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Describe the course of infection from contact with the pathogen to its exit from the host.

Include your opinion on whether all infections travel the same course

Provide an example to support your opinion.

Discussion expectations:

This should be a substantive response (between 75-150 words minimum) to the topic (s) in your own words, referencing (using APA format)

You can use resources other than your textbook to support your publications; however, you should mention the source (s) you used in your publications using in-text citations and reference lists in APA format.

Microbiology FUNDAMENTALS A Clinical Approach Third Edition

Marjorie Kelly Cowan


Heidi Smith


Jennifer Lusk


©McGraw-Hill Education. All rights reserved. Authorized only for instructor use in the classroom.  No reproduction or further distribution permitted without the prior written consent of McGraw-Hill Education.

Chapter 11

Interactions Between Microbes and Humans

©McGraw-Hill Education

Learning Outcomes Section 11.1

Differentiate among the terms colonization, infection, and disease.

Enumerate the sites where normal biota is found in humans.

Discuss how the Human Microbiome Project is changing our understanding of normal biota.

©McGraw-Hill Education

The Human Microbiome(1)

Humans and other mammals have the form and physiology that they have due to having been formed in intimate contact with their microbes

Human microbiome:

The sum total of all microbes found on and in a normal human

Critically important to the health and functioning of its host organism

©McGraw-Hill Education

Colonization, Infection, Disease

For the most part, our resident microbiota colonize us for the long term and do not cause disease

Infection: microbes get past host defenses, enter tissues, and multiply

Disease: deviation from health; pathologic state that results when cumulative effects of infection damage or disrupt tissues and organs

Infectious disease: a pathogenic state caused directly by microorganisms or their products

©McGraw-Hill Education

The Human Microbiome(2)

Human Microbiome Project (HMP):

A worldwide research effort under way since 2008

Characterize microbes living on human bodies when healthy

Determine how the microbiome differs in various diseases

Utilizes powerful techniques of genome sequencing and “big data” tools

©McGraw-Hill Education

Important and Surprising Results of HMP

Human cells: 21,000 protein-encoding genes

Microbiota: 8 million protein-encoding genes

Microbes are found in locations previously thought to be sterile

100 million viruses per gram of human feces

All healthy people seem to harbor potentially dangerous pathogens in low numbers

The makeup of one’s intestinal biota can influence overall health

©McGraw-Hill Education

Sites with Microbiota

Sites previously known to harbor normal microbiota:

Skin and adjacent mucous membranes, upper respiratory tract, gastrointestinal tract (including mouth), outer portion of urethra, external genitalia, vagina, external ear canal, external eye (lids, conjunctiva)

Additional sites now thought to harbor at least some normal microbiota (or their DNA):

Lungs (lower respiratory tract), bladder (and urine), breast and breast milk, amniotic fluid and fetus

Sites in which DNA from microbiota has been detected:

Brain, bloodstream

©McGraw-Hill Education

Acquiring the Microbiota

Human body has a variety of environmental niches (variations in temperature, pH, nutrients, and oxygen tension) and supports a wide range of microbes

Microbial antagonism:

Normal biota are unlikely to be displaced by incoming microbes

Limited number of attachment sites

Chemical or physiological environment created by resident biota is hostile to other microbes

Normal biota is beneficial or, at worst, commensal to the host in good health with a functioning immune system

©McGraw-Hill Education

Factors That Weaken Host Defenses and Increase Susceptibility to Infection

Old age and extreme youth (infancy, prematurity)

Genetic defects in immunity and acquired defects in immunity (AIDS)

Surgery and organ transplants

Underlying disease: cancer, liver malfunction, diabetes

Chemotherapy/immunosuppressive drugs

Physical and mental stress


Other infections

©McGraw-Hill Education

Colonization of the Fetus

Until recently, the uterus and its contents were thought to be sterile during embryonic and fetal development:

Analysis of newborns’ stools sampled before their first meal show a diversity of bacteria

This indicates that their intestines are colonized in utero

©McGraw-Hill Education

Colonization of the Newborn

Important source of microbiota for a newborn is its trip through the vagina:

Lactobacillus provides the baby with the necessary enzymes to digest milk

Other species protect the baby from skin disorders and other conditions

Human milk contains around 600 species of bacteria and sugars the baby cannot digest but that are digested by healthy gut bacteria

©McGraw-Hill Education

Where Babies Get a Microbiome

©Jim Connely (ultrasound); ©Adam Gault/SPL/Getty Images (birth); ©Jose Luis Pelaez Inc/Blend Images LLC (breast feeding); ©Pixtal/SuperStock (bottle);

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Concept Check (1)

Which of the following body sites previously thought to be microbe-free harbor at least some normal microbiota?

Skin and mucous membranes

External genitalia

Gastrointestinal tract

Breast milk

Upper respiratory tract

©McGraw-Hill Education

Learning Outcomes Section 11.2(1)

Differentiate between a microbe’s pathogenicity and its virulence.

List the steps a microbe has to take to get to the point where it can cause disease.

Explain the significance of polymicrobial infections.

List several portals of entry and exit.

Define infectious dose, and explain its role in establishing infection.

Describe three ways microbes cause tissue damage.

Compare and contrast major characteristics of endotoxin and exotoxins.

©McGraw-Hill Education

Learning Outcomes Section 11.2(2)

Provide a definition of virulence factors.

Draw a diagram of the stages of disease in a human.

Differentiate among the various types of reservoirs, providing examples of each.

List several different modes of transmission of infectious agents.

Define healthcare-associated infection, and list the three most common types.

List Koch’s postulates, and discuss when they might not be appropriate in establishing causation.

©McGraw-Hill Education

When Colonization Leads to Disease

Pathogen: a microbe whose relationship with its host is parasitic and results in infection and disease

Pathogenicity: an organism’s potential to cause disease

True pathogens: capable of causing disease in healthy persons with normal immune defenses

Opportunistic pathogens: cause disease when the host’s defenses are compromised or when the pathogens become established in a part of the body that is not natural to them

©McGraw-Hill Education



Relative severity of a disease caused by a particular microbe

Degree of pathogenicity

Virulence of a microbe is determined by its ability to:

Establish itself in a host

Cause damage

Virulence factor: any characteristic or structure of the microbe that contributes to its ability to establish itself in the host and cause damage

©McGraw-Hill Education

Polymicrobial Infections

Majority of infections are polymicrobial, with contributions from more than one microbe

Influenza infection frequently leads to pneumonia

Several types of skin infections are caused by either Staphylococcus or Streptococcus species:

When these two are cultivated with Moraxella, the three of them together lead to disease symptoms

©McGraw-Hill Education

Step One: Becoming Established—Portals of Entry(1)

Portal of entry: the route that a microbe takes to enter the tissues of the body to initiate an infection

Exogenous: microbe originating from a source outside the body from the environment or another person or animal

Endogenous: microbe already existing on or in the body—normal biota or a previously silent infection

©McGraw-Hill Education

Step One: Becoming Established—Portals of Entry(2)

The majority of pathogens have adapted to a specific portal of entry, one that provides a favorable habitat for further growth and spread

If certain pathogens enter the “wrong” portal, they will not be infectious:

Inoculation of the nasal mucosa with the influenza virus will result in the flu, but if the virus contacts the skin, no infection occurs

Occasionally, an infectious agent can enter by more than one portal:

Mycobacterium tuberculosis can enter through both the respiratory and gastrointestinal tracts

Streptococcus and Staphylococcus can enter through the skin, urogenital tract, and the respiratory tract

©McGraw-Hill Education

Portals of Entry(3)

Portal of Entry Organism/Disease How Access Is Gained
Skin Staphylococcus aureus, Streptococcus pyogenes, Clostridium tetani Via nicks, abrasions, punctures, areas of broken skin
Herpes simplex (type 1) Via mucous membranes of the lips
Helminth worms Burrow through the skin
Viruses, rickettsias, protozoa (i.e., malaria, West Nile virus) Via insect bites
Haemophilus aegyptius, Chlamydia trachomatis, Neisseria gonorrhoeae Via the conjunctiva of the eye
Gastrointestinal tract Salmonella, Shigella, Vibrio, Escherichia coli, poliovirus, hepatitis A, echovirus, rotavirus, enteric protozoans (Giardia lamblia, Entamoeba histolytica) Through eating/drinking contaminated foods and fluids Via fomites (inanimate objects contaminated with the infectious organism)
Respiratory tract Bacteria causing meningitis, influenza, measles, mumps, rubella, chickenpox, common cold, Streptococcus pneumoniae, Klebsiella, Mycoplasma, Cryptococcus, Pneumocystis, Mycobacterium tuberculosis, Histoplasma Via inhalation of offending organism
Urogenital tract HIV, Trichomonas, hepatitis B, syphilis, Treponema pallidum, Neisseria gonorrhoeae, Chlamydia trachomatis, herpes, genital warts Enter through the skin/mucosa of penis, external genitalia, vagina/cervix, urethra; may enter through an unbroken surface or through a cut or abrasion

©McGraw-Hill Education

Quantity of Microbes in the Inoculating Dose

Infectious dose (ID):

The minimum number of microbes necessary to cause an infection to proceed

Microorganisms with smaller infectious doses have greater virulence

ID for Q fever is a single cell

ID for tuberculosis, giardiasis, and coccidioidomycosis is about 10 cells

ID for gonorrhea is 1,000 cells

ID for typhoid fever is 10,000 cells

ID for cholera is 1,000,000,000 cells

©McGraw-Hill Education

Step Two: Becoming Established—Attaching to Host Cells


Process by which microbes gain a more stable foothold on host tissues

Dependent on binding between specific molecules on both the host and pathogen

Pathogen is limited to only those cells (and organisms) to which it can bind

Firm attachment is almost always a prerequisite for causing disease, since the body has so many mechanisms for flushing microbes from tissues

©McGraw-Hill Education

Adhesion Mechanisms

Bacterial, fungal, and protozoal pathogens attach by:

Fimbriae (pili)

Surface proteins

Adhesive slimes or capsules

Viruses attach by specialized receptors

Parasitic worms fastened by suckers, hooks, and barbs

©McGraw-Hill Education

Step Three: Becoming Established—Surviving Host Defenses

Phagocytes: cells that engulf and destroy host pathogens by means of enzymes and antimicrobial chemicals

Antiphagocytic factors:

Virulence factors used by some pathogens to avoid phagocytes

Leukocidins: kill phagocytes outright

Extracellular surface layer (slime or capsule) makes it difficult for the phagocyte to engulf the pathogen

Some bacteria survive inside the phagocyte

©McGraw-Hill Education

Step Four: Causing Disease

Virulence factors are simply adaptations a microbe uses to establish itself in a host

Three ways that microorganisms cause damage to their host:

Directly through the action of enzymes or toxins (both endotoxins and exotoxins)

Indirectly by inducing the host’s defenses to respond excessively or inappropriately

Epigenetic changes made to host cells by microbes

©McGraw-Hill Education

Three Ways Microbes Damage the Host

©McGraw-Hill Education

Extracellular Enzymes


Enzymes secreted by microbes that break down and inflict damage on tissues

Dissolve the host’s defense barriers to promote the spread of disease to other tissues

Examples of enzymes:

Mucinase: digests the protective coating on mucous membranes

Hyaluronidase: digests the ground substance that cements animal cells together

Coagulase: causes clotting of blood or plasma

Kinase: dissolves fibrin clots

©McGraw-Hill Education

Bacterial Toxins: A Potent Source of Cellular Damage

Toxin: a specific chemical product of microbes that is poisonous to other organisms

Toxins are named according to their target:

Neurotoxins act on the nervous system.

Enterotoxins act on the intestine

Hemotoxins lyse red blood cells

Nephrotoxins damage the kidneys

©McGraw-Hill Education


Hemolysins: class of bacterial exotoxin that disrupts the cell membrane of red blood cells

Cause the RBC to hemolyze, to burst and release hemoglobin pigment

©McGraw-Hill Education/Lisa Burgess, photographer

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Lipopolysaccharide (LPS), part of the outer membrane of gram-negative cell walls

Has a variety of systemic effects on tissues and organs

Causes fever, inflammation, hemorrhage, and diarrhea

Blood infections by Salmonella, Shigella, Neisseria meningitidis, and Escherichia coli are particularly dangerous and can lead to shock

©McGraw-Hill Education

Origins and Effects of Circulating Exotoxins and Endotoxin

©McGraw-Hill Education

Will Disease Result?

©Dave and Les Jacobs/Kolostock/Blend Images

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Definitions of Infection Types

Type of Infection Definition Example
Localized infection Microbes enter the body, remain confined to a specific tissue Boils, warts, fungal skin infections
Systemic infection Infection spreads to several sites and tissue fluids—usually via the bloodstream—but may travel by other means such as nerves (rabies) and cerebrospinal fluid (meningitis) Mumps, rubella, chickenpox, AIDS, anthrax, typhoid, syphilis
Focal infection Infectious agent spreads from a local site and is carried to other tissues Tuberculosis, streptococcal pharyngitis
Mixed infection (polymicrobial infection) Several agents establish themselves simultaneously at the infection site Human bite infections, wound infections, gas gangrene
Primary infection The initial infection Can be any infection
Secondary infection A second infection caused by a different microbe, which complicates a primary infection; often a result of lowered host immune defenses Influenza complicated by pneumonia, common cold complicated by bacterial otitis media
Acute infection Infection comes on rapidly, with severe but short-lived effects Influenza
Chronic infection Infection that progresses and persists over a long period of time HIV

©McGraw-Hill Education

Warning Signals of Disease

Sign: objective evidence of disease as noted by an observer

Symptom: subjective evidence of disease as sensed by the patient

Syndrome: a disease identified by a certain complex of signs and symptoms

©McGraw-Hill Education

Signs and Symptoms of Inflammation

Symptoms of inflammation:





Signs of inflammation:

Edema: the accumulation of fluid in afflicted tissue

Granulomas and abscesses: walled-off collections of inflammatory cells and microbes in the tissues

Lymphadenitis: swollen lymph nodes

©McGraw-Hill Education

Signs of Infection in the Blood

Signs of infection:

Leukocytosis: increase in white blood cell levels

Leukopenia: decrease in white blood cell levels

Septicemia: a general state in which microorganisms are multiplying in the blood and are present in large numbers

Bacteremia or viremia: bacteria or viruses are present in the blood but not multiplying

©McGraw-Hill Education

Infections That Go Unnoticed

No noticeable symptoms are produced

Microbe is active in host tissues

Host does not seek medical attention

These infections are known as asymptomatic, or subclinical (inapparent)

©McGraw-Hill Education

Step Five: Vacating the Host—Portals of Exit

Portal of exit:

Specific avenue by which pathogens exit

Shed through secretion, excretion, discharge, or sloughed tissue

High number of microbes in these materials increases the likelihood that the pathogen will reach other hosts

Portal of exit is usually the same as the portal of entry, but some pathogens use a different route

©McGraw-Hill Education

Major Portals of Exit of Infectious Diseases

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Steps Involved When a Microbe Causes Disease in a Host

©McGraw-Hill Education

Long-Term Infections and Long-Term Effects

Latency: a dormant state of microbes in certain chronic infectious diseases

Viral latency: herpes simplex, herpes zoster, hepatitis B, AIDS, Epstein-Barr

Bacterial/protozoan latency: syphilis, typhoid fever, tuberculosis, malaria

Sequelae: long-term or permanent damage to tissues or organs caused by infectious disease

Meningitis: deafness

Strep throat: rheumatic heart disease

Lyme disease: arthritis

Polio: paralysis

©McGraw-Hill Education

Course of an Infection(1)

Incubation period:

The time from initial contact with the infectious agent to the appearance of symptoms

Agent is multiplying at the portal of entry but has not caused enough damage to elicit symptoms

Varies according to host resistance, degree of virulence, and distance between the target organ and the portal of entry

Ranges from several hours to several years

Majority of infections range from 2 to 30 days

©McGraw-Hill Education

Course of an Infection(2)

Prodromal stage:

1- to 2-day period when the earliest notable symptoms of infection appear

Vague feeling of discomfort: head and muscle aches, fatigue, upset stomach, general malaise

Acute phase:

Infectious agent multiplies at high levels, exhibits its greatest virulence, becomes well established in its target tissue

Marked by fever and other prominent and specific signs and symptoms

Extremely variable in length of this period

©McGraw-Hill Education

Course of an Infection(3)

Convalescent period:

Patient begins to respond to the infection and symptoms decline

Patient’s strength and health gradually return due to the healing nature of the immune response

Many patients stop taking antibiotics during this period, even though pathogens are still in their system, leading to antibiotic resistance

Continuation phase:

Only some infections have this phase

Either the organism lingers for months, years, or indefinitely after the patient is well or the organism is gone but symptoms continue

©McGraw-Hill Education

Stages in the Course of Infection and Disease

©McGraw-Hill Education

Reservoirs: Where Pathogens Come From


Primary habitat in the natural world from which a pathogen originates

Often a human or animal carrier

Also soil, water, and plants

Transmitter: individual or object from which an infection is acquired

Syphilis: reservoir and transmitter are the same

Hepatitis A: reservoir is a human, transmitter is food

©McGraw-Hill Education

Reservoirs and Transmitters

Living Reservoirs Transmission Examples
Animals (Other than humans and arthropods) Mammals, birds, reptiles, etc. Pathogens from animals can be directly transmitted to humans, as in the example of bats transmitting rabies to humans can be transmitted to humans via vectors, as with fleas passing the plague from rats to people can be transmitted through vehicles such as water, as in the case of leptospirosis, which is often transmitted from animal urine to human skin via bodies of water
Humans Actively ill A person suffering from a cold contaminates a pen, which is then picked up by a healthy person. That is indirect transmission. Alternatively, a sick person can transmit the pathogen directly by sneezing on a healthy person.
Humans Carriers A person who is fully recovered from his hepatitis but is still shedding hepatitis A virus in his feces may use suboptimal hand-washing technique. He contaminates food, which a healthy person ingests (indirect transmission). Carriers can also transmit through direct means, as when an incubating carrier of HIV, who does not know she is infected, transmits the virus through sexual contact.
Arthropods Biological vectors When an arthropod is the host (and reservoir) of the pathogen, it is also the mode of transmission.
Nonliving Reservoirs Transmission Examples
Soil, Water, Air The built environment Some pathogens, such as the TB bacterium, can survive for long periods in nonliving reservoirs. They are then directly transmitted to humans when they come in contact with the contaminated soil, water, or air.

Top: ©Thinkstock/Getty Images (writing); ©Ingram Publishing (pen in mouth); Middle: Source: CDC; Bottom: ©McGraw-Hill Education/Christopher Kerrigan, photographer

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Living Reservoirs

A great number of infections that affect humans have their reservoirs in other humans

Persons or animals with symptomatic infection are obvious sources:

Carrier: an individual who inconspicuously shelters a pathogen, spreads it to others without any notice, and who may not have experienced disease due to the microbe

©McGraw-Hill Education

Carrier States

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Animals as Reservoirs and Sources

The majority of animal reservoir agents are arthropods such as fleas, mosquitoes, flies, and ticks

Larger animals can also spread infection:

Mammals: rabies

Birds: psittacosis

Lizards: salmonellosis

Biological vector: actively participates in a pathogen’s life cycle, serving as a site in which it can multiply or complete its life cycle

Mechanical vector: carries the microbe more or less accidentally on its body parts

©McGraw-Hill Education


Zoonosis: an infection indigenous to animals but naturally transmissible to humans

Humans are essentially dead-end hosts that do not contribute to the natural persistence of the microbe

Some zoonotic infections have multihost involvement

Some have complex life cycles in the wild

Zoonotic spread of disease is promoted by close associations between humans and animals

Make up a full 70% of all new emerging diseases worldwide

Impossible to eradicate without also eradicating the animal reservoir

©McGraw-Hill Education

Common Zoonotic Infections

Disease Primary Animal Reservoirs
Rabies Mammals
Yellow fever Wild birds, mammals, mosquitoes
Viral fevers Wild mammals
Hantavirus Rodents
Influenza Chickens, birds, swine
West Nile virus Wild birds, mosquitoes
Rocky Mountain spotted fever Dogs, ticks
Psittacosis Birds
Leptospirosis Domestic animals
Anthrax Domestic animals
Brucellosis Cattle, sheep, pigs
Plague Rodents, fleas
Salmonellosis Mammals, birds, reptiles, and rodents
Tularemia Rodents, birds, arthropods
Ringworm Domestic mammals
Toxoplasmosis Cats, rodents, birds
Trypanosomiasis Domestic and wild mammals
Trichinosis Swine, bears
Tapeworm Cattle, swine, fish

©McGraw-Hill Education

Nonliving Reservoirs

Microorganisms have adapted to nearly every habitat in the biosphere:

Thrive in soil, water, air

Surfaces in homes, offices, and other structures in the “built environment”

Most are saprobic and cause little harm and considerable benefit

Some are opportunists

A few are regular pathogens

Because humans are in regular contact with environmental sources, acquisition of pathogens from nonliving reservoirs is always a possibility

©McGraw-Hill Education

Transmission of Infectious Agents(1)

Communicable: a disease in which an infected host can transmit the infectious agent to another host and establish infection in that host

Infectious is sometimes used interchangeably with communicable, but this is not precise usage

Contagious: a disease that is highly communicable, especially through direct contact

Influenza and measles are highly contagious

Hansen’s disease (leprosy) is only weakly communicable

©McGraw-Hill Education

Transmission of Infectious Agents(2)

Noncommunicable: an infectious disease that does not arise through transmission of the infectious agent from host to host

Compromised person is invaded by their own microbiota

Individual has accidental contact with a microbe that exists in a nonliving reservoir

Infected persons do not become a source of disease to others

©McGraw-Hill Education

Patterns of Transmission in Communicable Diseases(1)

Direct or indirect contact with animate or inanimate objects

Horizontal transmission: disease is spread through a population from one infected individual to another

Three major modes of transmission:

Direct contact – close contact between people

Indirect transmission – an object or substance carries the agent from one person to another

Vector transmission – arthropods that harbor an infectious agent and transfer it to a human

Vertical transmission: disease transmitted from parent to offspring via ovum, sperm, placenta, milk

©McGraw-Hill Education

Patterns of Transmission in Communicable Diseases(2)

Vertical – transmission is from parent to offspring via the ovum, sperm, placenta, or milk

Horizontal – disease is spread through a population from one infected individual to another

Direct (contact) transmission

Indirect transmission

Fomite – inanimate object

Vehicle – natural, nonliving material like air, water, soil, and food

Vector transmission

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