Chapter 1: What is Microbiology and Why Does it Matter
Germ theory of disease (R Koch, 1800’s): states that microbes are the cause of infectious
diseases.
The first golden age of microbiology (1875-1910), when microbes were directly associated
with the diseases they caused.
In the first half of the twentieth century, scientists studied the structure, physiology and
genetics of microbes and found links between microbial properties and the development and
symptoms of infectious diseases. During this period, the discovery of penicillin in 1929 and
sulfonamide drugs in 1936 opened the door for effective treatments. By the end of the
twentieth century, better sanitation methods and advances in the fields of molecular biology
and genetics had increased our knowledge at the molecular level, contributing to the
development of vaccines and antibiotics. Now in the twenty-first century, infectious diseases
we thought were conquered are reappearing, and resistance to treatments is beginning to
grow. New diseases are emerging and organisms that were thought to be harmless are now
being found to cause disease in certain circumstances. The potential for bioterrorism has
gone from fiction to fact.
Immunocompromised: a condition in which the immune system is not functioning properly.
Nosocomial infection: hospital acquired infection.
O157:H7 (enterohemorrhagic strain of e.coli) can cause bacterial hemorrhagic disease and
O104:H4 causes serious food poisoning.
1
,For most pathogens, the basic aspects of how they cause disease can be looked at as:
epidemiology (the study of factors determining the frequency and distribution of disease),
pathogenesis (the study of how disease develops) and host defense.
Epidemiology
Pathogens must accomplish five steps to cause disease successfully:
- Step 1: get into the body or cell.
- Step 2: be able to stay in.
- Step 3: defeat the host defenses.
- Step 4: cause damage to the host.
- Step 5: be able to be transmitted to a new host.
Pathogenesis
Virulence factors are required for the organism to persist in the host, cause disease and
escape the host defenses so that the infection can continue.
Host defense
There are two basic types of defense against infection.
1. Innate immune response:
The nonspecific defense, the one you are born with and representing the first line of defense
by the host. Involve a variety of cellular mechanisms coupled with chemical and mechanical
factors. In many cases, these are all that are needed to defeat infection.
2. Adaptive immune response:
The second line of defense, which you acquire through being exposed to your environment.
The adaptive immune response is specific and has the benefit of memory., which means that
if you have that same infection later, the response will be immediate and powerful.
Chapter 4: An Introduction to Cell Structure and Host-Pathogen Relationships
Highly virulent: immediately lethal. Most pathogens are not highly virulent, because if the
host dies too quickly, it would prevent the spread of the pathogen.
Prokaryotes: bacteria and archaea, are less complex cells that lack a true nucleus and any
other structures enclosed by a membrane.
Eukaryotes: organisms made up of cells that do contain a membrane-enclosed nucleus as
well as other membrane-enclosed structures.
Bacteria
Bacteria are the smallest living organisms. The major bacterial shapes are spheres and ovoids
(cocci), straight rods (bacilli), very short rods (coccobacilli), curved rods (vibrio), rod-shaped
with tapered ends (fusiform bacilli) and spirals (spirilla if rigid, spirochetes if flexible).
2
,Bacteria can form distinctive multicell arrangements. One factor determining the shape of
these multicell arrangements is the degree of stickiness of the organism. For example, cocci
with two-cell arrangements (diplococci), chains and clusters.
For an additional degree of morphological classification, we use differential staining.
Staining
Staining is caused by dye molecules that bind to the microorganisms and give them color so
that they are visible. Microorganisms can be categorized according to which stains color
them. The most commonly used stains contain cations which are attracted to bacterial cells
because they have an overall negative charge on their surface (positive staining). Acidic dyes
are less common. Their anions give color to the background because they are repelled by the
negatively charged bacterial cells (negative staining).
There are two main types of staining procedures that use basic dyes:
- Simple stains (only one dye, used to identify shape and multicell arrangement).
- Differential stains (two or more dyes, used to distinguish between organisms or
different parts of the same organism).
1. The gram stain:
Can be used to separate most bacteria into four major groups: gram-positive, gram-negative,
gram-variable and gram-non reactive. The gram stain takes advantage of the differences in
cell wall of these groups of bacteria.
3
, Mordant: a substance that sets the color inside the cell and makes it permanent.
Any gram-variable bacteria are recognizable by the way in which they stain unevenly.
Gram-nonreactive bacteria do not stain and must be stained by a different method to be
seen.
2. The negative stain
Can be used to identify bacterial shapes, in particular spirochetes. It can also be used to
identify the presence of a capsule, which is a structure that surrounds certain bacterial cells.
The capsule is important in bacteria that infect humans because it can facilitate adherence
and undermines the host’s defense mechanisms by inhibiting phagocytosis. It also limits the
access of antiseptics, disinfectants and antibiotics.
The negative staining procedure uses dyes such as nigrosin and India ink to color the
background surrounding encapsulated bacteria, making the capsule very visible. A second
dye can be added to color the bacterium inside each capsule.
3. The Ziehl-Neelsen acid-fast stain:
Can be used to detect mycobacterium tuberculosis/leprae. These bacteria have a cell wall
that contains mycolic acid and lipids which make the cell wall hard to penetrate. Therefore,
heat is used as a part of the staining procedure to break down mycolic acid and permit the
entry of stains. Dyed cells who do not lose their color when washed with acid are classified
as acid-fast. These are the cells with mycolic acid in the cell wall.
4. The endospore stain:
An endospore is a small, dormant structure that forms in bacterial cells and several types of
bacteria can undergo sporulation (the process in which endospores are formed). Endospore
stain is a differential stain in which a sample is colored by heating with malachite green.
Host-pathogen relationships
Pathogens: organisms that can infect humans and cause illness. From the perspective of the
pathogenic organism, however, being pathogenic is simply a strategy for survival.
Most of the microorganisms are harmless and in some cases perform useful functions such
as providing protection from pathogens, producing vitamins and aiding digestion. These
microorganisms are classified as mutualistic: they depend on us for their survival and we
benefit from their presence.
Organisms that cause disease by taking advantage of a host’s increased susceptibility to
infection are called opportunistic pathogens. In contrast to opportunistic pathogens, primary
(obligate) pathogens are those that can cause disease in individuals who are healthy. Primary
pathogens are restricted to humans, whereas others also infect animal hosts.
Infection by any pathogen requires that the pathogen 1) be able to multiply in sufficient
numbers to secure establishment in the host and 2) be transmissible to new hosts. In most
cases there is a subclinical resolution to the infection in which the pathogen causes damage
4
Germ theory of disease (R Koch, 1800’s): states that microbes are the cause of infectious
diseases.
The first golden age of microbiology (1875-1910), when microbes were directly associated
with the diseases they caused.
In the first half of the twentieth century, scientists studied the structure, physiology and
genetics of microbes and found links between microbial properties and the development and
symptoms of infectious diseases. During this period, the discovery of penicillin in 1929 and
sulfonamide drugs in 1936 opened the door for effective treatments. By the end of the
twentieth century, better sanitation methods and advances in the fields of molecular biology
and genetics had increased our knowledge at the molecular level, contributing to the
development of vaccines and antibiotics. Now in the twenty-first century, infectious diseases
we thought were conquered are reappearing, and resistance to treatments is beginning to
grow. New diseases are emerging and organisms that were thought to be harmless are now
being found to cause disease in certain circumstances. The potential for bioterrorism has
gone from fiction to fact.
Immunocompromised: a condition in which the immune system is not functioning properly.
Nosocomial infection: hospital acquired infection.
O157:H7 (enterohemorrhagic strain of e.coli) can cause bacterial hemorrhagic disease and
O104:H4 causes serious food poisoning.
1
,For most pathogens, the basic aspects of how they cause disease can be looked at as:
epidemiology (the study of factors determining the frequency and distribution of disease),
pathogenesis (the study of how disease develops) and host defense.
Epidemiology
Pathogens must accomplish five steps to cause disease successfully:
- Step 1: get into the body or cell.
- Step 2: be able to stay in.
- Step 3: defeat the host defenses.
- Step 4: cause damage to the host.
- Step 5: be able to be transmitted to a new host.
Pathogenesis
Virulence factors are required for the organism to persist in the host, cause disease and
escape the host defenses so that the infection can continue.
Host defense
There are two basic types of defense against infection.
1. Innate immune response:
The nonspecific defense, the one you are born with and representing the first line of defense
by the host. Involve a variety of cellular mechanisms coupled with chemical and mechanical
factors. In many cases, these are all that are needed to defeat infection.
2. Adaptive immune response:
The second line of defense, which you acquire through being exposed to your environment.
The adaptive immune response is specific and has the benefit of memory., which means that
if you have that same infection later, the response will be immediate and powerful.
Chapter 4: An Introduction to Cell Structure and Host-Pathogen Relationships
Highly virulent: immediately lethal. Most pathogens are not highly virulent, because if the
host dies too quickly, it would prevent the spread of the pathogen.
Prokaryotes: bacteria and archaea, are less complex cells that lack a true nucleus and any
other structures enclosed by a membrane.
Eukaryotes: organisms made up of cells that do contain a membrane-enclosed nucleus as
well as other membrane-enclosed structures.
Bacteria
Bacteria are the smallest living organisms. The major bacterial shapes are spheres and ovoids
(cocci), straight rods (bacilli), very short rods (coccobacilli), curved rods (vibrio), rod-shaped
with tapered ends (fusiform bacilli) and spirals (spirilla if rigid, spirochetes if flexible).
2
,Bacteria can form distinctive multicell arrangements. One factor determining the shape of
these multicell arrangements is the degree of stickiness of the organism. For example, cocci
with two-cell arrangements (diplococci), chains and clusters.
For an additional degree of morphological classification, we use differential staining.
Staining
Staining is caused by dye molecules that bind to the microorganisms and give them color so
that they are visible. Microorganisms can be categorized according to which stains color
them. The most commonly used stains contain cations which are attracted to bacterial cells
because they have an overall negative charge on their surface (positive staining). Acidic dyes
are less common. Their anions give color to the background because they are repelled by the
negatively charged bacterial cells (negative staining).
There are two main types of staining procedures that use basic dyes:
- Simple stains (only one dye, used to identify shape and multicell arrangement).
- Differential stains (two or more dyes, used to distinguish between organisms or
different parts of the same organism).
1. The gram stain:
Can be used to separate most bacteria into four major groups: gram-positive, gram-negative,
gram-variable and gram-non reactive. The gram stain takes advantage of the differences in
cell wall of these groups of bacteria.
3
, Mordant: a substance that sets the color inside the cell and makes it permanent.
Any gram-variable bacteria are recognizable by the way in which they stain unevenly.
Gram-nonreactive bacteria do not stain and must be stained by a different method to be
seen.
2. The negative stain
Can be used to identify bacterial shapes, in particular spirochetes. It can also be used to
identify the presence of a capsule, which is a structure that surrounds certain bacterial cells.
The capsule is important in bacteria that infect humans because it can facilitate adherence
and undermines the host’s defense mechanisms by inhibiting phagocytosis. It also limits the
access of antiseptics, disinfectants and antibiotics.
The negative staining procedure uses dyes such as nigrosin and India ink to color the
background surrounding encapsulated bacteria, making the capsule very visible. A second
dye can be added to color the bacterium inside each capsule.
3. The Ziehl-Neelsen acid-fast stain:
Can be used to detect mycobacterium tuberculosis/leprae. These bacteria have a cell wall
that contains mycolic acid and lipids which make the cell wall hard to penetrate. Therefore,
heat is used as a part of the staining procedure to break down mycolic acid and permit the
entry of stains. Dyed cells who do not lose their color when washed with acid are classified
as acid-fast. These are the cells with mycolic acid in the cell wall.
4. The endospore stain:
An endospore is a small, dormant structure that forms in bacterial cells and several types of
bacteria can undergo sporulation (the process in which endospores are formed). Endospore
stain is a differential stain in which a sample is colored by heating with malachite green.
Host-pathogen relationships
Pathogens: organisms that can infect humans and cause illness. From the perspective of the
pathogenic organism, however, being pathogenic is simply a strategy for survival.
Most of the microorganisms are harmless and in some cases perform useful functions such
as providing protection from pathogens, producing vitamins and aiding digestion. These
microorganisms are classified as mutualistic: they depend on us for their survival and we
benefit from their presence.
Organisms that cause disease by taking advantage of a host’s increased susceptibility to
infection are called opportunistic pathogens. In contrast to opportunistic pathogens, primary
(obligate) pathogens are those that can cause disease in individuals who are healthy. Primary
pathogens are restricted to humans, whereas others also infect animal hosts.
Infection by any pathogen requires that the pathogen 1) be able to multiply in sufficient
numbers to secure establishment in the host and 2) be transmissible to new hosts. In most
cases there is a subclinical resolution to the infection in which the pathogen causes damage
4
