baltimore classification).
• Host range (animal, plant, bacterial viruses).

Arboviruses

• Arthropod-borne viruses (transmitted by mosquitoes, ticks, etc.).
• Mostly RNA viruses.
• Enveloped; cause systemic infections such as encephalitis, hemorrhagic fever, fever with rash.
• Examples: West Nile virus, Dengue, Zika, Yellow Fever.

Paramyxoviruses

• Transmission: Respiratory droplets.
• Prevention: MMR vaccine (for measles, mumps), good hygiene.
• Features: Enveloped, negative-sense RNA; induce syncytia formation (multinucleated cells). Includes measles, mumps, RSV, parainfluenza.

Hepatitis Virus Transmission

• HAV: Fecal-oral route; prevention = vaccine, hygiene.
• HBV: Blood, sexual contact, perinatal; prevention = vaccine.
• HCV: Blood (IV drug use, transfusions); no vaccine available.

RNA vs DNA Viruses

• RNA viruses: Replicate in cytoplasm (except influenza, retroviruses), more mutation-prone.
• DNA viruses: Replicate in nucleus (except poxvirus), generally more stable.

RNA Viruses

• Positive-strand RNA: Acts like mRNA; can be directly translated.
• Negative-strand RNA: Must be transcribed to +RNA by RNA-dependent RNA polymerase before translation.

Coronaviruses

• Positive-sense RNA viruses, enveloped, crown-like spikes.
• Cause respiratory and gastrointestinal illness.
• Includes SARS-CoV, MERS-CoV, SARS-CoV-2 (COVID-19).
• Known for zoonotic transmission and high mutation/recombination rates.

Influenza

• Hemagglutinin (HA): Attachment to host cells.
• Neuraminidase (NA): Viral release from cells.
• M2 protein: Uncoating inside host cell.
• Ability to undergo antigenic variation (drift and shift).

Antigenic Variation

• Drift: Minor mutations in HA/NA genes; causes seasonal flu.
• Shift: Major genetic reassortment; creates new subtypes; can cause pandemics.

RSV (Respiratory Syncytial Virus)

• Paramyxovirus, enveloped, negative-sense RNA.
• Leading cause of bronchiolitis and pneumonia in infants.
• Causes syncytia. No vaccine, but palivizumab (monoclonal antibody) for high-risk infants.

Rabies

• Transmission: Bite of infected animal; virus in saliva.
• Features: Bullet-shaped virus, travels via nerves to CNS; causes encephalitis, hydrophobia.
• Prevention: Post-exposure prophylaxis (vaccine + rabies immunoglobulin).

HIV/AIDS

• Virus: Human immunodeficiency virus (retrovirus, enveloped, RNA).
• Target cells: $CD4^+$ T cells, macrophages.
• Transmission: Blood, sexual contact, perinatal.
• Mechanism: Reverse transcription of RNA to DNA, integrates into host genome.
• Disease progression:
  • Acute phase → Clinical latency → AIDS ($CD4$ count < $200/mm^3$ or opportunistic infections).
• Key markers: p24 antigen (early), anti-HIV antibodies.
• Diagnosis: ELISA, Western blot, PCR.
• Treatment: ART (antiretroviral therapy) – includes reverse transcriptase inhibitors, protease inhibitors, integrase inhibitors, entry inhibitors.
• Prevention: Safe sex, PrEP, screening blood supply, needle exchange, maternal treatment.