Infection, Infectious Diseases, and Epidemiology: Foundations of Microbiology

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Introduction to Microbiology

Definition and Scope

Microbiology is the study of microorganisms—organisms invisible to the naked eye, including bacteria, viruses, fungi, and parasites. While most microorganisms are harmless or beneficial, a small proportion are pathogenic and can cause disease in humans, animals, and plants.

Microorganisms: Single-celled microscopic organisms, including bacteria, viruses, fungi, and parasites.
Pathogens: Microorganisms that cause disease.
Many microbes are essential for processes such as fermentation, decomposition, and maintaining health.

Louis Pasteur in his laboratory

Basic Microbial Structures

Classification and Characteristics

Microorganisms vary in size, complexity, and growth requirements. Understanding their structure is fundamental to microbiology.

Viruses: Composed mainly of nucleic acids (DNA or RNA) and a protein shell (capsid). They require host cells for replication.
Chlamydia: Intracellular bacteria with a unique life cycle involving infectious elementary bodies and replicative reticulate bodies.
Mycoplasmas: The smallest self-replicating microbes, lacking a rigid cell wall, making them delicate and pleomorphic.
Bacteria: Prokaryotes with a rigid cell wall and circular chromosome. They lack membrane-bound organelles.
Eukaryotes: Organisms with a nucleus and membrane-bound organelles. Infectious eukaryotes include fungi, protists, and helminths (worms).

Diagram of naked and enveloped viruses Life cycle of chlamydias Colourized SEM of microbial community from human tongue scraping The protist Giardia intestinalis Cells of the Bacterium Streptococcus and Two Human Cheek Cells

Symbiotic Relationships Between Microbes and Their Hosts

Types of Symbiosis

Symbiosis refers to the close association between different species. Humans have numerous symbiotic relationships with microorganisms.

Mutualism: Both organisms benefit (e.g., bacteria in the human colon).
Commensalism: One benefits, the other is unaffected (e.g., mites in hair follicles).
Amensalism: One is harmed, the other is unaffected (e.g., fungus secreting antibiotics).
Parasitism: One benefits at the expense of the other (e.g., Mycobacterium tuberculosis in human lungs).

Wood eating termites depend on a protozoa which lives in their intestines to digest cellulose

The Human Microbiome

The human body is colonized by a vast array of microorganisms, collectively known as the microbiome. These organisms are typically harmless and may be beneficial.

Resident microbiota: Permanent inhabitants of the body, mostly commensal.
Transient microbiota: Temporary residents, unable to persist due to competition, immune responses, or environmental changes.
The microbiome begins to develop during birth and early life.

Resident microbiota in the human intestine SEM of resident microbiota on mucosal surface Table of some resident microbiota in the upper respiratory tract Newborn baby in skin-to-skin contact, illustrating early microbiome acquisition

Opportunistic Pathogens

Normal microbiota can become opportunistic pathogens under certain conditions, such as immune suppression, introduction to unusual body sites, or changes in the normal microbiota.

Reservoirs of Infectious Diseases

Types of Reservoirs

Reservoirs are sites where pathogens are maintained as sources of infection.

Animal reservoirs: Zoonoses are diseases naturally spread from animals to humans (e.g., rabies, malaria, ringworm).
Human carriers: Asymptomatic individuals who can transmit pathogens.
Nonliving reservoirs: Soil, water, and food contaminated with pathogens.

Cat with ringworm, a zoonotic fungal infection

Infection: The Invasion and Establishment of Microbes in Hosts

Contamination vs. Infection

Contamination: Presence of microbes on or in the body.
Infection: Successful invasion, multiplication, and establishment of a microbe in the host.

Bacterial interactions with mucous membranes: loose association, adherence, colonization

Portals of Entry

Skin: Pathogens enter through cuts, abrasions, or by burrowing.
Mucous membranes: Respiratory and gastrointestinal tracts are common entry points.
Placenta: Some pathogens can cross and infect the fetus.
Parenteral route: Circumvents normal barriers (e.g., via punctures, injections).

Diagram of portals of entry for infection SEM of bacteria on mucosal surface Diagram of parenteral route of infection

Adhesion and Host Specificity

Adhesion is the process by which microorganisms attach to host cells, a critical step for colonization and infection. Specific interactions between microbial adhesins and host cell receptors determine host and tissue specificity.

Fimbriae and pili: Protein structures aiding in attachment.
Adhesins: Molecules on microbial surfaces that bind to host receptors.
Biofilms: Communities of microbes attached to surfaces, often resistant to immune responses and antibiotics.

Dental plaque biofilm Fimbriae on bacterial cells Electron micrograph of Salmonella with fimbriae Pilus on Escherichia coli undergoing conjugation

The Nature of Infectious Disease

Manifestations of Disease

Symptoms: Subjective effects felt by the patient (e.g., pain, fatigue).
Signs: Objective, measurable effects (e.g., fever, rash).
Syndrome: A group of symptoms and signs that characterize a disease.
Asymptomatic (subclinical) infections: Infections without noticeable symptoms.

Terminology of Disease

Prefix/Suffix	Meaning	Example
-itis	Inflammation	Hepatitis (liver inflammation)
-emia	In the blood	Bacteremia (bacteria in blood)
-oma	Tumor or swelling	Papilloma (wart)
-osis	Condition of	Toxoplasmosis
-patho	Disease/abnormal	Pathology

Etiology: Causation of Disease

Etiology: The study of the cause of disease.
Koch’s postulates: Criteria to establish a causative relationship between a microbe and a disease.

Koch's Postulates

Virulence Factors

Virulence factors are microbial traits that contribute to pathogenicity and disease severity.

Adhesion factors: Enable attachment to host cells.
Biofilms: Protect microbes from host defenses.
Extracellular enzymes: Degrade host tissues and aid invasion.
Toxins: Harm host tissues or trigger damaging immune responses.
Antiphagocytic factors: Prevent destruction by host immune cells.

Comparison of microbial virulence between Streptococcus pneumoniae and Salmonella enterica in mice Diagram of extracellular enzyme action Botulinum toxin from Clostridium botulinum Tetanus toxin from Clostridium tetani Pore-forming exotoxin from Staphylococcus Alpha-toxin as a cytotoxin Diagram of endotoxin structure Comparison of bacterial exotoxins and endotoxins Bacterial capsule as an antiphagocytic factor Phagocytosis: Microbes that evade it Virulence factors: hiding from host defenses

Stages of Infectious Disease

Progression of Disease

Infectious diseases typically progress through five stages:

Incubation period: Time between infection and appearance of symptoms.
Prodromal period: Early, mild symptoms.
Illness: Most severe signs and symptoms.
Decline: Symptoms subside as immune response or treatment takes effect.
Convalescence: Recovery and return to normal function.

Transmission of Infectious Diseases

Modes of Transmission

Contact transmission: Direct (person-to-person), indirect (via fomites), or droplet (short-range aerosols).
Vehicle transmission: Airborne (long-range aerosols), waterborne, foodborne, or via bodily fluids.
Vector transmission: Biological (e.g., mosquitoes, ticks) or mechanical (e.g., flies, cockroaches).

Horizontal vs. Vertical Transmission

Horizontal transmission: Between individuals of the same generation.
Vertical transmission: From parent to offspring.

Classification of Infectious Diseases

By Duration and Spread

Term	Definition
Acute	Rapid onset, short duration
Chronic	Slow onset, long duration
Latent	Inactive for a period, then reactivates
Communicable	Transmitted from host to host
Noncommunicable	Not transmitted between hosts
Local	Confined to one area
Systemic	Spread throughout the body

Epidemiology: The Study of Disease in Populations

Measuring Disease Frequency

Incidence: Number of new cases in a given time period.
Prevalence: Total number of cases at a given time.

Types of Epidemiological Studies

Descriptive epidemiology: Collects data on occurrence, location, and time.
Analytical epidemiology: Determines cause, transmission, and prevention.
Experimental epidemiology: Tests hypotheses about disease causation.

Nosocomial (Healthcare-Associated) Infections

Exogenous: Acquired from the healthcare environment.
Endogenous: Arise from the patient’s own microbiota.
Iatrogenic: Result from medical procedures.
Superinfections: Occur when antimicrobial therapy disrupts normal microbiota.
Prevention: Handwashing is the most effective measure.

Public Health and Disease Control

Public health agencies (e.g., WHO, CDC) monitor, report, and control infectious diseases.
Efforts include sanitation, immunization, vector control, and public education.