parasite, pathogens
Administrative announcements
Homework due Sunday at midnight; reminder sent over the holiday weekend; plan to set aside time to work on it so you don’t have too much to do.
iClicker grades can be confusing if you look in the iClicker app because the instructor’s account has three sections in one.
In iClicker, you may see zeros for questions from sections you didn’t participate in; Canvas will have the correct grade after syncing.
Today after this class around 11:00, the teaching assistant and the instructor will sync grades into Canvas.
In Canvas, you’ll see the correct grade (e.g., 4 out of 4 for that day).
In iClicker, the app may show, e.g., 4 out of 12 because it aggregates three sections; don’t rely on iClicker for the final grade.
The grade that matters is the Canvas grade after transfer.
If you miss a question in iClicker (don’t click in time or bathroom break), you still get a point in iClicker; the grade can be adjusted in Canvas after it’s posted there.
Do not email about iClicker issues; it’s easier to fix in person either before or after class because the instructor cannot easily change grades on a phone due to the Okta login and Canvas limitations.
You must wait until your grade is in Canvas before asking for a fix; the iClicker app cannot be the source of truth for grading.
Now starting the main topic: parasites and pathogens, with definitions, examples, and terminology.
The biological definitions: parasite, pathogen, ecto-/endo- and examples
A parasite is an organism that lives on or in a host and typically derives benefit at the host’s detriment; the host suffers a negative impact while the parasite gains benefit.
A pathogen is a microorganism that can cause disease; from a strict biological standpoint, all pathogens are parasites.
In common medical language vs. biological language there can be overlap and informal differences in usage.
Prefixes:
means outside (lives on the outside of the body; example: toe fungus / athlete’s foot).
means inside (an endoparasite is inside the body; example: certain worms).
Examples:
Ectoparasite: toe fungus described as living on the outside of the body (athlete’s foot).
Endoparasite: a worm that lives inside the body (filariasis/elephantiasis) blocking the lymphatic system and causing edema.
Treatments by type:
Antiparasitic medicines for parasites (e.g., worms).
Antifungal creams for fungal infections (e.g., athlete’s foot are common and sold in grocery stores).
Microbes thrive in warm, moist environments with dead skin available for nutrients; athlete’s foot can crack and scab if severe.
Key notes on terminology:
In medicine, the terms pathogen and parasite can be used differently in informal language; however, in a strict biological sense, pathogens are a subset of parasites.
Other major parasite/pathogen groups used in medicine:
Protists (single-celled eukaryotes with a nucleus): malaria (Plasmodium falciparum), giardiasis, trichomoniasis, etc.
Worms (multicellular parasites).
Mites (ectoparasites).
Associated disease and pathogen examples:
Malaria (protozoan parasite).
Urinary tract infections often involve pathogenic E. coli (a bacterium) that may require specific adhesion mechanisms (e.g., p pili) to attach to urogenital epithelial cells.
Distinction between pathogen types in medicine:
Pathogen: organisms that cause disease (bacteria, fungi, viruses, parasites).
In medical publications, pathogens and parasites are named and grouped with varying emphasis; colloquial use can differ from formal usage.
Pathogenicity and virulence: key concepts and metrics
Pathogenicity: the ability of an organism to cause disease.
Example: E. coli strains that are pathogenic have specific genes (e.g., adhesion factors) enabling them to cause urinary tract infections.
Pathogenic vs non-pathogenic strains:
Many E. coli strains are commensal in the colon and do not cause disease; pathogenic strains carry extra genes that enable disease.
Primary pathogens vs opportunistic pathogens:
Primary pathogens cause disease in a healthy host (e.g., Ebola).
Opportunistic pathogens cause disease when normal defenses are compromised (e.g., Candida albicans in antibiotic-treated individuals, Staphylococcus aureus in a wound).
Significance of infection types:
Acute infections: rapid onset and resolution (e.g., acute influenza).
Chronic infections: long-lasting with latent periods; example: herpes simplex virus type 1 (HSV-1) causing cold sores with latency in the trigeminal nerve; can reactivate under stress or immune suppression.
Examples of latency and reactivation: chickenpox (varicella) causing shingles (herpes zoster) later in life; long-term virus persistence in nervous tissue.
Immunocompromised conditions:
Pneumocystis jirovecii pneumonia is an opportunistic infection common in AIDS patients.
HIV/AIDS link:
HIV is the etiologic agent of AIDS; AIDS is a syndrome with characteristic opportunistic infections such as Kaposi’s sarcoma and Pneumocystis pneumonia.
Signs that reflect disease rather than mere infection:
Signs: objective measurements (e.g., fever, rash, high blood pressure).
Symptoms: subjective experiences reported by the patient (e.g., fatigue, pain).
Syndromes:
A syndrome is a constellation of signs and symptoms that often accompany a disease (e.g., AIDS is a syndrome with specific opportunistic infections).
HIV causes AIDS; SARS-CoV-2 virus causes the disease COVID-19.
Immunopathology:
Some disease manifestations are caused by the host immune response (fever, inflammation) rather than direct pathogen damage.
Immunopathology can also contribute to tissue damage during infection.
Long-term sequelae and long-term symptoms:
Long COVID: persistent symptoms after initial infection; variable organ involvement, including pulmonary, neurological, and other system damage.
Invasiveness and tissue spread (virulence factors):
Invasiveness refers to the ability of a pathogen to invade tissues and disseminate (e.g., Salmonella invading intestinal cells and disseminating via lymphatics and bloodstream).
The lysosome is the cellular organelle that fuses with endocytic vesicles to digest pathogens; some pathogens block fusion to survive inside cells.
Epidemiology and dose concepts:
Infectious dose 50 (ID_{50}): the number of organisms needed to infect 50% of hosts.
Lethal dose 50 (LD_{50}): the number of organisms needed to kill 50% of hosts.
Example narrative: If we give each of 4 people 75 cells of Mycobacterium tuberculosis, and 50% become infected, that dose corresponds to ID_{50} = 75.
In contrast, if 400 cells kill 50% of hosts, then LD_{50} = 400.
Infections can occur with doses below ID{50} if the host immune system is strong; exposure above ID{50} increases infection probability.
Practical notes on ID{50} and LD{50}:
These measurements are typically obtained in animal models (not humans) due to ethical constraints.
The graph of virulence often plots dose (x-axis) versus response (infection or death) (y-axis).
The infectious dose and lethal dose can vary by strain and host species and across different exposure routes.
Real-world exposure may involve multiple routes and presences of vaccines or prior immunity that alter effective ID{50} or LD{50}.
Historical and ethical context:
Human experimentation without consent has occurred in the past; informed consent is now required for clinical trials.
Animal testing is used to assess safety and efficacy; legal and ethical frameworks govern how data are translated to humans.
Public health relevance:
Public health agencies track ID-like and LD-like concepts when modeling outbreaks and assessing risk.
Vaccinations and prior immunity can reduce effective infection and mortality burden in populations.
Invasiveness, host range, and examples of pathogenic spread
Invasiveness:
The ability of a pathogen to invade tissues and spread within a host; some organisms remain localized, others disseminate systemically.
Example: Salmonella invades intestinal cells; it can block lysosome fusion, enter macrophages, travel via lymph nodes and bloodstream, and cause systemic infection.
Host range:
Host range is the number of species a microbe can infect.
HIV has a narrow host range (humans only).
SARS-CoV-2 has a broader host range (humans and many mammals; original reservoir identified as bats; spread to deer and other species).
Transmission modes and reservoirs:
Direct contact and vehicle transmission (airborne, water, contaminated surfaces).
Fomites: inanimate objects that harbor pathogens (e.g., door handles, beds, medical instruments).
Parenteral route: infections introduced directly into the bloodstream via needles (e.g., intravenous drug use); sterile technique and safe injection practices are critical.
Vertical transmission: mom-to-child transmission during childbirth or transplacentally; transplacental infection examples (syphilis can affect the baby, causing congenital disease).
Horizontal transmission: person-to-person or animal-to-human transmission (most routes are horizontal).
Arthropod vectors: living organisms that harbor and transmit pathogens (biological vectors) or simply carry them mechanically (mechanical vectors).
Fomites and infection control:
Fomites are a major vector in healthcare settings (e.g., door handles, patient beds, equipment).
Antimicrobial materials (e.g., silver or copper threads) can reduce microbial survival on surfaces and fabrics.
Vectors: biological vs mechanical:
Biological vectors: the pathogen’s life cycle includes an intermediate host (e.g., ticks carrying Rickettsia rickettsii — RMSF; malaria parasites in mosquitoes).
Mechanical vectors: vectors carry pathogens on their bodies without hosting the pathogen’s life cycle (e.g., a fly carrying pathogens on its legs from feces to food).
Zoonoses and reservoirs:
Zoonotic diseases involve animal reservoirs or vectors (e.g., Lyme disease with deer as reservoir, ticks as vectors; Ebola with bats and primates; SARS-CoV-2 linked to bats initially and later found in other mammals).
Reservoirs can be asymptomatic or symptomatic; some pathogens persist in animal reservoirs and repeatedly spill over to humans.
Case study ideas and examples:
Bubonic plague: Yersinia pestis; 1884 Chinese outbreak; buboes (enlarged lymph nodes) are characteristic; primary reservoir rats; flea vector; historical context includes the European Black Death.
Lyme disease: Borrelia burgdorferi; deer are reservoir; deer ticks transmit to humans; geographic distribution influenced by deer/tick populations.
Rocky Mountain spotted fever: RMSF; transmission by ticks; fever and rash as clinical signs.
Respiratory pathogens and vaccine history: polio eradication efforts and vaccination campaigns; measles outbreaks in areas with reduced vaccination coverage; public health strategies rely on vaccination campaigns and surveillance.
Signs, symptoms, disease, and syndromes
Signs vs. symptoms:
Signs are objective, measurable abnormalities (e.g., fever, rash, high blood pressure).
Symptoms are subjective experiences reported by the patient (e.g., fatigue, pain).
Disease vs infectious disease:
A disease is a condition involving a dysfunction of body systems with signs and symptoms.
An infectious disease is a disease caused by a pathogen that can be spread to others.
Syndromes:
A syndrome is a collection of signs and symptoms that may be caused by more than one disease (e.g., AIDS as a syndrome with opportunistic infections).
Case example: syphilis case study (from early chapter):
Primary sign: a genital lesion (chancre) that is painless and may leak fluid; a sign because it’s observable.
Symptom: patient reports no pain at the lesion; this helps differentiate syphilis from other STIs with painful lesions.
Immunopathology and long-term symptoms:
Some symptoms arise from the host immune response (fever and inflammation) rather than direct pathogen damage.
Long-term sequelae can include organ damage (e.g., heart or nervous system) after an infection like strep throat leading to rheumatic fever or other complications; long COVID is an example of chronic symptoms after infection.
Infections’ five phases (time course):
Incubation period: time between exposure and onset of replication; patient may be asymptomatic.
Prodromal phase: early nonspecific symptoms; immune system begins to respond.
Acute phase: classic signs and symptoms prominent; pathogen replicates; symptoms are noticeable.
Decline phase: symptoms begin to improve as the immune system and/or treatment reduces pathogen burden.
Convalescent/ Chronic phase: recovery or chronic/latent infection depending on pathogen.
Long-term effects and chronic infections:
Examples include prolonged lung damage after severe respiratory infections; neuropathies or chronic fatigue after certain viral infections; long-term complications after streptococcal infections affecting the heart (rheumatic fever) in some histories.
Zoonotic disease and public health relevance:
Infectious disease surveillance relies on documentation of notifiable diseases to monitor outbreaks and inform public health responses.
Public health surveillance, reporting, and epidemiology
CDC and notifiable diseases:
Morbidity (incidence of disease) and mortality (deaths) statistics are tracked; the CDC provides an ongoing Morbidity and Mortality Weekly Report (MMWR).
Notifiable diseases must be reported by clinicians and laboratories to local health departments, which then report to the state health department and the CDC.
The CDC aggregates data to inform national and international surveillance (WHO) and to guide public health actions.
Local disease tracking example:
Clinicians may assess regional disease incidence (e.g., syphilis) by city and week; data may be organized by disease in modern systems.
Practical public health implications:
Outbreak detection and response depend on timely reporting and data collection to identify clusters and implement interventions.
Public health data support diagnosis, vaccination strategies, and outbreak containment.
Case example: a college student case and tick-borne disease:
Patient history is crucial for diagnosis (recent travel, exposure to ticks, camping in North Carolina).
Rocky Mountain spotted fever was considered when a tick bite exposure was reported; not all exposed individuals become ill, illustrating variable host response.
Transmission, vectors, and disease ecology
Modes of transmission (summary):
Direct contact (person-to-person via touch, droplets).
Vehicle transmission (airborne, water, food, fomites via environment).
Vector-borne transmission (biological vectors with a pathogen; mechanical vectors that carry pathogens on their bodies).
Fomites (inanimate objects):
Examples include surfaces, door handles, surgical tools, bed rails; significant in healthcare settings.
Countermeasures: disinfection, sterilization, and using antimicrobial materials (e.g., silver threads) can reduce transmission.
Vertical vs horizontal transmission:
Vertical: mother to baby (transplacental or perinatal during childbirth).
Horizontal: all other modes of transmission (person-to-person, animal-to-human, etc.).
Transplacental transmission:
A mechanism for some pathogens to reach the fetus; can cause congenital infections (e.g., syphilis).
Parenteral route and injection safety:
Parenteral portal of entry refers to direct entry of pathogens into the bloodstream (e.g., via needles).
Safe injection practices are essential in clinical settings to prevent iatrogenic infections.
Arthropod vectors and reservoirs:
Biological vectors: pathogens complete part of their life cycle in the vector (e.g., ticks transmitting RMSF).
Mechanical vectors: pathogens are carried on the vector’s body without replication in the vector (e.g., a fly transferring pathogens on its legs).
Animal reservoirs can be asymptomatic or symptomatic and serve as sources for spillover to humans (e.g., deer for Lyme disease; bats and primates for Ebola).
Zoonosis and reservoir concepts:
Zoonotic diseases originate in animals and can be transmitted to humans (zoo + notos: animals).
Reservoir species maintain the pathogen in nature; spillover to humans can occur under ecological or behavioral changes.
Biosafety, lab safety levels, and standard precautions
Biosafety levels (BSL) overview:
BSL-1: Basic microbiology, non-pathogenic organisms; minimal precautions.
BSL-2: Work with human pathogens that pose moderate hazards; requires PPE, biosafety cabinet (BSC) for certain procedures; example: the on-campus BSL-2 lab.
BSL-3: Pathogens that can be inhaled and cause serious illness; requires specialized facilities, containment, and PPE; not in the provided campus lab.
BSL-4: Highest containment for exotic, deadly, untreatable pathogens (e.g., smallpox, Ebola); requires space suits and highly controlled entry/exit protocols; only a small number of labs exist worldwide.
Laboratory practices and equipment:
Biosafety cabinets (BSC) protect both the worker and the environment; they maintain airflow and filter pathogens; some cabinets use filters with 0.2-micron HEPA filters; some cabinets include antimicrobial filters (e.g., silver threads) for added protection.
Proper sterilization and disinfection protocols are essential; many instruments and surfaces require cleaning and disinfection between uses.
PPE: gloves, lab coats, eye protection, respirators as required by the risk level.
Universal and standard precautions:
Treat all body fluids as potentially infectious; assume the possibility of asymptomatic infection (e.g., TB can be asymptomatic in about 10% of cases).
Respiratory hygiene/cough etiquette; safe injection practices; handling sharps safety; patient isolation when contagious; proper sterilization/disinfection.
Practical notes on lab training:
Institutions may have limited spaces for student laboratory work due to biosafety constraints.
Students in microbiology majors typically learn lab safety and pathogen handling, with strict adherence to BSL guidelines.
Ethical and public health considerations:
Historical context of human experimentation without consent informs current ethics and informed consent requirements for clinical trials.
Public health surveillance depends on safe, ethical lab practices and transparent reporting.
Five-phase infection timeline and clinical implications
Incubation period: time from initial exposure to the onset of pathogen replication and symptoms; varies by pathogen (e.g., HIV has a long incubation period).
Prodromal phase: early, nonspecific symptoms before the disease fully manifests.
Acute phase: classic signs and symptoms; high pathogen activity; clinical management often critical.
Decline: symptoms abate; pathogen load decreases; patient begins to recover.
Convalescence: recovery; signs and symptoms disappear; some pathogens may persist in latent form (latency) or cause long-term sequelae (e.g., long COVID).
Long-term consequences and sequelae:
Some infections cause lasting damage to organs (e.g., lungs after severe infections; nervous system involvement).
Latent infections can reactivate later (e.g., herpesviruses).
Quick reference: key terms recap
Infectious disease: disease caused by a pathogen that can be transmitted to others.
Sign: objective measurement (fever, rash, abnormal vitals).
Symptom: subjective experience reported by the patient (pain, fatigue).
Syndrome: collection of signs and symptoms that may reflect more than one disease.
Portal of entry: any site where a pathogen can enter the body (eyes, ears, nose, mouth, urogenital tract, skin breaches).
Parenteral route/portal: entry through injections or breaches in the skin.
Parenteral precautions: sterile technique, safe injection practices.
Portal of entry vs. portal of exit: entry is how the pathogen enters; exit is how it leaves the host (e.g., coughing, diarrhea).
Vector (biological vs mechanical): an organism that transmits a pathogen (biological includes pathogen life cycle within the vector; mechanical is incidental carriage on the vector).
Fomite: an inanimate object that harbors a pathogen.
Endemic: a disease that is always present in a population or region.
Epidemic: rapid increase of disease in a population or region.
Pandemic: disease outbreak spanning multiple countries or continents.
Zoonotic disease: disease that can be transmitted from animals to humans.
Virulence: the degree to which a pathogen can cause disease; includes infectious dose (ID{50}) and lethal dose (LD{50}).
ID_{50}: the dose of pathogen needed to infect 50% of hosts.
LD_{50}: the dose of pathogen needed to kill 50% of hosts.
Host range: number of species a pathogen can infect.
Immunopathology: disease symptoms caused by host immune response rather than direct pathogen damage.
Latency: period where a pathogen persists in the host with no symptoms, potentially reactivating later.
Notifiable diseases: infections that must be reported to local and national health authorities to enable surveillance and intervention.
Final practical takeaways
Always rely on Canvas for final grades after grade syncing; iClicker may display misleading totals due to multi-section settings.
When studying pathogens, focus on the vocab: signs vs symptoms, disease vs infectious disease, syndrome, virulence (ID{50}, LD{50}), invasiveness, host range, transmission modes, vectors, fomites, vertical vs horizontal transmission, and biosafety levels.
Public health context matters: surveillance, reporting chains, and outbreak response depend on accurate data collection and transmission knowledge.
Remember common real-world examples tied to these terms: Lyme disease (deer reservoir, tick vector), RMSF (tick-borne), bubonic plague (Yersinia pestis, rats, fleas), syphilis (chancre), herpesviruses (latency and reactivation), malaria (Plasmodium), SARS-CoV-2 (bat origin, broad host range), and long-term issues like long COVID.
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