Principles of Disease and Epidemiology: Microbiology Study Notes

Principles of Disease and Epidemiology

Pathology, Infection, and Disease

Pathology is the scientific study of disease, focusing on its causes, development, and effects. Understanding the distinctions between infection and disease is fundamental in microbiology.

• Pathology: Study of disease.

• Etiology: The cause of a disease.

• Pathogenesis: The manner in which a disease develops.

• Infection: Invasion or colonization of the body by pathogens.

• Infectious disease: Occurs when an infection results in any change in the state of health.

• Disease: May result when a microorganism locates in a part of the body where it is not normally found.

The Human Microbiome

The human microbiome consists of the collection of microorganisms that inhabit various regions of the human body. These microbes play essential roles in health and disease.

• Establishment: Begins in utero; placental microbiome includes Enterobacteriaceae and Propionibacterium.

• Colonization: Lactobacilli colonize neonates during vaginal birth; more microbes acquired from food, people, and pets.

• Normal microbiota (flora): Permanently colonize the host and do not cause disease under normal conditions.

• Transient microbiota: Present for days, weeks, or months, then disappear.

• Human Microbiome Project: Analyzes relationships between microbial communities and human health.

Factors Influencing the Normal Microbiota

The distribution and composition of normal microbiota are determined by numerous factors, including environmental and host-related variables.

• Nutrients: Availability affects microbial growth.

• Physical and chemical factors: pH, temperature, moisture, etc.

• Mechanical factors: Movement of fluids, chewing, blinking.

• Body’s defenses: Immune system activity.

• Other factors: Age, diet, geography, hygiene, occupation, lifestyle.

Representative Normal Microbiota by Body Region

Normal microbiota vary by body region, each with unique environmental conditions and microbial populations.

Region	Principal Components	Comments
Skin	Propionibacterium, Staphylococcus, Corynebacterium, Micrococcus, Acinetobacter, Brevibacterium, Candida, Malassezia	Secretions inhibit microbes; keratin is a barrier; low pH and moisture
Eyes (Conjunctiva)	Staphylococcus epidermidis, S. aureus, diphtheroids, Propionibacterium, Corynebacterium, streptococci, Micrococcus	Tears and blinking remove/inhibit microbes; lysozyme present
Nose and Throat	S. aureus, S. epidermidis, diphtheroids, Streptococcus pneumoniae, Haemophilus, Neisseria	Microbial antagonism; mucus and ciliary action remove microbes
Mouth	Streptococcus, Lactobacillus, Actinomyces, Bacteroides, Veillonella, Neisseria, Haemophilus, Fusobacterium, Treponema, Staphylococcus, Corynebacterium, Candida	Moisture, warmth, food support diverse microbes; saliva dislodges microbes
Large Intestine	E. coli, Bacteroides, Fusobacterium, Lactobacillus, Enterococcus, Bifidobacterium, Enterobacter, Citrobacter, Proteus, Klebsiella, Candida	Largest numbers; microbial antagonism; mucus and shedding prevent attachment
Urinary and Genital Systems	Staphylococcus, Micrococcus, Enterococcus, Lactobacillus, Bacteroides, diphtheroids, Pseudomonas, Klebsiella, Proteus, Clostridium, Candida albicans, Trichomonas vaginalis	Acid-tolerant; urine flow removes microbes; acidity inhibits/kills microbes

Exploring the Microbiome: Birth and Health Conditions

The mode of birth influences the initial microbiome composition, which can affect health outcomes.

• Vaginal birth: Lactobacillus and Bacteroides are prevalent.

• Cesarean birth: Microbiome resembles human skin; Staphylococcus aureus is common.

Relationships Between the Normal Microbiota and the Host

Normal microbiota interact with the host in various ways, including protection and symbiosis.

• Microbial antagonism (competitive exclusion): Normal microbiota protect the host by competing for nutrients, producing harmful substances, and affecting pH and oxygen.

• Clostridium difficile: Causes severe intestinal infections if normal microbiota are reduced by antibiotics; fecal microbial transfer (FMT) can treat infections.

Types of Symbiosis

• Commensalism: One organism benefits, the other is unaffected.

• Mutualism: Both organisms benefit.

• Parasitism: One organism benefits at the expense of the other; many pathogens are parasites.

• Opportunistic pathogens: Normal microbiota that can cause disease under certain conditions.

Koch’s Postulates

Establishing Disease Causation

Koch’s postulates are a set of criteria used to prove the cause of an infectious disease.

• The same pathogen must be present in every case of the disease.

• The pathogen must be isolated from the diseased host and grown in pure culture.

• The pathogen from the pure culture must cause the disease when inoculated into a healthy, susceptible laboratory animal.

• The pathogen must be isolated from the inoculated animal and shown to be the original organism.

Exceptions: Some pathogens cause multiple diseases, only infect humans, or cannot be cultured. Multiple pathogens may cause similar symptoms.

Classifying Infectious Diseases

Symptoms, Signs, and Syndromes

Diseases are classified based on their transmission, symptoms, and signs.

• Symptoms: Subjective changes felt by the patient.

• Signs: Objective changes measurable or observable.

• Syndrome: Specific group of signs and symptoms accompanying a disease.

Types of Diseases

• Communicable disease: Spread from one host to another (e.g., COVID-19, influenza).

• Contagious disease: Easily and rapidly spread.

• Noncommunicable disease: Not spread from host to host (e.g., tetanus).

Occurrence of Disease

Incidence and prevalence are key epidemiological measures.

• Incidence: Number of new cases during a specific time period.

• Prevalence: Total number of cases at a specified time, including old and new cases.

Patterns of Disease Occurrence

• Sporadic disease: Occurs occasionally.

• Endemic disease: Constantly present in a population.

• Epidemic disease: Acquired by many people in a short time.

• Pandemic disease: Worldwide epidemic.

Severity and Duration of Disease

Classification by Duration

• Acute disease: Rapid onset, short duration.

• Chronic disease: Slow development, long duration.

• Subacute disease: Intermediate between acute and chronic.

• Latent disease: Inactive for a time, then activates.

• Herd immunity: Immunity in most of a population.

Classification by Severity

• Asymptomatic: No signs or symptoms.

• Mild: Fever, dry cough, tiredness, muscle pain, sore throat.

• Moderate: Breathlessness, tachycardia, persistent cough, higher fever.

• Severe: Pneumonia, extreme breathlessness, chest pain, high temperature, bluish lips/face.

• Critical: Severe acute respiratory syndrome (SARS), inflamed alveoli, may require ventilator.

• Sepsis: Extreme inflammatory syndrome in response to severe infection.

Fatality Ratios

• Infection fatality ratio (IFR): $\frac{\text{Number of deaths}}{\text{Total infected individuals}}$

• Case fatality ratio (CFR): $\frac{\text{Number of deaths}}{\text{Number diagnosed}}$

Extent of Host Involvement

Types of Infection

• Local infection: Pathogens limited to a small area.

• Systemic infection: Spread throughout the body via blood and lymph.

• Focal infection: Systemic infection that began as a local infection.

Blood-related Conditions

• Sepsis: Toxic inflammatory condition from spread of microbes or toxins.

• Bacteremia: Bacteria in the blood.

• Septicemia: Growth of bacteria in the blood.

• Toxemia: Toxins in the blood.

• Viremia: Viruses in the blood.

Infection Progression

• Primary infection: Acute infection causing initial illness.

• Secondary infection: Opportunistic infection after a primary infection.

• Subclinical infection: No noticeable signs or symptoms.

Predisposing Factors

• Nutrition, sex, genetic inheritance, climate, environment, vaccination, age, lifestyle, compromised host.

Development of Disease

Stages of Disease

The progression of disease follows distinct stages, from initial infection to recovery.

• Incubation period: Interval between infection and first signs/symptoms.

• Prodromal period: Early, mild, nonspecific symptoms.

• Period of illness: Disease is most severe.

• Period of decline: Signs and symptoms subside.

• Period of convalescence: Recovery; body returns to prediseased state.

Reservoirs of Infection

Types of Reservoirs

Reservoirs are continual sources of infection, classified as human, animal, or nonliving.

• Human reservoirs: People with symptoms or carriers (asymptomatic, incubating, convalescent, chronic, passive).

• Animal reservoirs: Zoonoses are diseases primarily in animals that can be transmitted to humans.

• Nonliving reservoirs: Soil, water, foods.

Selected Zoonoses

Disease	Reservoir	Causative Agent	Transmission
Influenza	Swine, birds	Alphainfluenzavirus	Direct contact
Rabies	Bats, skunks, foxes, dogs, raccoons	Lyssavirus	Direct contact (bite)
West Nile encephalitis	Horses, birds	Flavivirus	Mosquito bite
Anthrax	Domestic livestock	Bacillus anthracis	Contact with contaminated hides/animals, air, food
Ringworm	Domestic mammals	Trichophyton, Microsporum, Epidermophyton	Direct contact, fomites
Malaria	Monkeys	Plasmodium spp.	Mosquito bite
Tapeworm (pork)	Pigs	Taenia solium	Ingestion of undercooked pork

Transmission of Disease

Contact Transmission

Contact transmission involves direct or indirect transfer of pathogens between hosts.

• Direct contact: Close association between infected and susceptible host.

• Congenital transmission: From mother to fetus/newborn at birth.

• Indirect contact: Via nonliving object (fomite).

• Droplet transmission: Airborne droplets less than 1 meter.

Vehicle Transmission

Vehicle transmission occurs via inanimate reservoirs such as air, water, or food.

• Airborne: Pathogens carried by dust or droplets.

• Waterborne: Pathogens spread through contaminated water.

• Foodborne: Pathogens spread through contaminated food; cross-contamination possible.

Vector Transmission

Vectors, primarily arthropods, transmit disease by mechanical or biological means.

• Mechanical transmission: Pathogen carried on vector's body parts.

• Biological transmission: Pathogen reproduces in vector; transmitted via bites or feces.

Representative Arthropod Vectors and Diseases

Arthropod Vector	Causative Agent	Disease
Anopheles (mosquito)	Plasmodium spp.	Malaria
Glossina (tsetse fly)	Trypanosoma brucei	African trypanosomiasis
Triatoma (kissing bug)	T. cruzi	Chagas' disease
Aedes (mosquito)	Flavivirus yellow fever virus	Yellow fever
Ixodes spp. (tick)	Ehrlichia spp.	Ehrlichiosis
Xenopsylla cheopis (rat flea)	Yersinia pestis	Plague