, INTRODUCTION TO MICROBIOLOGY
Microbiology is the science that studies microorganisms (“micro” = small, “bios” = life) and their
interaction with the host and the environment. It includes not only organisms that cause disease, but also
microorganisms that normally live in the body and may be beneficial.The four main groups of medically
important microorganisms are:
•Bacteria—unicellular prokaryotic organisms without a true nucleus or membrane-bound organelles.
They reproduce by binary fission and usually possess a rigid cell wall made of peptidoglycan.
•Viruses—acellular particles made of nucleic acid (DNA or RNA) surrounded by a protein coat,
sometimes with an envelope. They cannot reproduce alone and must enter a living cell.
•Fungi—eukaryotic organisms with a nucleus and organelles,existing as yeasts (unicellular) or molds
(filamentous). Some are dimorphic.
•Parasites—eukaryotic organisms that may be unicellular (protozoa) or multicellular (helminths).
The distinction between prokaryotes and eukaryotes is fundamental because it explains why bacteria behave
differently from fungi and human cells, and why antibacterial drugs can selectively attack bacteria.
Why this matters clinically- Many antibiotics work because they target structures that exist only in bacteria:
•β-lactams → peptidoglycan cell wall
•Macrolides, tetracyclines, aminoglycosides → 70S ribosomes
Colonization—presence, multiplication, and persistence of a microorganism in or on the body without
tissue damage.Example Staphylococcus aureus in the nose
Infection—penetration and multiplication of microorganisms within the host that may or may not produce
symptoms.
Disease—appears when the interaction between microorganism and host produces tissue damage and
clinical symptoms.
“Infection is not always followed by disease, but infection is the prerequisite for disease.”
HOST–MICROBE INTERACTION
Host–microbe interaction is a dynamic interaction that continuously changes depending on the
microorganism, the host, and the environment. The final outcome depends on three groups of factors:
Microbial factors:
•Virulence •Inoculum size •Ability to adhere •Ability to invade •Toxin production
The more virulent a microorganism is, the more easily it causes disease.
Opportunistic pathogens— harmless organisms that cause disease only if host defenses are impaired. EX:
•Candida albicans •Staphylococcus epidermidis
Situations favoring opportunistic infections:
•Immunosuppression •Chemotherapy •Steroid therapy
,Host factors:
•Age •Nutrition •Vaccination •Chronic disease •Stress •Integrity of skin and mucosa
Environmental factors:
•Smoking •Alcohol •Drugs •Pollution •Climate •Hygiene
TYPES OF RELATIONSHIP BETWEEN HOST AND MICROBE
The relationship between microorganism and host may take different forms:
Parasitism—microorganism benefits and the host is harmed.Ex •Malaria •Tuberculosis
Mutualism—both microorganism and host benefit.Ex •Intestinal microbiota synthesizing vitamin K
Commensalism—microorganism benefits while the host is not significantly affected. Ex •Skin flora
Latent or Silent Infection—occurs when the microorganism remains in the body after the acute infection
has resolved, but does not actively replicate or produces minimal replication. The microorganism may
reactivate later. Important features:
•No symptoms during latency •The pathogen persists •Reactivation may occur if immunity decreases
Examples •Tuberculosis •Herpes simplex
Healthy Carrier— is an asymptomatic individual who harbors a pathogen and can transmit it to others. The
person may or may not have had the disease in the past. Examples:
•Nasal carrier of Staphylococcus aureus
•Intestinal carrier of Salmonella typhi
ROUTES OF TRANSMISSION OF EXOGENOUS / ENDOGENOUS INFECTIONS
Exogenous infections are infections caused by microorganisms that come from outside the body. The
pathogen enters the host through specific portals and reaches a susceptible tissue. The route of entry is very
important because many microorganisms cause disease only if they enter through a specific route. Main
routes of transmission:
1. Inhalation / Airborne Transmission—The microorganism enters through the respiratory tract after
inhalation of droplets or aerosols.
•Droplets = larg particles that travel a short distance
•Aerosols = small particles that remain suspended longer
Examples •Tuberculosis •COVID-19
2. Ingestion / Fecal–Oral Transmission—The microorganism enters through the mouth via contaminated
food, water or hands.This route is typical of intestinal pathogens.Examples •Salmonellosis •Cholera
3. Direct Contact—Transmission occurs through direct contact with skin, mucosa or contaminated
surfaces.Ex •Impetigo •Herpes simplex •Scabies
The microorganism enters through •Small wounds •Scratches •Mucosal surface
4. Blood Transmission—The pathogen enters directly into the bloodstream.Sources:
, •Needles •Blood transfusion •Intravenous drug use •Accidental puncture
Examples •Hepatitis B\C
5. Vector Transmission—A vector is an arthropod that transmits a pathogen from one host to another.
•Malaria → mosquito •Lyme disease → tick •Plague → flea
6. Zoonoses—Zoonoses are infections transmitted from animals to humans.Examples:
•Rabies •Brucellosis •Toxoplasmosis
Sources—•Bites •Scratches •Animal secretions
Endogenous infection is an infection caused by microorganisms that are already present in the patient’s body
(The pathogen originates from the host) , usually as part of the normal microbiota or as colonizing
organisms, but that become pathogenic by: Typical mechanisms:
1.Change of Habitat—Many microorganisms are harmless in their normal location but become pathogenic if
they move elsewhere.Classic example:
Escherichia coli normally lives in the colon and is part of the intestinal flora. In the intestine it is usually
harmless and may even be beneficial. But if it ascends from the perianal area into the urinary tract, it can
cause cystitis,pyelonephritis or recurrent urinary tract infection.This is an endogenous infection because the
bacterium already existed in the body before the disease appeared.
2.Alteration of the Normal Flora—The normal microbiota usually prevents pathogens from growing by
•competing for nutrients •producing antimicrobial substances
If the normal flora is altered, microorganisms that are normally controlled may overgrow.Most common
cause: broad-spectrum antibiotics.Antibiotics kill sensitive bacteria, but resistant organisms survive and
multiply.Example: Clostridioides difficile may normally be present in small numbers in the intestine. After
prolonged antibiotic therapy, the intestinal flora is destroyed and Clostridioides difficile can overgrow,
producing toxins A and B and causing pseudomembranous colitis.Symptoms watery diarrhea,abdominal
pain,fever.
3.Reduced Host Defenses—Microorganisms that are harmless in healthy individuals can become pathogenic
when immunity decreases.Conditions favoring endogenous infections:
•AIDS •Chemotherapy •Corticosteroids •Diabetes •Malnutrition •Old age
Examples:
•Candida albicans in immunocompromised patients
•Staphylococcus epidermidis in catheterized patients
4. Entry Into Normally Sterile Sites—A microorganism may become pathogenic if it enters a body site that is
normally sterile like blood,cerebrospinal fluid,pleural cavity or peritoneum.
Example: Staphylococcus epidermidis often infects prosthetic valves, catheters and prostheses because it is
part of the skin flora and gains access during medical procedures.
Microbiology is the science that studies microorganisms (“micro” = small, “bios” = life) and their
interaction with the host and the environment. It includes not only organisms that cause disease, but also
microorganisms that normally live in the body and may be beneficial.The four main groups of medically
important microorganisms are:
•Bacteria—unicellular prokaryotic organisms without a true nucleus or membrane-bound organelles.
They reproduce by binary fission and usually possess a rigid cell wall made of peptidoglycan.
•Viruses—acellular particles made of nucleic acid (DNA or RNA) surrounded by a protein coat,
sometimes with an envelope. They cannot reproduce alone and must enter a living cell.
•Fungi—eukaryotic organisms with a nucleus and organelles,existing as yeasts (unicellular) or molds
(filamentous). Some are dimorphic.
•Parasites—eukaryotic organisms that may be unicellular (protozoa) or multicellular (helminths).
The distinction between prokaryotes and eukaryotes is fundamental because it explains why bacteria behave
differently from fungi and human cells, and why antibacterial drugs can selectively attack bacteria.
Why this matters clinically- Many antibiotics work because they target structures that exist only in bacteria:
•β-lactams → peptidoglycan cell wall
•Macrolides, tetracyclines, aminoglycosides → 70S ribosomes
Colonization—presence, multiplication, and persistence of a microorganism in or on the body without
tissue damage.Example Staphylococcus aureus in the nose
Infection—penetration and multiplication of microorganisms within the host that may or may not produce
symptoms.
Disease—appears when the interaction between microorganism and host produces tissue damage and
clinical symptoms.
“Infection is not always followed by disease, but infection is the prerequisite for disease.”
HOST–MICROBE INTERACTION
Host–microbe interaction is a dynamic interaction that continuously changes depending on the
microorganism, the host, and the environment. The final outcome depends on three groups of factors:
Microbial factors:
•Virulence •Inoculum size •Ability to adhere •Ability to invade •Toxin production
The more virulent a microorganism is, the more easily it causes disease.
Opportunistic pathogens— harmless organisms that cause disease only if host defenses are impaired. EX:
•Candida albicans •Staphylococcus epidermidis
Situations favoring opportunistic infections:
•Immunosuppression •Chemotherapy •Steroid therapy
,Host factors:
•Age •Nutrition •Vaccination •Chronic disease •Stress •Integrity of skin and mucosa
Environmental factors:
•Smoking •Alcohol •Drugs •Pollution •Climate •Hygiene
TYPES OF RELATIONSHIP BETWEEN HOST AND MICROBE
The relationship between microorganism and host may take different forms:
Parasitism—microorganism benefits and the host is harmed.Ex •Malaria •Tuberculosis
Mutualism—both microorganism and host benefit.Ex •Intestinal microbiota synthesizing vitamin K
Commensalism—microorganism benefits while the host is not significantly affected. Ex •Skin flora
Latent or Silent Infection—occurs when the microorganism remains in the body after the acute infection
has resolved, but does not actively replicate or produces minimal replication. The microorganism may
reactivate later. Important features:
•No symptoms during latency •The pathogen persists •Reactivation may occur if immunity decreases
Examples •Tuberculosis •Herpes simplex
Healthy Carrier— is an asymptomatic individual who harbors a pathogen and can transmit it to others. The
person may or may not have had the disease in the past. Examples:
•Nasal carrier of Staphylococcus aureus
•Intestinal carrier of Salmonella typhi
ROUTES OF TRANSMISSION OF EXOGENOUS / ENDOGENOUS INFECTIONS
Exogenous infections are infections caused by microorganisms that come from outside the body. The
pathogen enters the host through specific portals and reaches a susceptible tissue. The route of entry is very
important because many microorganisms cause disease only if they enter through a specific route. Main
routes of transmission:
1. Inhalation / Airborne Transmission—The microorganism enters through the respiratory tract after
inhalation of droplets or aerosols.
•Droplets = larg particles that travel a short distance
•Aerosols = small particles that remain suspended longer
Examples •Tuberculosis •COVID-19
2. Ingestion / Fecal–Oral Transmission—The microorganism enters through the mouth via contaminated
food, water or hands.This route is typical of intestinal pathogens.Examples •Salmonellosis •Cholera
3. Direct Contact—Transmission occurs through direct contact with skin, mucosa or contaminated
surfaces.Ex •Impetigo •Herpes simplex •Scabies
The microorganism enters through •Small wounds •Scratches •Mucosal surface
4. Blood Transmission—The pathogen enters directly into the bloodstream.Sources:
, •Needles •Blood transfusion •Intravenous drug use •Accidental puncture
Examples •Hepatitis B\C
5. Vector Transmission—A vector is an arthropod that transmits a pathogen from one host to another.
•Malaria → mosquito •Lyme disease → tick •Plague → flea
6. Zoonoses—Zoonoses are infections transmitted from animals to humans.Examples:
•Rabies •Brucellosis •Toxoplasmosis
Sources—•Bites •Scratches •Animal secretions
Endogenous infection is an infection caused by microorganisms that are already present in the patient’s body
(The pathogen originates from the host) , usually as part of the normal microbiota or as colonizing
organisms, but that become pathogenic by: Typical mechanisms:
1.Change of Habitat—Many microorganisms are harmless in their normal location but become pathogenic if
they move elsewhere.Classic example:
Escherichia coli normally lives in the colon and is part of the intestinal flora. In the intestine it is usually
harmless and may even be beneficial. But if it ascends from the perianal area into the urinary tract, it can
cause cystitis,pyelonephritis or recurrent urinary tract infection.This is an endogenous infection because the
bacterium already existed in the body before the disease appeared.
2.Alteration of the Normal Flora—The normal microbiota usually prevents pathogens from growing by
•competing for nutrients •producing antimicrobial substances
If the normal flora is altered, microorganisms that are normally controlled may overgrow.Most common
cause: broad-spectrum antibiotics.Antibiotics kill sensitive bacteria, but resistant organisms survive and
multiply.Example: Clostridioides difficile may normally be present in small numbers in the intestine. After
prolonged antibiotic therapy, the intestinal flora is destroyed and Clostridioides difficile can overgrow,
producing toxins A and B and causing pseudomembranous colitis.Symptoms watery diarrhea,abdominal
pain,fever.
3.Reduced Host Defenses—Microorganisms that are harmless in healthy individuals can become pathogenic
when immunity decreases.Conditions favoring endogenous infections:
•AIDS •Chemotherapy •Corticosteroids •Diabetes •Malnutrition •Old age
Examples:
•Candida albicans in immunocompromised patients
•Staphylococcus epidermidis in catheterized patients
4. Entry Into Normally Sterile Sites—A microorganism may become pathogenic if it enters a body site that is
normally sterile like blood,cerebrospinal fluid,pleural cavity or peritoneum.
Example: Staphylococcus epidermidis often infects prosthetic valves, catheters and prostheses because it is
part of the skin flora and gains access during medical procedures.
