CHARACTERIZING AND CLASSIFYING VIRUSES, VIROIDS, AND PRIONS
A. CHARACTERISTICS OF VIRUSES
o
o
o
o
o
o
o
o
o
Cause many infections of humans, animals, plants, and bacteria
Cannot carry out any metabolic pathway
Neither grow nor respond to the environment
Cannot reproduce independently
Recruit the cell’s metabolic pathways to increase their numbers
Cause most of the diseases that plague the industrialized world
Virus – miniscule, acellular, infectious agent having one or
several pieces of either DNA or RNA
No cytoplasmic membrane, cytosol, organelles (with one
exception)
Have extracellular and intracellular state
o
EXTRACELLULAR STATE
o Called virion
o Protein coat (capsid) surrounding nucleic acid
o Nucleic acid and capsid also called nucleocapsid
o Some have phospholipid envelope
o Outermost layer provides protection and recognition sites
for host cells
o
INTRACELLULAR STATE
o Capsid removed
o Virus exists as nucleic acid
GENETIC MATERIAL OF VIRUSES
o
o
o
o
o
o
Show more variety in nature of their genomes than do cells
May be DNA or RNA, but never both
Primary way scientists categorize and classify viruses
Can be dsDNA, ssDNA, dsRNA, ssRNA
May be linear and composed of several segments or single and
circular
Much smaller than genomes of cells
HOSTS OF VIRUSES
o
o
o
Most viruses infect only particular host’s cells
o Due to affinity of viral surface proteins or glycoproteins for
complementary proteins or glycoproteins on host cell
surface
May be so specific they only infect particular kind of cell in a
particular host
Generalists – infect many kinds of cells in many different hosts
CAPSID MORPHOLOGY
o
o
o
Capsids – protein coats that provide protection for viral nucleic
acid and means of attachment to host’s cells
Capsid composed of proteinaceous subunits called capsomeres
Some capsids composed of single type of capsomere; others
composed of multiple types
THE VIRAL ENVELOPE
o
o
o
Acquired from host cell during viral replication or release;
envelope is portion of membrane system of host
Composed of phospholipid bilayer and proteins; some proteins
are virally coded glycoproteins (spikes)
Envelope’s proteins and glycoproteins often play role in host
recognition
VIRUSES VS CELLS
Characteristic
Cellular structure
External
membrane
covering
Size
Viruses
No
Outer envelope and
capsid
Cells
Yes
Cell membrane and cell
wall
Microscopic (10-400
nanometers)
Pathogenicity
Metabolism
Division and
growth
Intracellular
parasites
Genetic material
Genome type
Yes
No
No
Microscopic (200
nanometers to 12
centimeters)
Yes
Yes
Yes
Yes
No
DNA or RNA
dsDNA, ssDNA, RNA,
or ssRNA
Uses host cell
machinery
DNA and RNA
dsDNA
Reproduction
Self-replicating by
asexual and/or sexual
means
Family
Poxviridae
Herpesviridae
Strand Type
Double
Double
Papillomaviridae Double
Polyomaviridae
Double
Adenoviridae
Double
Hepadnaviridae
Parvoviridae
Partial single
and partial
double
Single
Poxviridae
Herpesviridae
Double
Double
Papillomaviridae Double
Polyomaviridae
Double
Adenoviridae
Double
Hepadnaviridae
Partial single
and partial
double
Single
Parvoviridae
Representative Genera (Diseases)
Orthopoxvirus (smallpox)
Simplexvirus (herpes simplex virus
type 1, herpes simplex virus type
2), Varicellovirus (chickenpox,
varicella-zoster virus),
Lymphocryptovirus (Epstein-Barr
virus), Cytomegalovirus
Papillomavirus (warts, cervical
cancer, penile cancer)
Polyomavirus (progressive
multifocal leukoencephalopathy)
Mastadenovirus (respiratory
infections, conjunctivitis)
Orthohepadnavirus (hepatitis B)
Erythrovirus (erythema
infectiosum)
Orthopoxvirus (smallpox)
Simplexvirus (herpes simplex virus
type 1, herpes simplex virus type
2), Varicellovirus (chickenpox,
varicella-zoster virus),
Lymphocryptovirus (Epstein-Barr
virus), Cytomegalovirus
Papillomavirus (warts, cervical
cancer, penile cancer)
Polyomavirus (progressive
multifocal leukoencephalopathy)
Mastadenovirus (respiratory
infections, conjunctivitis)
Orthohepadnavirus (hepatitis B)
Erythrovirus (erythema
infectiosum)
B. VIRAL REPLICATION
o
o
o
Dependent on hosts’ organelles and enzymes to produce new
virions
Replication cycle usually results in death and lysis of host cell →
lytic replication
Stages of lytic replication cycle
o Attachment
o Entry
o Synthesis
o Assembly
o Release
LYSOGENY
o
o
o
o
Modified replication cycle
Infected host cells grow and reproduce normally for generations
before they lyse
Temperate phages
o Prophages – inactive phages
Lysogenic conversion results when phages carry genes that alter
phenotype of a bacterium
REPLICATION OF ANIMAL VIRUSES
o
o
Same basic replication pathway as bacteriophages
Differences result from
o Presence of envelope around some viruses
o Eukaryotic nature of animal cells
o Lack of cell wall in animal cells
1. ATTACHMENT OF ANIMAL VIRUSES
o
o
o
Chemical attraction
Animal viruses do not have tails or tail fibers
Have glycoprotein spikes or other attachment molecules
that mediate attachment
2. SYNTHESIS OF ANIMAL VIRUSES
o
o
o
o
Each type of animal virus requires different strategy
depending on its nucleic acid
DNA viruses often enter the nucleus
RNA viruses often replicated in the cytoplasm
Must consider
o How mRNA is synthesized
o What serves as template for nucleic acid replication
3. ASSEMBLY AND RELEASES OF ANIMAL VIRUSES
o
o
o
o
o
Most DNA viruses assemble in and are released from nucleus
into cytosol
Most RNA viruses develop solely in cytoplasm
Number of viruses produced and released depends on type
of virus and size and initial health of host cell
Enveloped viruses cause persistent infections
Naked viruses are released by exocytosis or may cause lysis
and death of host cell
4. LATENCY OF ANIMAL VIRUSES
o
o
o
o
When animal viruses remain dormant in host cells
May be prolonged for years with no viral activity, signs, or
symptoms
Some latent viruses do not become incorporated into host
chromosome
When provirus is incorporated into host DNA, condition is
permanent, becomes physical part of host’s chromosome
Feature
Bacteriophage
Animal Virus
Attachment
Proteins on tails
attach to proteins on
cell wall
Penetration
Genome is injected
into cell or diffuses
into cell
Spikes, capsids, or envelope
proteins attach to proteins or
glycoproteins on cell
membrane
Capsid enters cell by direct
penetration, fusion, or
endocytosis
Uncoating
None
Site of synthesis
In cytoplasm
Site of assembly
In cytoplasm
Mechanism of
release
Lysis
Removal of capsid by cell
enzymes
RNA viruses in cytoplasm;
most DNA viruses in nucleus
RNA viruses in cytoplasm;
most DNA viruses in nucleus
Naked virions: exocytosis or
lysis; enveloped virions:
budding
C. THE ROLE OF VIRUSES IN CANCER
o
o
o
o
Normally, animal’s genes dictate that some cells can no longer
divide and those that can divide are prevented from unlimited
division
Genes for cell division are “turned off” or genes that inhibit
division are “turned on”
Neoplasia – uncontrolled cell division in multicellular animal;
mass of neoplastic cells is tumor
Benign vs. malignant tumors
o Metastasis
o Cancers
Feature
Benign Tumor
Malignant Tumor
Ability to
spread
Does not spread to
other parts of the
body
Growth rate
Grows slowly
Can spread to other parts of
the body through the
bloodstream or lymphatic
system
Grows quickly
Borders
Has distinct, smooth,
and regular borders
Has irregular and uneven
borders
Appearance
Typically looks like
normal tissue
Low risk of recurring
after removal
May look abnormal or distorted
Cannot metastasize
(spread to other parts
of the body)
May not require
treatment
Can metastasize (spread to
other parts of the body)
Risk of
recurrence
Metastasis
Treatment
Examples
Skin moles, uterine
fibroids, lipomas
High risk of recurring after
removal
Often requires treatment, such
as surgery, radiation therapy, or
chemotherapy
Lung cancer, breast cancer, skin
cancer
ENVIRONMENTAL FACTORS THAT CONTRIBUTE TO THE ACTIVATION OF
ONCOGENES
o
o
o
o
Ultraviolet light
Radiation
Carcinogens
Viruses
o
Viruses cause 20-25% of human cancers in several ways
o Some carry copies of oncogenes as part of their genomes
o Some promote oncogenes already present in host
o Some interfere with tumor repression when they insert
into host’s repressor gene
o Several specific DNA and RNA viruses are known to cause
~15% of human cancers
o Burkitt’s lymphoma
o Hodgkin’s disease
o Kaposi’s sarcoma
o Cervical cancer
D. CULTURING VIRUSES IN THE LABORATORY
o
Culturing Viruses in Whole Organisms
o
o
o
Culturing Viruses in Embryonated Chicken Eggs
o
o
In bacteria
In plants and animals
Ideal because they are inexpensive, among the largest of
cells, free of contaminating microbes, and contain a
nourishing yolk
Culturing Viruses in Cell (Tissue) Culture
o
Culturing Viruses in Cell (Tissue) Culture
o
o
Cell cultures consist of cells isolated from an organism and
grown on a medium or in a broth
Two types of cell cultures
o Diploid cell cultures
o Continuous cell cultures
E. OTHER PARASITIC PARTICLES: VIROIDS AND PRIONS
o
CHARACTERISTICS OF VIROIDS
o
o
o
Extremely small, circular pieces of RNA that are infectious and
pathogenic in plants
Similar to RNA viruses, but lack capsid
May appear linear due to H bonding
o
CHARACTERISITCS OF PRIONS
o
Proteinaceous infectious agents
o
Composed of single protein PrP
o
All mammals contain gene that codes for primary sequence of
amino acids in PrP
o
Two stable tertiary structures of PrP
o Normal functional structure with α-helices called cellular
PrP
o Disease-causing form with β-sheets called prion PrP
o
Prion PrP converts cellular PrP into prion PrP by inducing
conformational change
o
Normally, nearby proteins and polysaccharides force PrP into
cellular shape
o
Excess PrP production or mutations in PrP gene result in initial
formation of prion PrP
o
When prions are present, they cause newly synthesized cellular
PrP to refold into prion PrP
o
All prion diseases involve fatal neurological degeneration,
deposition of fibrils in brain, and loss of brain matter
o
Large vacuoles form in brain; characteristic spongy appearance
o
Spongiform encephalopathies – BSE, CJD, kuru
o
Prions only destroyed by incineration or autoclaving in 1N NaOH
Characteristic
Bacteria
Viruses
Viroids
Size
200-2000 nm
10-400 nm
2 nm
5 nm
Structure
Prokaryotic
cell with a
cell wall, cell
membrane,
cytoplasm,
and
ribosomes
Singlestranded
RNA
molecule
without a
capsid
Misfolded
protein
Metabolism
Independent
Binary fission
Dependent
on host cell
Replication
of RNA
inside host
cell
Independent
Reproduction
Examples
* Escherichia
coli *
Salmonella
typhi *
Bacillus
subtilis
Genetic
material
(DNA or
RNA)
enclosed in
a protein
coat
(capsid)
Dependent
on host cell
Replication
of genetic
material
inside host
cell
* HIV *
Influenza
virus *
Ebola virus
* Potato
spindle
tuber viroid
* Peach
latent
mosaic
viroid
Prions
Misfolding of
normal
proteins into
prion
proteins
*
CreutzfeldtJakob disease
* Mad cow
disease *
Kuru
F. ARE VIRUSES ALIVE?
o
o
Some scientists consider them complex pathogenic chemicals
that lack the characteristics of life
Other scientists consider them to be the least complex living
entities because they
o Use sophisticated methods to invade cells
o Have the ability to take control of their host cell
o Are able to replicate themselves
INFECTION, INFECTIOUS DISEASES, AND EPIDEMIOLOGY
A. SYMBIOTIC RELATIONSHIPS BETWEEN MICROBES AND THEIR
HOSTS
o
o
o
Symbiosis means “to live together”
We have symbiotic relationships with countless microorganisms
Types of symbiosis
o Mutualism
o Commensalism
o Parasitism
NORMAL MICROBIOTA IN HOSTS
o
o
o
Also termed normal flora and indigenous microbiota
Refers to the organisms that colonize the body’s surfaces
without normally causing disease
Two types
o Resident microbiota
o Transient microbiota
1. RESIDENT MICROBIOTA
o
o
Are a part of the normal microbiota throughout life
Are mostly commensal
2. TRANSIENT MICROBIOTA
o
o
o
Remain in the body for only hours to months before
disappearing
Found in the same regions as resident microbiota
Cannot persist in the body
o Competition from other microorganisms
o Elimination by the body’s defense cells
o Chemical or physical changes in the body
3. ACQUISITION OF NORMAL MICROBIOTA
o
o
o
Development in the womb is generally free of
microorganisms (axenic)
Microbiota begins to develop during the birthing process
Much of one’s resident microbiota is established during the
first months of life
HOW NORMAL MICROBIOTA BECOMES OPPORTUNISTIC PATHOGENS
o
o
o
o
o
Opportunistic pathogens are normal microbiota or other
normally harmless microbes that can cause disease under
certain circumstances
Conditions that provide opportunities for pathogens
Immune suppression
Changes in the normal microbiota – changes in relative
abundance of normal microbiota may allow opportunity for a
member to thrive and cause disease
Introduction of normal microbiota into unusual site in the body
B. RESERVOIRS OF INFECTIOUS DISEASES OF HUMANS
o
o
o
Most pathogens cannot survive for long outside of their host
Sites where pathogens are maintained as a source of infection
are termed reservoirs of infection
Three types of reservoirs
o Animal reservoir
o Human carriers
o Nonliving reservoir
1. ANIMAL RESERVOIRS
o
o
o
Zoonoses – diseases that are naturally spread from their
usual animal host to humans
Acquire zoonoses through various routes
o Direct contact with animal or its waste
o Eating animals
o Bloodsucking arthropods
Humans are usually dead-end host to zoonotic pathogens
2. HUMAN CARRIERS
o
o
o
Infected individuals who are asymptomatic themselves but
infective to others
Some individuals will eventually develop illness while others
never get sick
Healthy carriers may have defensive systems that protect them
from illness
3. NONLIVING RESERVOIRS
o
Soil, water, and food can be reservoirs of infection
o Presence of microorganisms is often due to contamination
by feces or urine
C. THE MOVEMENT OF MICROBES INTO HOSTS: INFECTION
EXPOSURE TO MICROBES: CONTAMINATION AND INFECTION
o
o
Contamination – the mere presence of microbes in or on the
body
Infection – results when the organism has evaded the body’s
external defenses, multiplied, and become established in the
body
PORTALS OF ENTRY
o
o
Sites through which pathogens enter the body
Four major pathways
o Skin
o Mucous membranes
o Placenta
o Parenteral route
1. SKIN
o
o
o
Outer layer of packed, dead, skin cells usually acts as a
barrier to pathogens
Some pathogens can enter through openings or cuts
Others enter by burrowing into or digesting the outer
layers of skin
2. MUCOUS MEMBRANES
o
o
Line the body cavities that are open to the environment
Provide a moist, warm environment that is hospitable to
pathogens
Respiratory tract is the most common site of entry – entry
is through the nose, mouth, or eyes
Pathogens able to survive the acidic pH of the stomach
may use the gastrointestinal tract as a route of entry
o
o
3. PARENTAL ROUTE
o
o
Not a true portal of entry but a means by which the
portal of entry can be circumvented
Pathogens deposited directly into tissues beneath the
skin or mucous membranes
THE ROLE OF ADHESION IN INFECTION
o
o
o
Process by which microorganisms attach themselves to cells
Required to successfully establish colonies within the host
Uses adhesion factors
o Specialized structures
o Attachment proteins
o
Attachment proteins help in adhesion
o Found on viruses (attachment proteins) and many bacteria
(adhesins)
o Surface lipoproteins or glycoproteins, called ligands, bind
host cell receptors
o
Interaction of ligand with host receptor can determine
specificity for host cells
o
Ability to change or block the ligand or its receptor can prevent
infection
o
Inability to make attachment proteins or adhesins renders the
microorganisms avirulent
o
Some bacterial pathogens attach to each other to form a biofilm
D. THE NATURE OF INFECTIOUS DISEASE
o
o
o
Infection is the invasion of the host by a pathogen
Disease results only if the invading pathogen alters the normal
functions of the body
Disease is also referred to as morbidity
MANIFESTATIONS OF DISEASE: SYMPTOMS, SIGNS, AND SYNDROMES
o
Symptoms – subjective characteristics of disease felt only by the
patient
o
Signs – objective manifestations of disease that can be observed
or measured by others
o
Syndrome – group of symptoms and signs that characterize a
disease or abnormal condition
o
Asymptomatic, or subclinical, infections lack symptoms but may
still have signs of infection
Prefix/Suffix
carcincol-, colodermatemia
endo-gen, gen-genesis
hepatidio-itis
Meaning
cancer
colon
skin
pertaining to the blood
inside
give rise to
development
liver
unknown
inflammation of a structure
-oma
-patho,
pathosepti-
tumor
abnormal
teratotox-
literally, rotting; refers to
presence of pathogens
defects
poison
Example
carcinogenic
colitis
dermatitis
viremia
endocarditis
pathogen
pathogenesis
hepatitis
idiopathic
meningitis,
endocarditis
melanoma
pathology
septicemia
teratogenic
toxin
CAUSATION OF DISEASE: ETIOLOGY
o
o
o
Study of the cause of disease
Germ theory of disease – disease caused by infections of
pathogenic microorganisms
Robert Koch developed a set of postulates one must satisfy to
prove a particular pathogen causes a particular disease
Category
Hereditary
Congenital
Degenerative
Nutritional
Endocrine
(hormonal)
Mental
Immunological
Neoplastic
(tumor)
Infectious
Description
Examples
Caused by errors in the
genetic code received
from parents
Anatomical and
physiological (structural
and functional) defects
present at birth
Result from aging
Sickle cell anemia, diabetes
mellitus, Down syndrome
Result from lack of
some essential
nutrients in diet
Due to excesses or
deficiencies of
hormones
Emotional or
psychosomatic
Hyperactive or
hypoactive immunity
Fetal alcohol syndrome,
deafness from rubella
infection
Renal failure, age-related
farsightedness
Kwashiorkor, rickets
Dwarfism
Abnormal cell growth
Skin rash, gastrointestinal
distress
Allergies, autoimmune
diseases,
agammaglobulinemia
Benign tumors, cancers
Caused by an infectious
agent
Colds, influenza, herpes
infections
Iatrogenic
Idiopathic
Nosocomial
Caused by medical
treatment or
procedures
Unknown cause
Disease acquired in
health care setting
Surgical error, yeast
vaginitis resulting from
antimicrobial therapy
Alzheimer's disease,
multiple sclerosis
Pseudomonas infection in
burn patient
CAUSATION OF DISEASE: ETIOLOGY
o
Exceptions to Koch’s postulates
o
Using Koch’s postulates is not feasible in all cases
o Some pathogens can’t be cultured in the laboratory
o Some diseases are caused by a combination of
pathogens and other cofactors
o Ethical considerations prevent applying Koch’s
postulates to pathogens that require a human host
o
Difficulties in satisfying Koch’s postulates
o Diseases that can be caused by more than one
pathogen
o Pathogens that are ignored as potential causes of
disease
VIRULENCE FACTORS OF INFECTIOUS DISEASE
o
o
Pathogenicity – ability of a microorganism to cause disease
Virulence – degree of pathogenicity
o Virulence factors contributing to an organism’s virulence
o Adhesion factors
o Biofilms
o Extracellular enzymes
o Toxins
o Antiphagocytic factors
o
Extracellular enzymes
o Secreted by the pathogen
o Dissolve structural chemicals in the body
o Help pathogen maintain infection, invade further, and avoid
body defenses
o
Toxins
o Chemicals that harm tissues or trigger host immune
responses that cause damage
o Toxemia refers to toxins in the bloodstream that are carried
beyond the site of infection
o Two types
o Exotoxins
o Endotoxins
Characteristic
Source
Exotoxins
Endotoxins
Produced by both Grampositive and Gramnegative bacteria
Proteins
Produced by Gramnegative bacteria only
Toxicity
Highly toxic
Less toxic than exotoxins,
but can still be fatal
Heat stability
Heat labile (destroyed by
heat)
Mode of
action
Bind to specific receptors
on host cells and cause a
variety of effects, such as
cell death, tissue damage,
and disruption of cellular
processes
Tetanospasmin, botulinum
toxin, diphtheria toxin
Heat stable (can
withstand high
temperatures)
Activate the host immune
system, which can lead to
inflammation, fever, and
shock
Chemical
nature
Examples
Lipopolysaccharides (LPS)
Lipopolysaccharide (LPS)
from Salmonella, E. coli,
and other Gram-negative
bacteria
o
Antiphagocytic factors
o
Certain factors prevent phagocytosis by the host’s phagocytic
cells
o Bacterial capsule
o Often composed of chemicals found in the body and
not recognized as foreign
o Can be slippery, making it difficult for phagocytes to
engulf the bacteria
o
Antiphagocytic chemicals
o Some prevent fusion of lysosome and phagocytic
vesicles
o Leukocidins directly destroy phagocytic white blood
cells
SUMMARY OF VIRULENCE FACTORS OF INFECTIOUS DISEASE
Factor
Pathogenicity
Virulence
Extracellular
enzymes
Definition
Types (if had one)
ability of a microorganism
to cause disease
degree of pathogenicity
Secreted by Pathogens
Help pathogen maintain
infection, invade further,
and avoid body defenses
Toxins
Chemicals that harm tissues
or trigger host immune
responses that cause
damage
Exotoxins - are
proteins that are
secreted by bacteria
into the surrounding
environment.
Endotoxins - are
lipopolysaccharides
(LPS) that are found
in the outer
membrane of Gramnegative bacteria.
They are released
when the bacteria
die and lyse.
Antiphagocytic
factors
Certain factors prevent
phagocytosis by the host’s
phagocytic cells
are substances produced by
pathogens that help them
evade phagocytosis, the
process by which immune
cells engulf and destroy
foreign invaders.
Bacterial capsule
- Can be slippery,
making it difficult for
phagocytes to engulf
the bacteria
Antiphagocytic
chemicals
- Some prevent
fusion of lysosome
and phagocytic
vesicles
THE STAGES OF INFECTIOUS DISEASE
o
o
Following infection, a sequence of events called the disease
process occurs
Many infectious diseases have five stages following infection
o Incubation period
o Prodromal period
o Illness
o Decline
o Convalescence
E. THE MOVEMENT OF PATHOGENS OUT OF HOSTS: PORTALS OF EXIT
o
o
o
Pathogens leave host through portals of exit
Many portals of exit are the same as portals of entry
Pathogens often leave hosts in materials the body secretes or
excretes
F. MODES OF INFECTIOUS DISEASE TRANSMISSION
o
Transmission is either from a reservoir or a portal of exit to
another host’s portal of entry
o
Three groups of transmission
o
Contact transmission
o Direct, indirect, or droplet
o
Vehicle transmission
o Airborne, waterborne, or foodborne
o
Vector transmission
o Biological or mechanical
Mode of
Transmission
Contact
Transmission
Direct contact
Indirect contact
Droplet
transmission
Airborne
transmission
Vehicle
transmission
Vector
transmission
Mechanical
transmission
Biological
transmission
Examples of Diseases
Spread
Cuts, anthrax, gonorrhea,
herpes, rabies,
staphylococcal infections
Person-to-person
transmission through
physical touch
Transmission via
contaminated objects or
surfaces
Respiratory droplets from
coughs or sneezes
Pathogens suspended in
the air
Transmission through
contaminated food, water,
or other vehicles
Carried by vectors (e.g.,
mosquitoes, ticks)
Pathogens carried
mechanically (e.g., on flies’
legs)
Pathogens multiply within
vectors before transmission
Transmission
Skin-to-skin contact
Direct physical contact
Touching
contaminated surfaces
Close proximity to an
infected person
Inhalation of airborne
particles
Ingestion or exposure
to contaminated
substances
Bites from infected
vectors
Physical transport by
vectors
Vectors serve as hosts
for pathogen
development
G. CLASSIFICATION OF INFECTIOUS DISEASES
o
Diseases can be classified in number of ways
o The taxonomic groups of the causative agent
o The body system they affect
o Their longevity and severity
o How they are spread to their host
o The effects they have on populations (rather than on
individuals)
H. EPIDEMIOLOGY OF INFECTIOUS DISEASES
FREQUENCY OF DISEASE
o
Track occurrence of diseases using two measures
o Incidence – number of new cases of a disease in a
given area during a given period of time
o Prevalence – number of total cases of a disease in a
given area during a given period of time
o
Occurrence also evaluated in terms of frequency and
geographic distribution
EPIDEMIOLOGICAL STUDIES
o
Descriptive epidemiology
o Careful tabulation of data concerning a disease
o Record information about the location and time
of the cases of disease
o Collect patient information
o
Try to identify the index case (or first case) of the disease
o
Analytical Epidemiology
o
o
o
o
Experimental epidemiology
o
o
o
Seeks to determine the probable cause, mode of
transmission, and methods of prevention
Useful in situations in which Koch’s postulates can’t be
applied
Often retrospective – investigation occurs after an
outbreak has occurred
Involves testing a hypothesis concerning the cause of a
disease
Application of Koch’s postulates is experimental
epidemiology
Hospital Epidemiology: Nosocomial Infections
o
o
Types of nosocomial infections
o Exogenous – pathogen acquired from the health care
environment
o Endogenous – pathogen arises from normal
microbiota due to factors within the health care
setting
o Iatrogenic – results from modern medical procedures
Control of nosocomial infections
o Involves precautions designed to reduce the factors
that result in disease
o Hand washing is the most effective way to reduce
nosocomial infections
EPIDEMIOLOGY AND PUBLIC HEALTH
o
Agencies at the local, state, national, and global level share
information concerning disease
o The United States Public Health Service is the national
public health agency
o World Health Organization (WHO) coordinates public
health services internationally
o
Public health agencies work to limit disease transmission
o Monitor water and food safety
o
Public health agencies campaign to educate the public on
healthful choices to limit disease
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
A. FOOD MICROBIOLOGY
o
Microorganisms are involved in producing many foods and
beverages
o
Characteristic flavors, aromas, and consistencies of various
foods result from the process of fermentation
o
Microbial metabolism also acts as a preservative, destroys many
pathogenic microbes and toxins, and can add nutritional value in
the form of vitamins and other nutrients
o
Microbes are used in food production and to control microbial
activity that would otherwise result in food spoilage
THE ROLES OF MICROORGANISMS IN FOOD PRODUCTION
BREAD
o Fermentation in food microbiology refers to any desirable
change that occurs to a food or beverage as a result of
microbial growth
o Spoilage denotes unwanted change to a food that could occur
for various reasons
o Undesirable metabolic reactions
o Growth of pathogens
o Presence of unwanted microorganisms in the food
o
Commercial food and beverage production often rely on the
use of a starter culture
o Starter cultures are composed of known
microorganisms that perform specific fermentations
consistently
o
Many common products are the result of fermentation of
vegetables, meats, and dairy products
PRODUCTS OF ALCOHOLIC FERMENTATION
o
Alcoholic fermentation is the process by which various
microorganisms convert simple sugars such as glucose into
alcohol (ethanol) and carbon dioxide (CO2)
o
Specific starter cultures are used in the large-scale commercial
applications of alcohol fermentation
o
Various alcoholic products can be made through fermentation
Food
Starting Material
Miso
Representative Culture
Microorganisms
Aspergillus oryzae and
Bacillus subtilis
Aspergillus oryzae and
Saccharomyces cerevisiae
Lactic acid bacteria (e.g.,
Lactobacillus)
Lactic acid bacteria (e.g.,
Lactobacillus)
Soy sauce
Soybeans, rice, or
other grains
Soybeans and wheat
Sauerkraut
Cabbage
Kimchi
Yogurt
Napa cabbage,
radish, and
seasonings
Milk
Kefir
Milk
Lactic acid bacteria (e.g.,
Lactobacillus)
Lactic acid bacteria and yeast
Tempeh
Soybeans
Rhizopus oligosporus
Natto
Soybeans
Bacillus subtilis
Sourdough
bread
Cheese
Flour and water
Wild yeast (e.g.,
Saccharomyces)
Various bacteria and molds
Vinegar
Various starting
materials (e.g., wine)
Malted barley, hops,
water, and yeast
Grapes
Beer
Wine
Milk
Acetic acid bacteria (e.g.,
Acetobacter)
Saccharomyces cerevisiae
Saccharomyces cerevisiae
THE CAUSES OF FOOD SPOILAGE
o
Food spoilage results from intrinsic or extrinsic factors
o
o
Intrinsic factors are those that are inherent properties of
the food itself
Extrinsic factors are those involved with the processing or
handling of food rather than with the food itself
Intrinsic
Factors
Nutritional
composition
Water activity
pH
Physical
structure
Microbial
competition
Description
The composition of the food, such as its protein,
carbohydrate, and fat content, can affect the growth of
microorganisms. Foods that are high in nutrients are more
likely to spoil than foods that are low in nutrients.
Water activity is a measure of the available water in a food
that microorganisms can use for growth. Foods with high
water activity, such as meat and milk, are more likely to
spoil than foods with low water activity, such as dried fruits
and nuts.
The pH of a food is a measure of how acidic or alkaline it is.
Most microorganisms cannot grow in acidic environments,
so foods with a low pH, such as orange juice and pickles, are
less likely to spoil than foods with a neutral pH, such as
bread.
The physical structure of a food, such as its surface area,
can affect the growth of microorganisms. Foods with a large
surface area, such as ground meat, are more likely to spoil
than foods with a small surface area, such as whole fruits
and vegetables.
Some foods contain naturally occurring microorganisms
that can compete with harmful microorganisms. For
example, pickles contain lactic acid bacteria, which produce
acids that inhibit the growth of other microorganisms.
Extrinsic
Factors
Degree of
processing
Description
Amount of
preservatives
Storage
temperature
Storage
packaging
Processed foods are often less likely to spoil than
unprocessed foods. This is because processing methods,
such as canning and freezing, can kill microorganisms and
inactivate enzymes that can cause spoilage.
Preservatives can help to prevent spoilage by killing or
inhibiting the growth of microorganisms. Preservatives can
be added to foods naturally, such as the salt in cured
meats, or artificially, such as the sodium benzoate in soft
drinks.
Microorganisms grow more quickly at warmer
temperatures. Therefore, foods should be stored at cold
temperatures, such as in the refrigerator or freezer, to slow
the growth of microorganisms and prevent spoilage.
Packaging can help to protect foods from microorganisms
and other contaminants. For example, vacuum-sealed
packaging can remove air from the food, which can help to
prevent the growth of aerobic microorganisms.
CLASSIFYING FOODS IN TERMS OF POTENTIAL FOR SPOILAGE
Three categories based on likelihood of spoilage
o
o Perishable
Tend to be nutrient rich, moist, and unprotected by rinds or
coverings and need to be kept cold
o
Semi-perishable
o Can store in sealed containers for months without
spoiling
o Many fermented foods are semi-perishable
o
Nonperishable
o Usually dry or canned foods that can be stored almost
indefinitely without spoiling
o Often are nutrient poor, dried, fermented, or preserved
THE PREVENTION OF FOOD SPOILAGE
FOOD PROCESSING METHODS
o Industrial canning
o Eliminates mesophilic bacteria and endospores
o Hyperthermophilic microbes remain but they cannot grow at
room temperature
o
Pasteurization
o Lowers the number of microbes but some microbes
survive
o Used most with delicate foods and beverages
o
Lyophilization
o Foods are frozen and then a vacuum draws off the ice
crystals
o
Gamma radiation
o Penetrates foods and damages the DNA of microbes
o Can achieve complete sterilization
USE OF PRESERVATIVES
o
Various substances are used as preservatives of foods and
beverages
o
o
o
o
o
Salt and sugar remove water from the food
Garlic contains the antimicrobial compound, allicin,
which inhibits enzyme function
Benzoic acid interferes with enzymatic function
Certain spices and herbs produce oils that interfere with
the membrane functions of microorganisms
Chemical preservatives can be purposely added to foods
(many inhibit microbial growth but don’t kill the
microbes)
ATTENTION TO TEMPERATURE DURING PROCESSING AND STORAGE
o
High temperatures are desirable during food processing and
preparation to prevent food spoilage
o High temperatures kill pathogens because proteins and
enzymes become denatured
o
Low temperatures are desirable for food storage
o Cold rarely kills microbes but retards their growth by
slowing their metabolism
o Listeria monocytogenes can grow while in cold storage
and can be found in certain dairy products
FOODBORNE ILLNESSES
o
o
Can occur from consumption of spoiled foods or foods that
contain harmful microbes or their products
Two categories of food poisoning
o Food infections
o Result from the consumption of living microorganisms
o Food intoxications
o Caused by the consumption of microbial toxins rather
than the microbe itself
o
Symptoms include nausea, vomiting, diarrhea, fever, fatigue,
and muscle cramps
Organism
Campylobacter
jejuni
Clostridium
botulinum
Affected Food
Products
Raw and
undercooked meats,
raw milk, untreated
water
Home-prepared
foods
Comments
Most common cause of
diarrhea of all foodborne
agents
Produces a neurotoxin
Escherichia coli
O157:H7
Meat, raw milk
Produces an enterotoxin
Listeria
monocytogenes
Dairy products, raw
and undercooked
meats, seafood,
produce
Raw and
undercooked eggs,
meat, dairy products,
fruits and vegetables
Salads, milk and
other dairy products,
water
Cooked high-protein
foods
Common in soils and water,
contamination from these
sources occurs easily, grows
at refrigerator temperature
Second most common cause
of foodborne illness in the
United States
Meat (pork in
particular)
Raw and
undercooked seafood
Pork, dairy products,
produce
Parasitic protozoan
Salmonella spp.
Shigella spp.
Staphylococcus
aureus
Toxoplasma
gondii
Vibrio vulnificus
Yersinia
enterocolitica
Third most common cause
of foodborne illness in the
United States
Produces a potent toxin that
is not destroyed by cooking
Causes primary septicemia
(bacteria in the blood)
Causes generalized diarrhea
and severe cramping that
mimics appendicitis, grows
at refrigerator temperature
B. INDUSTRIAL MICROBIOLOGY
o Industrial microbiology is an important field within the
microbiological sciences
o Industrial microbiology is used in various applications
o Microbes in fermentation
o Microbes in the production of several industrial products
o Treatment of water and wastewaters
o Disposal and cleanup of biological wastes
o Treatment of mine drainage
THE ROLES OF MICROBES IN INDUSTRIAL FERMENTATIONS
o
o
Industrial fermentations involve the large-scale growth of
particular microbes for producing beneficial compounds
Examples include amino acids or vitamins
o
Primary metabolites
o Produced during active growth and metabolism
o Either required for reproduction or by-products of active
metabolism
o
Secondary metabolites
o Produced after the culture has moved from log phase of
growth and has entered the stationary phase
o Substances are not immediately needed for growth
INDUSTRIAL PRODUCTS OF MICROORGANISMS
o
Microorganisms, particularly bacteria, produce a large array of
industrially useful chemicals during their metabolic activities
o
Recombinant organisms add to this diversity by producing
substances not normally manufactured by microbial cells
Product
Yogurt
Starting
Material
Representative Culture Microorganisms
Cheese
Pasteurized skim
milk
Milk curd
Streptococcus thermophilus and
Lactobacillus bulgaricus
Starter culture as in cottage cheese plus
Penicillium camemberti or Penicillium
roqueforti
Beer
Barley
Saccharomyces cerevisiae
Bread
Flour, salt, etc.
Saccharomyces cerevisiae
Wine
Grapes
Saccharomyces cerevisiae
Sake
Cooked rice
Aspergillus oryzae and Saccharomyces spp.
Vinegar
Fruits,
vegetables, or
grains
Acetobacter or Gluconobacter bacteria
Sauerkraut
Cabbage
Various lactic acid bacteria, including
Lactobacillus plantarum, Lactobacillus
brevis, and Leuconostoc mesenteroides
Kombucha
Tea and sugar
Kefir
Milk
Sourdough
bread
Flour and water
Symbiotic culture of bacteria and yeasts
(SCOBY)
Kefir grains, which contain a variety of
bacteria and yeasts
Lactic acid bacteria and wild yeasts
Kimchi
Cabbage, radish,
and other
vegetables
Various lactic acid bacteria, including
Lactobacillus plantarum, Lactobacillus
brevis, and Leuconostoc mesenteroides, as
well as yeasts and fungi such as Candida
krusei and Saccharomyces cerevisiae
Pickles
Cucumbers,
peppers, beets,
and other
vegetables
Various lactic acid bacteria, including
Lactobacillus plantarum, Lactobacillus
brevis, and Pediococcus pentosaceus
INDUSTRIAL PRODUCTS OF MICROORGANISMS
o
BIOSENSORS AND BIOREPTORS
o Are relatively new applications of microorganisms to solve
environmental problems
o
Biosensors
o Devices that combine bacteria or microbial products with
electronic measuring devices to detect other bacteria,
bacterial products, or chemicals in the environment
o
Bioreporters
o Sensors composed of microbes with innate signaling
capabilities, such as the ability to glow in the presence of
biological or chemical compounds
o
Used to detect the presence of environmental pollutants
and monitor efforts to remove harmful substances
WATER AND WASTEWATER TREATMENT
o
Treatment of drinking water
o Potable water is water considered safe to drink
o Does not imply that the water is devoid of all
microorganisms and chemicals
o The levels of microorganisms and chemicals in the
water are low enough that it is not a health concern
o
The presence of coliforms in water indicates fecal contamination
and an increased likelihood that disease- causing microbes are
present
o
Treatment of drinking water involves three stages
o Sedimentation and Flocculation
o Filtration
o Disinfection
WATER QUALITY TESTING
o
Technique that uses the presence of certain indicator organisms
to signal the possible presence of pathogens in water
o
Majority of water-borne illnesses are caused by and spread via
fecally contaminated water
o
E. coli or other coliforms in water indicates other pathogens may
be present
o E. coli is a good indicator organism
o Consistently found in human waste
o Survives in water as long as most pathogens
o Easily detected by simple tests
TREATMENT OF WASTEWATER
o
Wastewater (sewage) is water that leaves homes or businesses
after being used for washing or flushed from toilets
o
Wastewater contains a variety of contaminants
o
Treatment is intended to remove or reduce contaminants to
acceptable levels
o
Wastewater is processed to reduce the biochemical oxygen
demand (BOD)
o
BOD is a measure of the amount of oxygen required by aerobic
bacteria to metabolize wastes in water
o
Effective sewage treatment reduces the BOD to levels too low to
support microbial growth
o
Various types of wastewater treatments are used
o Municipal wastewater treatment, wastewater treatment in
rural areas, treatment of agricultural wastes, and artificial
wetlands
BIOREMEDIATION
o
o
o
Uses organisms to clean up toxic, hazardous, or recalcitrant
compounds by degrading them to harmless compounds
Most widely known application is the use of bacteria, such as
Pseudomonas, to clean oil spills
TWO TYPES OF BIOREMEDIATION
o
Natural bioremediation
o Microbes are “encouraged” to degrade toxic substances in
soil or water
o Occurs by the addition of nutrients that stimulate growth
or of chemicals that facilitate microbial access and activity
by increasing the solubility of toxic compounds
o
Artificial bioremediation
o Microbes are genetically modified by recombinant DNA
technology to specifically degrade certain chemicals
THE PROBLEM OF ACID MINE DRAINAGE
o
Drainage results from the exposure of certain metal ores to
oxygen and microbial action
o
The resulting compounds are carried into streams and rivers
where they reduce the pH
– The lowered pH can kill fish, plants, and other organisms
o
Subsurface mines can significantly reduce the levels of acid mine
drainage
C. ENVIRONMENTAL MICROBIOLOGY
o
o
Studies the microorganisms as they occur in their natural
habitats
Microbes are important to microbial ecology, biogeochemical
cycles, soil microbiology, and aquatic microbiology
MICROBIAL ECOLOGY
o
o
Study of the interrelationships among microorganisms and their
environment
Two aspects to consider
o Levels of microbial associations in the environment
o Role of adaptation in microbial survival
ROLE OF ADAPTATION IN MICROBIAL SURVIVAL
o
Most microorganisms live in harsh environments
o The harsher the environment, the more specially adapted
a microbe must be to survive
o
Microbes must be capable of adapting in environments that
cycle between excess and depletion
o
Biodiversity held in balance by various checks
o
o
o
Competition – best-adapted microorganisms have traits
that provide them advantages
Antagonism – microbe makes some product that actively
inhibits the growth of another
“Cooperation” – a microbe’s metabolic activities make the
environment more favorable for other microbes or
provide them with waste products to use for their own
metabolism
ROLE OF MICROORGANISMS IN BIOGEOCHEMICAL CYCLES
o
Biogeochemical cycles are the processes by which organisms
convert elements from one form to another
o
o
Elements are often converted between the oxidized and
reduced forms
The actions of organisms recycling are the major
components of biogeochemical cycles
MICROBIAL ECOLOGY
o
Biogeochemical cycling entails three processes
o
Production
o Conversion of inorganic compounds into the organic
compounds of biomass
o
Consumption
o Organisms feed on producers and other consumers
converting organic molecules into other organic
molecules
o
Decomposition
o Conversion of organic compounds in dead organisms
into inorganic compounds
PHOSPHOROUS CYCLE
o
o
o
Phosphorus undergoes little change in oxidation state in the
environment
Movement of phosphorus from insoluble to soluble forms
available for uptake by organisms
Conversion of phosphorus from organic to inorganic forms by
pH–dependent processes
CYCLING OF TRACE METALS
o
o
Metal ions are important microbial nutrients
Cycling primarily involves a transition from an insoluble to a
soluble form so trace metals can be used by organisms
SOIL MICROBIOLOGY
o
o
Examines the roles played by organisms living in soil
Nature of soils
o Soil arises from the weathering of rocks and through the
actions of microorganisms
ENVIRONMENTAL FACTORS AFFECTING MICROBIAL ABUNDANCE IN
SOIL
o
Moisture content
o Moist soils support microbial growth better than dry soils
o
Oxygen
o Oxygen dissolves poorly in water so moist soils are lower in
oxygen than dry soils
o
pH
o Highly acidic and highly basic soils favor fungi
o
Temperature
o Most soil organisms are mesophiles
o
Nutrient availability
o Size of a microbial community is determined by how much
rather than what type of organic material is available
MICROBIAL POPULATIONS IN SOIL
o
Perform a number of functions
o Cycle elements and convert them to usable form
o Degrade dead organisms
o Produce compounds with potential human uses
MICROBIAL POPULATIONS PRESENT IN SOIL
o
o
o
o
Archaea are present but inability to culture limits ability to study
them
Bacteria are numerous and diverse inhabitants of soil
Fungi are the next most populous group of microorganisms
Algae and protozoa are also present in the soil
Microorganism
Host
Disease
Bacillus anthracis
Humans
Anthrax
Cordyceps sinensis
Humans
Caterpillar fungus disease
Agrobacterium tumefaciens
Plants
Crown gall disease
Phytophthora infestans
Plants
Late blight
Histoplasma capsulatum
Humans
Histoplasmosis
Fusarium oxysporum
Plants
Fusarium wilt
Coccidioides immitis
Humans
Coccidioidomycosis
Rhizoctonia solani
Plants
Damping-off
Aspergillus flavus
Humans
Aspergillosis
Pythium spp.
Plants
Root rot
Blastomyces dermatitidis
Humans
Blastomycosis
Verticillium dahliae
Plants
Verticillium wilt
AQUATIC MICROBIOLOGY
o
o
o
Study of the microorganisms living in freshwater and marine
environments
Water ecosystems support fewer microbes than soil because
nutrients are diluted
TYPES OF AQUATIC HABITATS
o
o
o
Freshwater systems – characterized by low salt content
Marine systems – characterized by a salt content of about
3.5%
Specialized aquatic systems – salt lakes, iron springs, and
sulfur springs
WATER POLLUTION
o
o
o
Polluted waters are obvious in that one can either see, taste, or
smell the pollutant
Water pollution can occur three ways
o
Physically
o Presence of particulate matter
o
Chemically
o Presence of inorganic or organic compounds
o
Biologically
o Results from an overabundance of organisms or the
presence of non-native microorganisms
Polluted waters are high in organic compounds and support a
greater than normal microbial load
D. BIOLOGICAL WARFARE AND BIOTERRORISM
o
Microbes can be fashioned into biological weapons that are
directed at people, livestock, or crops
o
Bioterrorism
o Uses microbes or their toxins to terrorize human
populations
o
Agroterrorism
o Uses microbes to terrorize human populations by
destroying the food supply
ASSESSING MICROORGANISMS AS POTENTIAL AGENTS OF WARFARE
OR TERROR
o
o
Criteria for assessing biological threats to humans
Established to evaluate the potential of microorganisms to
be “weaponized”
CRITERIA FOR BIOLOGICAL THREATS TO HUMANS BASED ON
o
o
o
o
Public health impact – ability of hospitals and clinics
to handle the casualties
Delivery potential – how easily the agent can be
introduced into the population
Public perception – effect of public fear on the ability
to control an outbreak
Public health preparedness – existing response
measures
CRITERIA FOR ASSESSING BIOLOGICAL THREATS TO LIVESTOCK AND
POULTRY
o
o
Criteria used are similar to those used to evaluate potential
threats to humans
Include agricultural impact, delivery potential, and plausible
deniability
CRITERIA FOR ASSESSING BIOLOGICAL THREATS TO AGRICULTURE
CROPS
o
o
Plant diseases are generally not as contagious as animal or
human diseases
Criteria based on the predicted extent of crop loss, delivery and
dissemination potential, and containment potential
KNOWN MICROBIAL THREATS
o
Various microorganisms are currently considered threats as
agents of bioterrorism
o
Three types
o Human pathogens
o Animal pathogens
o Plant pathogens
Disease
Agent
Natural
Source
Smallpox
Variola major
(orthopoxvirus)
Rodents
Anthrax
Bacillus anthracis
Soil
Plague
Yersinia pestis
Rodents
Tularemia
Francisella tularensis
Rodents
Botulism
Clostridium botulinum
toxin
Soil
Order of
Concern
Category A
Threats:
Highest
Priority
Category A
Threats:
Highest
Priority
Category A
Threats:
Highest
Priority
Category A
Threats:
Highest
Priority
Category A
Threats:
Highest
Priority
Viral
hemorrhagic
fevers
Various viruses (e.g.,
Ebola, Marburg)
Rodents,
arthropods
Glanders
Burkholderia mallei
Horses
Melioidosis
Burkholderia
pseudomallei
Soil, water
Psittacosis
Chlamydia psittaci
Birds
Q fever
Coxiella burnetii
Livestock,
ticks
Ricin toxin
Ricinus communis
Castor
beans
Staphylococcal
enterotoxin B
Staphylococcus
aureus
Food
Typhus fever
Rickettsia prowazekii
Lice
Viral
encephalitis
Various viruses (e.g.,
Venezuelan equine
encephalitis, Eastern
equine encephalitis)
Various agents (e.g.,
Cryptosporidium,
Giardia)
Various agents (e.g.,
Salmonella, E. coli)
Mosquitoes
Water safety
threats
Food safety
threats
Water
Food
Category A
Threats:
Highest
Priority
Category B
Threats:
Moderate
Category B
Threats:
Moderate
Category B
Threats:
Moderate
Category B
Threats:
Moderate
Category B
Threats:
Moderate
Category B
Threats:
Moderate
Category B
Threats:
Moderate
Category B
Threats:
Moderate
Category C
Threats:
Low Risk
Category C
Threats:
Low Risk
ANIMAL PATHOGENS
o
o
o
Divided into categories based on level of danger
Some agents could potentially amplify an outbreak by infecting
wild animal populations in addition to livestock
Foot-and-mouth disease (FMD) is the most dangerous of the
agents
o It affects all wild and domestic cloven-hoofed animals
PLANT PATHOGENS
o
o
Most potential agents are fungi
o Their dissemination could easily result in contamination of
soils
All agents are naturally present so detecting the difference
between a natural outbreak and an intentional attack would be
difficult
DEFENSE AGAINST BIOTERRORISM
o
Much can be done to decrease the chances of a biological attack
or to limit its scope once it occurs
o
Depends on coupling surveillance with effective response
protocols
o
Agroterrorism is a concern because there is very little security
protecting the nation’s agricultural enterprises
o
o
o
Livestock and poultry are often moved around the
country without being tested for disease
Many agricultural facilities are open to the public
Screening of animals as well as restricting public access
to agricultural facilities could help defend against
agroterrorism
THE ROLES OF
BIOTERRORISM
o
GENETIC
TECHNOLOGY
IN
Could be used to create new biological threats or modify
existing ones
o
o
o
RECOMBINANT
Traits of various agents could be combined to create novel
agents for which no immunity exists in the population
Terrorists, in theory, could make their own microbes
Could be used to thwart bioterrorism
o
o
o
Scientist can identify unique genetic sequences that may
aid in tracking biological agents and determining their
source
Genetic techniques could help develop vaccines,
treatments, and pathogen-resistant crops