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(3.) Infectious Diseases and Epidemiology - Key Concepts (Lecture Notes)

Pandemic vs Epidemic vs Endemic vs Outbreak vs Sporadic

  • Pandemic: when an infection or disease breaks out and spreads worldwide; not confined to a single country or region.
  • Epidemic: a widespread occurrence of an infectious disease in a community at a particular time.
  • Endemic: something that's always present in that area.
  • Outbreak: a sudden increase in occurrences of a disease in a particular place/time.
  • Sporadic: random or isolated cases in different places; not clustered or following a pattern.
  • Visual representation: time vs number of cases graphs typically show endemic baseline, outbreaks/epidemics, and pandemics; sporadic events appear as isolated points.

Historical infectious diseases and naming conventions

  • Plague: historically devastating; transmission primarily by flea bites from rodents; Yersinia pestis is the causative organism.
  • Smallpox: highly prevalent in the past; caused by a virus (not bacteria).
  • Rodent/flea transmission details:
    • Fleas carry Yersinia pestis; bites transmit the organism to humans.
    • Rodent control is essential to control plague outbreaks.
  • Naming conventions for organisms:
    • Genus first, then species (binomial nomenclature).
    • First letter of the genus is capitalized; species is lowercase; both are italicized in proper formatting (e.g., Yersinia pestis).
  • Historical vaccination context:
    • Smallpox vaccine no longer routinely used because smallpox has been eradicated; individuals born after about 1977 typically did not receive this vaccination.
    • The vaccination history is tied to eradication status and longevity of immunity.
  • Infectious agents vary by type:
    • Some diseases are caused by viruses (e.g., measles, influenza, smallpox).
    • Some by bacteria (e.g., Bordetella pertussis, Borrelia burgdorferi, Chlamydia trachomatis, Staphylococcus aureus).
    • Some by protozoa (e.g., Cryptosporidium parvum).

Measles (examples and features)

  • Causative organism: measles virus (a virus).
  • Transmission: respiratory route; highly contagious.
  • Clinical features: fever, cough, coryza (runny nose), conjunctivitis (red watery eyes), Koplik spots (tiny white spots inside the mouth).
  • Surface survival: measles virus can survive on nonliving objects for about 2 ext{ hours}.
  • Prevention: vaccination (measles component in MMR); vaccination schedule and coverage not detailed here, but vaccines are key to control.
  • Note on clinical differentiation: measles rash pattern differs from other infections; Koplik spots are characteristic.

Influenza: types, transmission, and vaccines

  • Causative organisms: influenza viruses types A, B, and C; epidemics/pandemics primarily associated with type A.
    • Type A has multiple host species (humans and animals).
  • Nomenclature on the virus surface: two key surface proteins subject to mutation:
    • Hemagglutinin (HA)
    • Neuraminidase (NA)
  • Notation examples: H{1}N{1}, H{5}N{1} (subtypes), etc.
  • Antigenic changes:
    • Antigenic shifts cause epidemics and pandemics due to major changes in surface antigens.
    • Spike-like proteins (HA and NA) are the main targets of vaccines and immune responses; mutations in these proteins drive new strains.
  • Vaccination context:
    • Current vaccine is described as a trivalent vaccine containing two influenza A strains (e.g., H{1}N{1} and H{5}N{1}) and one influenza B strain.
    • The vaccine composition can change annually based on circulating strains.
  • Vaccine technology and speed:
    • RNA (mRNA) vaccines emerged and provided rapid development options; traditional virus-based vaccines required longer development times.
    • The rapid development of mRNA vaccines for COVID-19 is cited as an example of leveraging prior knowledge to tweak spike proteins for protection.
  • Antigenic drift vs shift:
    • Antigenic shifts involve major genetic changes that create new virus subtypes; these shifts contribute to epidemics/pandemics.
  • Transmission and control:
    • Transmission is primarily via respiratory droplets; prevention includes vaccination, hand hygiene, and other nonpharmaceutical measures.
  • Clinical notes:
    • Common symptoms include fever, cough, sore throat, fatigue; seasonal vaccine recommendations and surveillance data are tracked (CDC data cited as a real-time reference in class).

Bordetella pertussis and pertussis vaccination

  • Causative organism: Bordetella pertussis (bacterial).
  • Transmission: respiratory droplets; highly contagious in young children.
  • Symptoms: initial influenza-like cough with progressive coughing that can be severe (paroxysmal coughing) and lead to a characteristic whoop in some cases.
  • Vaccination: DTaP vaccine (Diphtheria, Tetanus, Acellular Pertussis).
    • D = Diphtheria; T = Tetanus; aP = Acellular Pertussis (acellular means without cells).
  • Vaccine evolution:
    • Whole-cell pertussis vaccine (earlier) caused more side effects; moved to acellular versions to reduce adverse effects.
    • The session includes discussion of subunit vaccines and toxoids as vaccine strategies (e.g., using inactivated toxins rather than whole organisms).
  • Pregnancy and adults:
    • Important for pregnant individuals and caregivers to be up-to-date on vaccines; timing relative to exposure and pregnancy is discussed.
  • Public health logic:
    • Vaccination reduces disease burden and severe outcomes, especially in children.

Chlamydia trachomatis and reproductive health

  • Disease type: bacterial sexually transmitted infection (STI).
  • Transmission: primarily sexually transmitted; high prevalence with significant morbidity.
  • Main symptoms in women: abnormal vaginal discharge, bleeding between periods, painful menses, painful urination; possible pelvic inflammatory disease (PID).
  • Urethral involvement in men: urethritis; potential progression if untreated.
  • Complications: PID can block fallopian tubes, causing infertility; ectopic pregnancy risk increases if tubes are scarred.
  • Screening and public health priority: community-wide screening of asymptomatic and symptomatic individuals is essential to prevent spread.
  • Treatment: antibiotic therapy is effective; early treatment reduces risk of infertility and ectopic pregnancy.
  • Broader context: a significant burden of sexually transmitted infections (STIs) with substantial costs; prevention relies on screening and safe practices.

Cryptosporidiosis and Cryptosporidium parvum

  • Causative organism: protozoan parasite Cryptosporidium parvum (protozoan, single-celled eukaryote).
  • Transmission: fecal-oral route; ingestion of contaminated water; also can be transmitted via contaminated fruits/vegetables and surfaces; zoonotic potential with animals (cows, rodents, dogs, cats).
  • Pathogenesis:
    • Attaches to the crypts of the small intestine, impairing absorption and causing diarrhea; infection leads to oocyst formation that can contaminate water and food.
    • Symptoms: GI symptoms (diarrhea, cramping, dehydration).
  • Hospital-acquired risk: can be transmitted in hospital settings, particularly affecting immunocompromised patients.
  • Prevention: avoid swallowing pool water; test and manage pet sources; ensure safe water and food handling; practice good hygiene.
  • Notable facts:
    • First reported case in the United States in 1976.
    • Causes a significant portion of diarrheal illness in developing countries; in some contexts up to about 30 ext{\%} of GI infections in those regions (as described).
  • Additional notes on cryptosporidiosis context:
    • It is a protozoan that infects the intestinal lining (crypts) and disrupts nutrient absorption, leading to watery diarrhea.
    • Treatment considerations differ from bacterial or viral causes because protozoa are eukaryotic and can be less responsive to some drugs.
  • Related topics mentioned: exposure through swimming and contaminated water bodies; potential spread via pets; importance of pool and water safety.

West Nile, Dengue, Chikungunya, and related vector-borne infections

  • Transmission: primarily via mosquitoes; birds often act as reservoir hosts (West Nile); humans are incidental hosts.
  • Dengue fever, chikungunya, and other arboviruses are discussed as examples of vector-borne diseases with global distribution and ongoing emergence.
  • Public health relevance: vector control and travel-related exposure are important components of prevention.

Staphylococcus aureus and MRSA; skin and soft tissue infections

  • Causative organism: Staphylococcus aureus; MRSA denotes methicillin-resistant S. aureus.
  • Epidemiology: one of the most common hospital- and community-acquired infections in the United States.
  • Disease spectrum: can start as a simple pimple or abscess, can invade deeper tissues, bones, kidneys, heart, and other organs; can cause bacteremia and sepsis.
  • Transmission and risk factors: spread via contact; high risk in athletes due to shared equipment and towels; surface contamination can contribute to spread.
  • Impetigo: superficial skin infection that can be caused by S. aureus or Streptococcus species; highly contagious.
  • MRSA specifics: resistance due to antibiotic resistance genes; MRSA can occur in the community and hospital settings.
  • Prevention and control:
    • Do not share personal items; practice good aseptic/ hygiene measures; screen hospital staff to prevent nosocomial spread.
    • In moist environments, S. aureus can survive on surfaces for extended periods (weeks to months); less so in dry environments.
  • Related terminology:
    • Aseptic techniques: methods to prevent contamination and infection.
    • Sepsis: systemic inflammatory response to infection.

Lyme disease and Borrelia burgdorferi

  • Causative organism: Borrelia burgdorferi (bacterial).
  • Transmission: tick-borne; bite by Ixodes ticks.
  • Symptoms and progression:
    • Early infection may present with a small bite or erythema migrans (bull’s-eye rash) in some cases; rash may be absent in others.
    • Flu-like symptoms in early stage; can progress to joint pain (arthritis), cardiac involvement (heart rate changes), and neurological symptoms (hearing loss, cognitive/psychiatric symptoms).
  • Prevention: protective clothing (pants tucked into socks, long sleeves, light-colored clothing to spot ticks), insect repellent (DEET or natural alternatives), and checking for ticks after exposure.
  • Disease stages and long-term concerns: untreated Lyme disease can become chronic with joint, cardiac, and neurological complications.

Epidemiology concepts: emergence, reemergence, and drivers

  • Emerging infectious diseases: diseases that are newly appearing in a population or showing up in a new area.
  • Reemerging infectious diseases: diseases that existed previously but are increasing again in incidence.
  • Examples mentioned: Ebola (global spread via travel), Dengue fever (global spread), West Nile, Chikungunya; discussion includes that some diseases may be endemic in certain regions.
  • Drivers of emergence/reemergence:
    • Ecological changes (deforestation, urbanization, climate changes) that bring humans into contact with new reservoirs.
    • International travel rapidly moving pathogens across the globe (e.g., within 24 hours).
    • Global commerce and movement of people and goods.
    • Technology and industry influencing transmission and distribution of pathogens.
    • Microbial adaptation and mutations enabling new host range or resistance.
    • Breakdowns or deficiencies in public health infrastructure and surveillance capacity.
  • CDC/WHO collaboration since 1995:
    • Four primary goals established in 1995 for infectious disease prevention and control:
    • Surveillance and monitoring of disease trends.
    • Deployment of trained personnel to respond to outbreaks.
    • Increased research funding and activity to understand and combat infections.
    • Prevention and control measures, including vaccine development and public health interventions.
    • Emphasis on global cooperation due to interconnectedness of markets, travel, and ecosystems.

Study guides, testing, and exam preparation (class format)

  • Course assessments include quizzes and exams on content covered; quizzes are used to provide practice and reinforce learning.
  • Quizzes contribute a substantial portion of the grade (e.g., around 30 ext{\%} of total score).
  • Quizzes are designed to reflect the exam content and help students pace their study; emphasis on understanding definitions, causative organisms, modes of transmission, and controls.
  • Study guides highlight the key topics and the way questions will be asked (e.g., matching organisms to their contributions or to a mode of transmission).
  • The instructor notes that not every detail from the readings will be tested; focus areas are defined in the study guides.

General microbiology concepts touched in the lecture

  • Cell types:
    • Prokaryotes vs eukaryotes: eukaryotic cells have a nucleus; prokaryotes lack a true nucleus.
    • The nucleus is derived from an ancestral cell evolution; its formation was a major step in cellular evolution.
  • Pathogenesis and immune response:
    • Lymph nodes as immune system hubs; when invaded, lymphocytes proliferate leading to swollen lymph nodes (buboes) in the context of certain infections like plague (bubonic stage).
    • Antigens trigger immune responses; antigens are substances that elicit antibody production.
  • Vaccines through history:
    • Whole-cell vaccines vs subunit vaccines vs toxoid vaccines vs DNA and RNA vaccines.
    • Example paths: whole-cell pertussis vaccine → acellular pertussis (subunit) vaccine to reduce adverse effects; toxoids for toxins; nucleic acid vaccines (DNA/RNA) enabling targeted antigen expression.
  • Asepsis and infection control:
    • Aseptic technique defined as “without contamination”; importance in preventing hospital-acquired infections.
    • Personal items, surfaces, and shared equipment as potential vectors for infection; emphasis on hygiene and disinfection.
  • Public health context:
    • Importance of vaccination not only for individual protection but for community (herd) immunity; estimated threshold for herd immunity around 75 ext{\%} ext{ to } 80 ext{\%} of the population.
    • The concept of exposure risk and prolonged exposure in transmission (e.g., measles via respiratory droplets, influenza via droplets, etc.).

Quick reference: key numerical and symbolic points

  • Herd immunity threshold: 75 ext{\%} ext{ to } 80 ext{\%}
  • Measles surface survival: ext{~2 hours} on inanimate objects
  • Measles first-dose vaccination window (contextual): 12 ext{--}15 ext{ months}; second dose prior to school entry
  • Influenza vaccine components (example; annual formulation): two A strains and one B strain; represented as subtypes like H{1}N{1} and H{5}N{1} for the A strains
  • Time to develop protective antibodies after vaccination: about 2 ext{ weeks}
  • Reported vaccine coverage and testing data vary with administrative changes; CDC data cited intermittently in class materials
  • Case counts cited for current respiratory infections: e.g., for measles and influenza surveillance, real-time data are accessible via CDC portals (example data referenced as of a specific date)
  • First US report of cryptosporidiosis: 1976

Notes on exam-style questions you might expect

  • Causative organism, mode of transmission, and control for a given disease (e.g., measles, influenza, pertussis, Lyme disease, MRSA).
  • Correct formatting of organism names (binomial nomenclature) and the rationale behind italicization and capitalization.
  • Distinctions between pandemic, epidemic, endemic, outbreak, and sporadic cases with real-world examples.
  • Explanation of antigenic shift vs drift and how these relate to outbreaks and vaccine design.
  • Vaccination strategy evolution (whole-cell vs acellular vs toxoid vs DNA/RNA vaccines) and rationale for current vaccine types.
  • Public health drivers of disease emergence: ecological changes, travel/commerce, microbial mutation, and infrastructure deficiencies.
  • Case scenario reasoning: choose the most likely infection given symptoms and exposure (e.g., bull's-eye rash → Lyme disease; bullous conjunctivitis and Koplik spots → measles; paroxysmal cough with a whoop → pertussis).
  • Interpreting surveillance data and understanding the role of vaccines in herd immunity and outbreak prevention.