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260 summer 2016
pathogenesis
Clicker questions about viral replication
• Which viruses can use the host’s replication
enzymes to make new genomes
• Which viruses have a genome that can be
directly used as an mRNA
• Which viruses require a RNA-dep RNA pol
• Which viruses need to carry the RNA-dep RNA
pol in the capsid
• Reverse transcriptase uses a ____ template to
make ____
A = DNA
all RNA
virusesC =C RNA
= all 
RNA
viruses except
retroviruses
DNAviruses

DNA BBB === dsRNA
DNA
virus
RNA
DNA
 not
RNA
AA==dsDNA
virus
C = “+”sense
RNA CD == RNA
“-”sense
RNA E= retrovirus
D=retroviruses only
About PCR
• Compare replication to PCR
• 1. list the things you need (reagents, enzymes)
for replication and in what order
• 2. list the things you put into your PCR tube
(reagents, enzymes).
• 3. compare – for the things in replication that
are missing in the PCR tube, what did you add
to fill that missing role?
The study of disease
Pathogenesis – the study of disease progression
Next class – epidemiology we’ll study disease
again but from a public health perspective
Pathogenesis (chapter 16)
Principles of disease aka
The Chapter of Many Definitions
Why do care?
• What specific agent causes disease
• How does the agent cause disease in the body
• How infectious agents are spread
A brief history
• Diseases and plagues attributed to
supernatural forces, incurable and terrifying
• Observation: disease seems to be
communicable
• 1600s there are microbes
• 1800s Microbes cause disease
• Robert Koch (German physician 1843-1910) –
systematic proof of causative agent
Koch’s Postulates
1. The same pathogen must be present in every case
of the disease
2. The pathogen must be isolated from the diseased
host and grown in pure culture
3. The pathogen from the pure culture must cause
the disease when it is inoculated into a healthy,
susceptible lab animal
4. The pathogen must be isolated from the inoculated
animal and must be shown to be the original
organism
Koch’s Postulates
Obtain pure culture of the organism
Same organism is present
in every case of the disease
Pure culture used to infect healthy
lab animal causes the disease
Figure 14.3
Koch’s Postulates
Organism cultured from infected animal is identical to original infection
Figure 14.3
Koch’s Postulates
• Koch's postulates can be used to prove the cause
of an infectious disease..
• But can Koch’s postulates be used to identify the
agent/microbe responsible for all diseases?
– Some pathogens can cause several disease conditions
– Some pathogens cause disease only in humans
– Some pathogens are not easily cultivated
Pathology, Infection, and Disease
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Pathology: The study of disease
Etiology: The study of the cause of a disease
Pathogenesis: The development of disease
Infection: Colonization of the body by pathogens
Disease: An abnormal state in which the body is not
functioning normally
Normal Microbiota and the Host
• Transient microbiota may be present for days,
weeks, or months then disappear
• Normal microbiota permanently colonize the host
• Symbiosis is the relationship between normal
microbiota and the host
Representative Normal Microbiota
Figure 14.1
Is this bad news?
Symbiosis
• In commensalism, one organism benefits, and the
other is unaffected
• In mutualism, both organisms benefit
• In parasitism, one organism benefits at the expense
of the other
• Some normal microbiota are opportunistic
pathogens such as?
Normal Microbiota on the Human Body
Table 14.1
What is the role of normal microbiota?
Normal Microbiota and the Host
• Microbial antagonism is a competition between
microbes.
• Normal microbiota protect the host by
– Occupying niches that pathogens might occupy
– Producing waste eg. acids
– Producing bacteriocins
• Probiotics: Live microbes applied to or ingested into
the body, intended to exert a beneficial effect
Effect of antibiotics
• Why are you at risk of a yeast infection or
bacterial GI illness after taking antibiotics?
Principles of disease
• Symptom: A subjective change in body function that
is felt by a patient as a result of disease
• Sign: An objective change in a body that can be
measured or observed as a result of disease
• Syndrome: A specific group of signs and symptoms
that accompany a disease
For example
• You catch a respiratory virus
• You feel tired, have a headache, your sinuses
itch, you have a sore throat
• The doctor finds swollen lymph nodes, notes
an elevated body temperature and views
redness in your throat and nasal passages
• What are the symptoms, signs
• How are the signs and symptoms related to
the concept of a syndrome
The Stages of a Disease
Figure 14.5
Development of disease
• Incubation period – from transmission to first
symptoms
• Prodromal period – early mild symptoms
• Period of illness – period of severe symptoms
• Period of decline – number of pathogens
declines (may overlap with severe symptoms)
• Period of convalescence (numbers continue to
drop; mild or no symptoms)
For example
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10/8 – your partner sneezes on you
10/10 – sore throat
10/12 – liquid goo phase, sneezing, fever
10/17 – back to salsa dancing!
Give the dates of the incubation period,
prodromal period and period of illness
Severity or Duration of a Disease
• Acute disease: Symptoms develop rapidly
• Chronic disease: Disease develops slowly
• Subacute disease: Symptoms in between acute and
chronic
• Subclinical disease: infection without noticeable
symptoms
• Latent disease: Disease with a period of no
symptoms when the causative agent is inactive
Order of disease
• Primary infection: Acute infection that causes the
initial illness
• Secondary infection: Opportunistic infection after a
primary (predisposing) infection
For example
• 1. a few weeks after the salsa dancing success,
you find you have a bacterial sinus infection
• 2. a patient with HIV develops thrush
Types of infection
• Local infection: Pathogens are limited to a small
area of the body
• Systemic infection: Microbe or toxins spread
throughout the body by the blood/lymph
• Focal infection: Infection that began as a local
infection spreads via the blood/lymph
Spread of disease – inside the body
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Bacteremia: Bacteria present in the blood
Toxemia: Toxins present in the blood
Viremia: Viruses present in the blood
Septicemia: “blood poisoning” - systemic infection
arising from multiplication of pathogens in the blood
Question
• What’s the difference between bacteremia
and bacterial septicemia
• What’s the difference between bacteremia
and toxemia
Spread of disease – in the population
• Communicable disease: A disease that is spread
from one host to another
• Contagious disease: A disease that is easily spread
from one host to another
• Noncommunicable disease: A disease that is not
transmitted from one host to another – SUCH AS??
For example
• Determine whether these are communicable
or not and if so, are they contagious
• HIV
• Influenza
• Botulism
Mechanisms of Pathogenicity
• Pathogenicity: Ability to cause disease
• Are all microbes pathogens?
• Virulence: The extent of pathogenicity
– ID50: Dose that causes infection in 50% of population
– LD50: Dose of toxin that is lethal for 50% of test
population
Questions
• For a given microbe, is the ID50 the same in
every situation?
• Which is less likely to cause disease – a
microbe with a higher ID50or lower ID50?
Toxins
Toxin
Botulinum
Shiga toxin
Staphylococcal enterotoxin
LD50
0.03 ng/kg
250 ng/kg
1350 ng/kg
Which organism has the most potent toxin??
reservoirs
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What do you think?
Human
Animal (zoonotic)
Environment
Carrier – human without symptoms
For example
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What is the reservoir for
HIV
Rabies
Mycobacterium tuberculosis
Clostridium botulinum
Modes of transmission
• Direct contact transmission – touch
• Indirect contact transmission - fomite
• Vehicle transmission – a vector brings the
pathogen
– Mechanical vector (rides the roof)
– Biological vector (rides inside)
question
• What is the reservoir for malaria
• What kind of transmission is it?
– Direct contact, indirect contact, zoonotic,
mechanical vector, biological vector
– More than one right answer
Portals of Entry
• Preferred route of entry
– Some have multiple routes (e.g. Yersina pestis causes
plague; B. anthracis causes anthrax)
– Other routes may not cause disease (e.g. Salmonella typhi
on skin; Streptococci pneumoniae that are ingested)
Portals of Entry
• How do microbes get into your body?
• Mucous membranes
– GI tract, respiratory tract most common
– Genitourinary tract, conjunctiva (membrane of eyes)
• Skin
– Major barrier to entry, mostly inaccessible to pathogens
– Some openings: hair follicles, sweat gland ducts
– Hookwork larvae can bore through skin; some fungi grow
on keratin
• Parenteral route
– Penetration of skin /mucous membranes
(punctures, cuts, bites, etc.)
Bacillus anthracis
Portal of Entry
Skin
ID50
10–50 endospores
Inhalation
10,000–20,000 endospores
Ingestion
250,000–1,000,000
endospores
Which portal is most likely to cause infection??
So for example
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Plasmodium (malaria) – what route?
C botulinum (botulism) – what route?
Influenzavirus – what route?
HIV (AIDS) – what route?
Bacillus anthracis (anthrax) – what route?
Why are these routes different?
biofilms
• ~65% of infections
– Dental plaque
– Implants
– Contact lenses
Adherence
capsules
• Can prevent phagocytosis – make cells
“invisible”
Alveolar macrophage attacking E. coli; RBC at top left
Capsules
• Capsules prevent phagocytosis
– Streptococcus pneumoniae; Haemophilus influenzae;
Bacillus anthracis
– Often avirulent without capsule since phagocytosed
(eg S. pneumoniae)
– Note - many nonpathogenic bacteria also produce capsules
(capsulation alone is not sufficient to designate a pathogen)
Alveolar macrophage attacking E. coli; RBC at top left
Cell Wall Components
– M protein resists phagocytosis
• Surface of fimbriae
 Streptococcus pyogenes (strep
throat, scarlet fever, TSS)
– Opa protein inhibits T helper cells
• fimbriae
 Neisseria gonorrhoeae
– Mycolic acid resists digestion
 Waxy lipid where?
 Mycobacterium tuberculosis
Hijacking host Cytoskeleton
Cytoskeleton filament - actin
Microbes (e.g. Salmonella; E. coli) produce invasins
that rearrange actin filaments of cytoskeleton 
membrane ruffling, penetration of cell
Some species use actin to propel themselves
through and between cells (e.g. Shigella; Listeria;
Ricksettia)
Membrane Ruffling
Invasins: alters host actin to enter host cell eg.Salmonella
Figure 15.2
Comet tails
Some bacteria organize actin behind them for propulsion
eg.Listeria, Shigella, Ricksettia
Damage to Host Cells
• Consumption of host’s nutrients
• Direct damage in vicinity of invasion
• TOXINS  blood/lymph  distant sites
Consumption of host nutrients
• Lack of iron limits bacterial growth
• Secrete siderophores to capture
• Take up from blood; some lyse cells
to release
Direct damage
• Disrupt host cell function
• Release wastes
• Rupture  release more viruses/bacteria
Human Herpes Virus 6 budding off
Toxins
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Toxin: Substance that contributes to pathogenicity
Toxigenicity: Ability to produce a toxin
Toxemia: Presence of toxin in the host's blood
Toxoid: Inactivated toxin used in a vaccine
Antitoxin: Antibodies against a specific toxin
All about toxins
• May be transported by blood or lymph
what is the important implication?
• May  fever, diarrhea, shock, cardiovascular and
nervous system disruption
• ~220 known types; ~40% damage cell membranes
• Two general types:
Exotoxins
Endotoxins
What do you think the difference is?
Exotoxins and Endotoxins
Proteins produced by bacteria and
secreted or released following lysis
Lipid A of lipopolysaccharides (LPS) of
outer membrane of Gram negatives
Figure 15.4
Exotoxins
• Specific for a structure or function in host cell
Figure 15.4a
Naming exotoxins
• By type of cell affected
– (e.g., neurotoxins, cardiotoxins, hepatotoxins,
leukotoxins, enterotoxins, cytotoxins)
– What does each affect?
• By associated disease
– (e.g., diphtheria toxin, tetanus toxin)
– What disease is associated with each toxin?
• By bacterium producing
– (e.g., botulinum toxin, Vibrio enterotoxin
– What organism produces each of these toxins?
What are exotoxins, really?
Proteins, usually enzymes  even small amounts harmful
1 mg botulinum exotoxin can kill 1 million guinea pigs
Genes usually carried on ?plasmids, phage – WHY??
Soluble in host fluids  transported widely
What are exotoxins, really?
Proteins, usually enzymes  even small amounts harmful
1 mg botulinum exotoxin can kill 1 million guinea pigs
Genes usually carried on ?plasmids, phage
Soluble in host fluids  transported widely
Mode of action– 3 main modes
Inhibit metabolism (usually protein synthesis)
Destroy parts of host cells
overactivate immune system
What are exotoxins, really?
Proteins, usually enzymes  even small amounts harmful
1 mg botulinum exotoxin can kill 1 million guinea pigs
Genes usually carried on ?plasmids, phage
Soluble in host fluids  transported widely
Mode of action
Inhibit metabolism (usually protein synthesis)
Destroy parts of host cells
overactivate immune system
Types
A-B
membrane-disrupting
superantigen
Exotoxin type: A-B Exotoxin
eg. diptheria,
botulinum,
tetanus,
vibrio (cholera)
Two parts – A and B, proteins
B (binding) – binds host receptor
A-B enter
A and B separate
A – enzyme,
usually inhibits
protein synthesis
Figure 15.5
Membrane-Disrupting exotoxin
Lyse host’s cells in one of two ways
 Making protein channels in the plasma membrane
– Leukocidins
Why is this bad?
– Hemolysins
– Streptolysins (b-hemolysis Streptococcus)
 Disrupting phospholipid bilayer
– Phospholipases remove polar head –gas gangrene (C. perfringens)
Exotoxin type: Superantigens
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Evoke intense immune response
Proliferation T cells (lymphocytes)  excess cytokines
Symptoms: fever, nausea, vomiting, diarrhea, shock, death
Eg. Staphylococcus (food poisoning, toxic shock syndrome)
Last words about exotoxins
Exotoxins are disease specific
Due to exotoxin, not bacterial infection
foodborne intoxication
botulism, staphylococcal food poisoning
Fighting exotoxins
Body makes antibodies (antitoxins)  provide immunity
Inactivate (heat, HCHO, iodine)  toxoids
Toxoids used as vaccine to stimulate antibody production
tetanus, diphtheria
Endotoxins – part of the cell
• Part of outer membrane of Gram-negatives
– Lipid portion of LPS, called lipid A
– Death and lysis of bacteria; antibiotics can worsen
• Stimulate macrophages -release high level cytokines
– Fever, nausea, vomiting, diarrhea, sometimes shock, death
(similar to but not as potent as superantigen exotoxins…)
Remember this?
Endotoxins and the Pyrogenic Response
Figure 15.6
Damage to Host Cells
Exotoxin
Source
Relation to microbe
Chemistry
Neutralized by antitoxin?
LD50
Gram?
?made/part of
What kind of molecule?
Y/N?
Need a little or a lot?
Figure 15.4a
Exotoxin
Source
Relation to microbe
Chemistry
Neutralized by antitoxin?
LD50
Mostly Gram +
Made by growing cell
Protein
Yes
Small
Figure 15.4a
Endotoxins
Source
Gram?
Relation to Microbe
Made/part?
Chemistry
Molecule?
Neutralized by Antitoxin?
LD50
Y/N?
How much you need?
Figure 15.4b
Endotoxins
Source
Relation to Microbe
Chemistry
Neutralized by Antitoxin?
LD50
Gram
Outer membrane
Lipid A
No
Relatively large
Figure 15.4b
Horizontal transmission
• Where do bacteria get their toxin genes?
Horizontal transmission
• Transformation
• Conjugation
• Transduction
A word about plasmids
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Circular small DNA containing 4-5 genes
What did we just transform into E. coli in lab?
What genes were on that plasmid?
DIAGRAM WHITE BOARD
Many antibiotic resistance genes are transmitted between
species by sharing plasmids
– Transformation and conjugation
Plasmids can code for
• Antibiotic resistance genes
– An example from lab?
• Metabolic enzymes
– Examples from this class?
• AND toxins
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Tetanus neurotoxin
Staphylococcal enterotoxin
Dextransucrase (Streptococcus mutans  tooth decay)
Adhesins and coagulase (Staphylococcus aureus)
Fimbria (Enteropathogenic E. coli)
Other ways to get toxins: transduction
• Lysogenic conversion: prophage in chromosome
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Shiga toxin of E. coli O157
Virbrio enterotoxin of Vibrio cholerae (cholera)
Botulinum neurotoxin
Capsule of Streptococcus pneumoniae (virulence factor)
Diphtheria toxin
Exotoxins due to Lysogenic Conversion
Exotoxin
Corynebacterium
diphtheriae
A-B toxin
Streptococcus
pyogenes
Membrane-disrupting
erythrogenic toxin
Clostridium botulinum
A-B toxin; neurotoxin
C. tetani
A-B toxin; neurotoxin
Vibrio cholerae
A-B toxin; enterotoxin
Staphylococcus
aureus
Superantigen
Pathogenicity of Viruses
• Gain entry via attachment sites for cell receptors
• Resulting damage termed cytopathic effects
– Production of virus particles (inclusion bodies)
– Inhibition of biosynthesis (DNA, RNA, protein synthesis)
– Host cell lysis
Inclusion body in brain tissue of rabies victim
Cytopathic effects
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Cause lysosomes to release enzymes
Cause cells to fuse into syncytium
Changes in host cell function
Production of interferon
Chromosomal damage
Loss of contact inhibition
Syncytium (giant cell) caused by measles virus
Pathogenic Properties of Fungi
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May cause disease, but usually lack toxins
Fungal waste products may cause symptoms
Chronic infections provoke an allergic response
Proteases
– Candida
• Capsule prevents phagocytosis
– Cryptococcus (meningitis)
Exceptions - Fungal toxins
• Ergot toxin - hallucinations
– Claviceps purpurea
• Aflatoxin (peanut butter)
– Aspergillus
• Mycotoxins (mushrooms)
– Neurotoxins: Phalloidin, amanitin
– Amanita phalloides
Pathogenic Properties of Protozoa
• Presence of protozoa
• Protozoan waste products may cause symptoms
• Avoid host defenses by
– Growing in phagocytes
– Antigenic variation
Plasmodium
• What disease?
• reproduction in host cells
Giardia
• Giardia lamblia (diarrhea) –
digest cells and tissue fluids
Trypanosomes
• African trypanosomiasis – sleeping sickness
• Chagas disease (US)
• reproduction inside host
Helminths
• Use host tissue and resources
• Interfere with host function
• Waste can cause symptoms
Algae
• A few species produce toxins
• Paralytic shellfish poisoning – “red tide”
– Dinoflagellates
– Saxitoxin
Portals of Exit
• Why do we care how the pathogen gets out?
Portals of Exit
• Important in spread of disease (epidemiology)
• Respiratory tract
– Coughing and sneezing
• Gastrointestinal tract
– Feces and saliva; “oral-fecal”
• Genitourinary tract
– STDs, urine
• Skin
– Wound infections; drainage
• Blood vectors important
– Biting arthropods and needles or syringes
Mechanisms of Pathogenicity
Figure 15.9