Microbiology of the GIT , Abdallh dwayat.pdf

Bacterial Infections- DigestiveSystem
Gram-Negative RodsRelatedtothe
EntericT
ract
Lecture15+16
Required Chapters:
1.Chapter 18
2.Viral infections (40,41)
3.Chapter 73
In addition to parasitology and mycology lectures by Dr.Ibrahim
Resources used in this file:
1.Review of medical
microbiology and immunology.
2.First Aid
3.Dr.Murad Lecture
Modified by: Abdallah
Dwayat

Gram-Negative Rods
Gram-Negative Rods are classified into three major groups:
1.Gram-Negative Rods related to respiratory tract, such as: Haemophilus, Bordutella.
2.Gram-Negative Rods related to Enteric Tract (Our lecture).
3.Gram-Negative Rods from animal sources (zoonotic), such as: Yersinia, Brucella.
What are the major clinical manifestations related to Enteric infections?
• Diarrhea (Bloody Diarrhea, or non-bloody Diarrhea(Watery Diarrhea), (Acute Diarrhea or
chronic diarrhea).
• Vomiting
• Dysphagia
• Abdominal pain, abdominal cramps
• Constipation
It is important to analyze these manifestations to reach definitive diagnosis.

Gram-Negative Rods
E.Coli: is related to non-bloody diarrhea, in special strains it is related to bloody diarrhea.
Shigella: Bloody Diarrhea (Mesentery infection)
Vibrio Cholera: Loss of large amounts of fluids, can lead to severe hypotension. (Rice Water
stool).
Gram-Negative Rods related to Enteric Tract can be classified into three major groups(depending
on site of the disease):
1. Pathogens that produce symptoms within or outside GI tract. (ex: E.coli, salmonella)
E.Coli can produce diarrhea, UTI, septicemia, neonatal meningitis.
2. pathogens that produce disease primarily within the enteric tract(Shigella, Helicobacter,
Campylobacter, Vibrio Cholera)
Helicobacter such as H.Pylori, Campylobacter such as: Campylobacter jejuni.
3.Pathogens that produce disease outside GI tract only(Klebsiella, Enterobacter)
Klebsiella, Enterobacter, which can cause pneumonia, Enterobacter can also cause UTI
Proteus is one of the most common of UTI
It is important to know the causative agent in order to know if we should administer
antibiotics, or give fluids and electrolytes only.

Gram-Negative Rods
• Enteric bacteria
• Repiratory bacteria
• Animal source bacteria

Enteric Bacteria
• Related to enteric tract:
-Pathogens both within and outside the
enteric tract
- Pathogens within the enteric tract
- Pathogens outside the enteric tract
• Lactose fermentation by Enteric rods depends on the type of
organism, for example: Salmonella and Shigella are non-
lactose fermenters, while E.Coli is a Lactose Fermenter.
• Facultative anaerobes include: E.Coli, Salmonella, Shigella.
• All Enteric Rods are Glucose Fermenters.

Clinical Case
A previously healthy 11- year old girl develops a
gastrointestinal infection with cramping and
watery stools. After several days, she begins to
pass blood per rectum, and is hospitalized for
dehydration. In the hospital, she is noted to have
decreasing urine output with rising blood urea
nitrogen (BUN). Total blood count reveals anemia
and thrombocytopenia, and the peripheral smear
is remarkable for fragmented red cells.

Clinical Case
Your patient is a 35-year-old woman who returned
from travelling in Eastern Europe 1 week ago.
While on the trip, she experienced anorexia,
nausea but no vomiting, and abdominal bloating.
For the last two days, she has had explosive
watery diarrhea. An examination of her stool
revealed pear shaped, flagellated, motile
organisms.

Note regarding cases
• First Case is related to a bacterial infection.
• Second case is related to a parasitic infection.

Enterobacteriaceae
• Enterobacteriaceae= Enteric Gram-Negative
Rods.
• Large family
• Gram-negative rods.
• There are general or major features for all Enterobacteriaceae
that distinguish them from other families.
• Facultative Anaerobes, Oxidase negative (they don’t
have ability to produce Cytochrome C, unlike P.Aeurogenosa,
which is one of the most common causes of UTI and Oxidase
+ve).
• Enterbacteriaceae can reduce nitrate to nitrite
• Found in colon of humans and other animals.

Enterobacteriaceae
• Escherichia – Salmonella (produce disease inside
or outside GI Tract).
• Shigella - Vibrio – Campylobacter –
Helicobacter (Produce disease only
inside GI Tract)
• Klebsiella - Enterobacter – Serratia – Proteus
(Produce disease only outside GI tract)
• Serratia is an important cause of pneumonia
especially in hospitalized patients. May cause UTI.
• Proteus is one of the most common causes of UTI.

Enterobacteriaceae
General Characteristics
• All facultative anaerobic
• All ferment glucose
• Oxidase negative
• Reduce nitrates to nitrites

Pathogenesis
• There are three important antigens for pathogenesis:
• Somatic or O Cell wall antigen is the outer polysaccharide portion of
lipopolysaccharide.
• H antigen is on the flagellar protein (important for establishment of infection, and
important in identification, such as using specific antiserum against H Antigen of
Salmonella).
 Only Flagellated bacteria have H Antigen.
 Because they have Flagella, E.Coli and Salmonella are
1. Motile.
2. Have H antigen.
 Klebsiella and Shiglella lack Flagella, so:
1. They are non-motile.
2. Lack H antigen
• The capsular or K polysaccharide (important in establishment of UTI by E.Coli, or
neonatal meningitis).
• Some Enterobacteriaceae may have all of these of antigens, or one or two of them
only.

Pathogenesis
• All members of the Enterobacteriaceae, being gram-
negative, contain endotoxin in their cell walls.
• Some of them have (Exotoxins):
 E.Coli has different exotoxins (heat stable or heat labile).
 E.Coli and V.Cholera produce Exotoxins called Enterotoxins.
 Mechanism of Action: Activation of adenylate cyclase
within the cells of the small intestine, causing diarrhea)
 Shiga toxin (found in Shigella and E.Coli).
 Shiga toxin of E.Coli O157 produces Hemolytic-Uremic
Syndrome

Laboratory Diagnosis
• Specimens suspected of containing members of the
Enterobacteriaceae and related organisms are usually inoculated onto
two media, a blood agar plate and a selective differential medium.
1. Blood agar plate
2. Mackonkey`s Agar or Eosin methylene blue (EMB).
 Eosin Methylene Blue is selective and differential.
 Mackonkey’s Agar is both selective and differential.
 Selective: suppresses unwanted gram-positive organisms.
 How? By bile salts or bacteriostatic dyes in the agar.
 The differential ability: is based on lactose fermentation.
• Triple sugar iron TSI: Differentiates between Gram-Negative enteric bacteria.

• On Differential Media (which differentiates based on Lactose
Fermentation):
 the non–lactose fermenters (e.g., Salmonella and Shigella) form
colorless colonies.
 whereas the lactose fermenters (e.g., E. coli) form colored colonies.
MacConkey Agar:
• Notice that Lactose Fermenting
Bacteria formed colored(pink)
colonies, while non-lactose
fermenting bacteria appeared
colorless (Differential Ability).
 Crystal Violet and Bile salts inhibit
the growth of Gram-Positive
bacteria.

• On Differential Media (which differentiates based on Lactose
Fermentation):
 the non–lactose fermenters (e.g., Salmonella and Shigella) form
colorless colonies.
 whereas the lactose fermenters (e.g., E. coli) form colored colonies.
Eosin Methylene Blue:
 This media is both selective and differential.
 On EMB agar, E. coli colonies have a
characteristic green sheen.
 The figure shows the growth of E.coli on EMB
agar.

• Triple Sugar Iron Media:
• TSI contains three sugars: glucose, lactose, sucrose, and Ferrous sulfate.
• The medium in the tube consists of two parts
1. Butt
2. Slant (Angled)
A
• The organism is inoculated into the butt and across the surface of the slant.
• There is a phenol red indicator.
• There are four possible results to this test:
1. Production of yellow color in both the butt and slant.
2. Red butt, red slant.
3. Yellow butt, red slant
4. Black Color
 General Rules:
1. If there a sugar fermentation, then there will be acid production, and change of the phenol red indicator
from red to yellow.
2. If there is no fermentation, then the color of the tube will remain red.
3. Color of Butt and Slant after fermentation depends on fermented sugar.
 If Lactose (or sucrose) are fermented, then butt and slant will change to yellow color.
 If glucose is the fermented sugar, only the butt will turn yellow.
Item Butt Slant
Site Bottom Top
Oxygenation Poorly Oxygenated Well-Oxygenated

TSI Media
Note: Glucose is present in 110 the concentration of the other two sugars.

TSI Media
• Bottom part is the butt, upper angular part is the slant.
• In A, B, C, there is acid production.
• In A and B: The fermented sugar is Lactose (or sucrose). Why? Because the color of both the
butt and slant turned yellow.
• In C: The fermented sugar is glucose, because only the butt color turned yellow.
• In D: There is production of Hydrogen sulfide (H2S) which produces the black color.
• In E: There is no sugar fermentation, because the color of the butt and slant did not change.
What is the difference between A and B?
• The production of Gas, which produced bubbles in the butt.
• Black Color means that H2S was produced, and Ferrous sulfate was converted into Ferrous
sulfide.

TSI Media
• E.Coli is a Gram-Negative rod, that appears on laboratory tests as the following:
1. MacConkey Agar: Pink Colonies (Lactose Fermenter)
2. EMB: Characteristic Green Colonies.
3. TSI: Yellow color in both the butt and slant, and there is gas production, so there will be
bubbles, but no H2S is produced.
• Salmonella is a Gram-Negative Rod, that appears on laboratory tests as the following:
1. MacConkey Agar: Colorless(non-lactose fermenter)
2. EMB: Colorless(non-lactose fermenter)
Remember that:
1. Alll Enterobacteriaceae ferment glucose, which produces yellow butt, red slant appearance
2. Lactose fermentation depends on the type. E.Coli ferments lactose, Salmonella and Shigella
do not.

• Antibiotic sensitivity test:
It is important to perform antibiotic sensitivity test, because generally
enteric bacteria are resistant to penicillin, because of beta-lactamase
production.
The specific choice usually depends on the results of antibiotic
sensitivity tests.
• Different antibiotics can be used: Fluoroquinolones,
Sulfamethoxazole and Trimethoprim (Folic Acid Synthesis
inhibitors), or combination of antibiotics, when treating H.Pylori
(Causative agent of peptic ulcer) for example.
• Highly antibiotic resistant: Due to B-Lactamase
production.
• Using of antibiotics also depend on severity and type of organism.
Antibiotic Therapy

E.Coli can cause:
1. Enterotoxin-mediated disease (Enterotoxigenic E.Coli that produces heat
labile or heat stable toxin).
2. Invasive inflammatory disease.
 Enterotoxin mediated disease causes watery diarrhea.
 Invasive E.Coli causes Hemolytic-Uremic Syndrome.
• In Enterotoxin-mediated disease: No Leukocytes in stool.
• In Invasive-inflammatory disease: there are leukocytes in stool.
• E.Coli 0157:H7 is a hemorrhagic strain. H7=flagellar antigen.

Heat Labile Enterotoxin of E.Coli
 The Enterotoxin of E.Coli is an A-B Exotoxin.
 Binding subunit is responsible for binding the exotoxin to specific receptors on the
membrane of the human cell.
 Main Mode of Action: The heat-labile toxin (LT) acts by stimulating adenylate cyclase.
 Both LT and cholera toxin act by catalyzing the addition of adenosine diphosphate-ribose (a
process called ADP ribosylation) to the G protein that stimulates the cyclase.
 This irreversibly activates the cyclase.
 The resultant increase in intracellular cyclic adenosine monophosphate (AMP) concentration
stimulates cyclic AMP–dependent protein kinase.
 cyclic AMP–dependent protein kinase phosphorylates ion transporters in the membrane.
 The transporters export ions, which cause an outpouring of fluid, potassium, and chloride
from the enterocytes into the lumen of the gut, resulting in watery diarrhea.
 Note that cholera toxin has the same mode of action.

Heat Labile vs Heat Stable Enterotoxin
Item Heat-Labile Toxin Heat-Stable toxin
Stability with heat • Labile(inactivated by
heat)
• which is inactivated at
65°C for 30 minutes.
• Stable
• Polypeptide that is not
inactivated by boiling
for 30 minutes.
Type of cyclase Adenylate Cyclase Guanylyl Cyclase
2nd messenger cAMP cGMP
Main cause of diarrhea  outpouring of fluid,
potassium, and chloride
from the enterocytes
into the lumen of the
gut,
 Inhibits the
reabsorption of sodium
ions and causes
diarrhea.
Type of diarrhea  Watery Diarrhea  Watery Diarrhea
Heat-stable toxin: Polypeptide that is not inactivated by boiling for 30 minutes. The
heat-stable toxin affects cyclic guanosine monophosphate (GMP) rather than cyclic
AMP. It stimulates guanylate cyclase and thus increases the concentration of cyclic
GMP, which inhibits the reabsorption of sodium ions and causes diarrhea.

Non-Lactose fermenters: “SSPPS”
• Salmonella
• Shigella
• Proteus
• Pseudomonas
• Serratia

Pathogens Both within & Outside the
Enteric Tract
E.Coli and Salmonella.
Major Characteristics of E.Coli:
 Normal Flora of the Colon.
 Motile organism, because it has flagella.
 Has the H antigen.
 Glucose Fermenter.
 Lactose Fermenter.
 Appear Pink on MacConkey agar.
 Appear Green on EMB agar.
 Produces yellow butt, yellow slant appearance with bubbles on TSI media.
 Facultative Anaerobic bacteria.
 Can produce enterotoxin-mediated disease, or invasive-inflammatory disease.
 Can produce heat-labile enterotoxin, or heat stable enterotoxin.
 Can cause watery diarrhea, or bloody diarrhea.
 Most common cause of UTI.
 Can cause neonatal sepsis, meningitis.

Escherichia
• E. coli
• UTI
• Neonatal sepsis
• Traveler`s diarrhea
• Enterohaemorhagic e. coli and bloody diarhea

E. coli
• Gram-negative rods
• Lactose fermenter
• Green sheen (characteristic green appearance
on EMB).
• Reservoir of E. coli includes both humans and
animals

E.Coli appearance on MacConkey agar:
• There are three results to enteric rod growth on MacConkey agar:
 Colored colonies, lactose fermenters.
 Colorless colonies, non-lactose fermenters.
 Slow positive, grow slowly.

E.Coli appearance on EMB agar “Green Sheen”:

E. coli
• Pili
• Enterotoxins (non invasive strains, watery
diarrhea
• Verotoxin (haemorrhagic / bloody diarrhea)
• Capsule (meningitis) and endotoxin (sepsis)
“K antigen”.

E. coli
• Pili: Helps the E.Coli in causing UTI.
• Galactose- Galactose Pili.
• Attachment to epithelium of urinary
bladder.
• Colonization in urinary bladder.
 UTI (most common cause of it).
• Uropathic Strains.
• Causes:
1. Cystitis (lower urinary tract infection)
2. Pyelonephritis(upper urinary tract
infection)
WBC in urine
+ve urine culture.

E.Coli
• Escherichia coli is the leading cause of community-acquired urinary tract infections.
• It is also the most frequent cause of nosocomial (hospital-acquired) urinary tract
infections.
• Community-acquired urinary tract infections by E.Coli occur primarily in women.
Why? this finding is attributed to three features that facilitate ascending infection into
the bladder.
1. A short urethra.
2. The proximity of the urethra to the anus
3. Colonization of the vagina by members of the fecal flora.
Nosocomial E.Coli infections occur equally frequently in both men and women and are
associated with the use of indwelling urinary catheters.

• Shiga toxin enters blood stream.
• Reaches renal system.
• Causes rupture of vessels in the kidneys.
 Haemolytic Uremic Syndrome.
• Pili mediates UTI caused by E.Coli.
• Enterotoxin mediate watery diarrhea
caused by E.Coli.
• Capusle (K antigen) mediates Neonatal
meningitis.
• Endotoxin Sepsis.

Treatment and Prevention
• Treatment of E.Coli depends on site of infection (GI
disease or,urinary tract disease, or meningitis).
• Antibiotic therapy is usually not indicated in E. coli
diarrheal diseases. Sometimes Trimethoprim-
sulfamethoxazole are used to shorten time of disease,
also loperamide is used (it reduces GI motility).
• Main intervention in Non-bloody diarrhea caused by
E.Coli: Fluids and Electrolyte replacement.
• Loperamide is contraindicated in Bloody
Diarrhea (increases risk of HUS).
• Antibiotics in case of E.Coli 0157 can increase
risk for HUS.

Treatment and Prevention
• Trimethoprim-sulfamethoxazole
• (Third generation Cephalosporin)+(Aminoglycoside)
For Neonatal Meningitis and sepsis.
• No specific vaccination: no active or passive immunization
against E.Coli
• Urinary tract infections can be classified into:
1. Lower Urinary Tract infection.
2. Upper Urinary Tract infection. (Pyelonephritis can be treated with Ciprofloxacin, or
ceftriaxone)
• In terms of complication:
1. Complicated UTI
2. Uncomplicated UTI. (Uncomplicated Cystitis Give Trimethoprim-Sulfamethoxazole)

Salmonella
• Gram-negative bacteria.
• Shape: Rod-shape
• Oxygen requirement: facultative anaerobic bacteria
• Fermentation: Ferments glucose, does not ferment lactose.
• Salmonellae live in the intestinal tract.
• In humans, Salmonella species cause
1. Salmonellosis: enteric fever (typhoid), resulting from
bacterial invasion of the bloodstream
2. Acute gastroenteritis: resulting from a foodborne
infection/intoxication.
3. Septicemia

Salmonella
Clinically, the Salmonella species are often thought of in two distinct
categories:
1. The typhoidal species (i.e., those that cause typhoid fever).
2. The nontyphoidal species (i.e., those that cause diarrhea [enterocolitis] and
metastatic infections, such as osteomyelitis)
Salmonella are Gram-Negative rods.

Acute Gastroenteritis by Salmonella
 Acute gastroenteritis: resulting from a foodborne infection/intoxication.
• Acute Gastroenteritis: clinical manifestations start after incubation period (12-
48 hours).
• The organisms penetrate both through and between the mucosal cells into the
lamina propria (in small and large intestines), with resulting inflammation and
diarrhea.
• Clinical Manifestations include: Abdominal pain, vomiting, diarrhea.
• Neutrophils limit the infection to the gut and adjacent mesenteric lymph nodes,
and because It is a self-limiting disease, there is no need for antibiotic
administration.
• enterocolitis begins with nausea and vomiting and then progresses to
abdominal pain and diarrhea.
• The infectious dose of Salmonella required is high, at least 100,000 organisms.
• Gastric acid is an important host defense; gastrectomy or use of antacids lowers
the infectious dose significantly.
• Special Care in childhood gastroenteritis, or HIV patients with gastroenteritis.
• In summary: Usually the disease lasts a few days, is self-limited, causes nonbloody
diarrhea, and does not require medical care except in the very young and very old

Enteric Fever(Typhoid) by Salmonella
• infection begins in the small intestine.
• The organisms enter, multiply in the mononuclear phagocytes of Peyer’s patches.
• Then spread to the phagocytes of the liver, gallbladder, and spleen.
Bacteremia
• This causes Fever (probably due to endotoxin).
• Characterized by: Fever, constipation. (maybe diarrhea at the beginning
of the disease).
• Acute Gastroenteritis(self-limiting): no need for antibiotic
administration.
• In enterocolitis, the organism is most easily isolated from a stool sample
• Enteric Fever there is a need for antibiotic administration.
• in the enteric fevers, a blood culture is the procedure most likely to
reveal the organism during the first 2 weeks of illness.
• Can cause intestinal perforation and hemorrhage.

Antigenic Structure
• Salmonella has three kinds of major antigens
with diagnostic or identifying applications
Somatic (O) or Cell Wall Antigens: Somatic
antigens are heat stable and alcohol
resistant
Capsular (Vi)
Flagellar (H) Antigens, important in
identification by using specific antibodies.

Pathogenesis of Salmomella
Infections in Human
• Bacteria enter the human digestive tract, penetrate the
intestinal mucosa (causing no lesion), and are stopped
in the mesenteric lymph nodes
• Bacterial multiplication occurs
• From the mesenteric lymph nodes, viable bacteria and
LPS (endotoxin) may be released into the bloodstream
resulting in septicemia
• Salmonella excretion by human patients may continue
long after clinical cure
• Asymptomatic carriers are potentially dangerous when
unnoticed

Clinical Findings
• S. typhi (Typhoid)
• Onset of illness is slow
• Fever, constipation
• Bacteremia
• Rose spots
• Leukopenia and anemia
• Liver function test: increase in liver enzyems (Alanine
transaminase, Aspratate Transaminase)
• Complications: Intestinal perforation and hemorrhage.

• Enterocolitis
- Invasion
- High infectious dose (large number of organisms to cause disease, in
contrast, shigella has low infectious dose).
-IP 12-48 h, nausea vomiting, abdominal pain and
diarrhea.
• Septicemia, occurs in one of two settings:
1. Chronic disease (sickle cell anemia, cancer).
2. Child with enterocolitis.
 Bacteremia results in seeding of many organs, with osteomyelitis,
pneumonia, and meningitis being the most common sequelae.
 Osteomyelitis in a child with sickle cell anemia is an important example of
this type of salmonella infection

Salmonella growth on
Medias:
On TSI media:
• It Does not ferment lactose or sucrose (no
yellow butt and slant appearance).
• An alkaline slant and an acid butt, frequently
with both gas and H2S (black color in the
butt)
• S. typhi is the major exception.
• It does not form gas and produces only a
small amount of H2S.
On EMB and MacConkey Agar:
non–lactose-fermenting bacteria
(colorless) colonies.

Treatment
• Antibiotics and Anti-motility drugs should not be
used in this case, why?
1. Prolong excretion of the organisms.
2. Prolong duration of symptoms (do not reduce illness).
3. Antibiotics Increase the frequency of the carrier state,
and resistant bacteria.
• Enterocolitis:
1. It is usually a self-limited disease that resolves without treatment.
2. Fluid and electrolyte replacement may be required.
Typhoid fever and septicemia:
 ceftriaxone and ciprofloxacin.

Vaccination Against Typhoid Fever
(1) Oral live-attenuated vaccine
(2) Parenteral heat-phenol-inactivated vaccine
(3)Newly licensed capsular polysaccharide
vaccine for parenteral use
• Remember that:
 E.Coli does not have a specific vaccine.
 Salmonella and E.Coli cause disease within
or outside GI tract.

Pathogens primarily within the
enteric tract
 Shigella
 Vibrio Cholera
 Helicobacter (e.g. Helicobacter Pylori).
 Campylobacter (e.g. Campylobacter Jejuni)
• Note: All Pathogens primarily within enteric tract are
oxidase positive, except for Shigella.

Shigella
• Gram-negative
• Motility: non-motile
• Spore Formation: non- spore forming
• Shape: rod-shaped bacteria
• Lactose Fermentation: non- lactose
fermenting bacteria.
• Hydrogen Sulfide Production: do not produce
H2S
• O antigens in the cell wall [+shiga toxin]
• Shigellosis is an infectious disease caused by
various species of Shigella.
• Human disease only. [No animal reservoir]
No flagella
No H antigen

Pathogenesis & Laboratory Diagnosis
• Very low ID
• Human Disease / fecal – oral (contamination
of food or water)
•Shiga toxins: destruction of intestinal mucosa.
• Blood diarrhea
• Colorless colonies on MacConkey`s - EMB
• Methylene blue stain.
• On TSI: Alkaline Slant, Acidic Butt (ferments
glucose, does not ferment lactose, doesn’t produce H2S)

Pathogenesis
• Incubation period is 1 to 4 days.
• Symptoms begin with fever and abdominal cramps
• Followed by diarrhea, which may be watery at first but later contains blood and
mucus.
• The disease varies from mild to severe depending on two major factors:
1. the species of Shigella.
2. the age of the patient.
 Young children and elderly people being the most severely affected.
 The diarrhea frequently resolves in 2 or 3 days.
 Antibiotics can shorten the course

 There are several vaccines against S.Typhi: live-
attenuated, inactivated, or conjugated.
 No Vaccine against other types of salmonella.
 No vaccine for Shigella.
• Salmonella Typhi can lead to
asymptomatic carrier state.
• Salmonella Typhi produces small
amount of H2S.

Treatment
• Fluid and electrolyte replacement
• Shigellosis can usually be treated with
antibiotics
• Severe Cases: Antibiotics administration, two
cases:
1. Fluoroquinolone sensitive: (ciprofloxacin)
2. Fluoroquinolone resistant:
trimethoprim/sulfamethoxazole

Vibrio
• Gram-negative curved rods (comma-shaped)
• Motile by means of a single polar flagellum
• Most species are oxidase-positive [E.Coli is oxidase-
negative].
• Vibrio cholera
• Acid Labile [large numbers of bacteria must be ingested
because the organism is particularly sensitive to stomach
acid].
 Susceptible individuals:Persons with little or no stomach
acid, such as those:
1. taking antacids.
2. those who have had gastrectomy.

Comma shaped appearance with single
polar flagella.

• V. cholerae and V. parahaemolyticus are
pathogens of humans
• Both produce diarrhea
• V. cholerae is noninvasive
• The pathogenesis of cholera is dependent
on colonization of the small intestine by the
organism and secretion of enterotoxin.

• Transmission to humans: is by water or food
• The natural reservoir of the organism is not
known
• V
. cholerae produces cholera toxin, the model for
enterotoxins, whose action on the mucosal
epithelium is responsible for the characteristic
diarrhea of the disease cholera
• A healthy person may become hypotensive within an
hour of the onset of symptoms and may die within
2-3 hours if no treatment is provided
V.Cholera: Transmission, reservoir,
complications

Pathogenesis
 Choleragen consists of an A (active) subunit and a B (binding) subunit.
 The B subunit, binds to a receptor on the surface of the enterocyte.
 The A subunit is inserted into the cytosol
 A subunit catalyzes the addition of ADP-ribose to the Gs protein (Gs is the stimulatory G
protein).
 This locks the Gs protein in the “on” position, which causes the persistent stimulation of
adenylate cyclase.
 The resulting overproduction of cyclic AMP activates cyclic AMP–dependent protein kinase,
an enzyme that phosphorylates ion transporters in the cell membrane
 resulting in the loss of water and ions from the cell. The watery efflux enters the lumen of
the gut, resulting in a massive watery diarrhea that contains neither neutrophils nor red
blood cells.
 Morbidity and death are due to:
1. dehydration
2. electrolyte imbalance

Clinical findings
• Cholera begins with sudden onset of massive
diarrhea (Rice-Water stool). [Watery diarrhea in
large volumes is the hallmark of cholera]
• There is no abdominal pain, and subsequent
symptoms are referable:
Marked dehydration
• Loss of fluids and electolytes lead to cardiac
and renal failure.

Diagnosis
• Clinical: Water-Rice stool.
• Slow lactose fermenter
• TSI: Acid slant and acid butt
• Oxidase positive
• No gas or H2s production
• Agglutination of organism polyvalent O1 or
non-O1 antiserum (specific antiserum
against O antigen).

Treatment of cholera
• Involves the rapid intravenous replacement
of the lost fluid and ions. (. Glucose is added to the
solution to enhance the uptake of water and electrolytes)
• Tetracyclines may shorten the duration
of diarrhea and reduce fluid loss.
• If treatment is instituted promptly, the
disease runs a self-limited course in up
to 7 days

Prevention
• Public health measures that ensure a
clean water and food supply
• Vaccine (killed or live-attenuated)
• Antibiotics (tetracyclines) to prevent
transmission to close contacts.

Campylobacter
• C. jejuni
• Curved gram negative rods
• Comma or S-shape
• Microaerophilic (grows best in 5% oxygen
rather than in the 20% present in the
atmosphere).

• Found in domestic animals, such as
cattle, dogs, and chickens.
• Types of transmission:
1. Animal to human transmission
2. Human to human transmission
• Fecal oral transmission (food and water
contamination)
• Food and water contaminated with
animal feces are the major sources of
human infection.
Reservoir&Transmission

Clinical Findings
• Enterocolitis
• Starts Watery, foul-smelling diarrhea
(enterotoxin mediated syndrome) followed by:
1. bloody diarrhea
2. Fever
3. abdominal pain
• Guillain Barre syndrome (the most common cause of
acute neuromuscular paralysis. Guillain-Barré syndrome is an
autoimmune disease attributed to the formation of
antibodies against C. jejuni that cross-react with antigens on
neurons).

• Stool culture on Blood agar:
stool specimen is cultured on a blood agar plate containing
antibiotics that inhibit most other fecal flora.
• Sensitive to nalidixic acid (Nalidixic acid is a
quinolone)

Treatment
• Macrolides or Ciprofloxacin
• No vaccine
• Public measures
1. Shigella
2. “Salmonella other than Typhi”
3. Campylobacter
4. E.Coli.
No Vaccine

Helicobacter
• H. pylori
• Curved gram negative rods
• Cause disease only within GI tract
• Urease positive (similar to proteus, unlike E.Coli)
• Can grow in human stomach.[The natural habitat of H. pylori is the
human stomach, and it is probably acquired by ingestion. However, it has not been isolated from
stool, food, water, or animals]
 Helicobacter is urease positive, while Campylobacter
is urease negative.
Item H.Pylori Campylobacter
Site of disease Restricted to GI Restricted to GI
Presence of oxidase Oxidase + Oxidase +
Presence of urease Urease + Urease -

Helicobacter
 Helicobacter is urease positive, while Campylobacter is urease negative.
 H.Pylori attaches to the mucus-secreting cells of the gastric mucosa(mostly in
the antrum).
 It causes two things:
1. Production of large amounts of ammonia from urea by the organism’s
urease.
2. An inflammatory response.
leads to damage to the mucosa.
 Loss of the protective mucus coating predisposes to gastritis and peptic ulcer.
• The ammonia does two things:
1. Damages the Gastric mucosa.
2. Neutralizes stomach acid, allowing the organism to survive.
• MALT lymphomas are: B-cell tumors located typically in the stomach.
• Association between H.Pylori and MALT lymphoma:
• Helicobacter pylori is often found in the MALT lesion.
• The chronic inflammation induced by the organism is thought to stimulate B-
cell proliferation and eventually a B-cell lymphoma.
• Antibiotic treatment directed against the organism often causes the tumor to
regress.

Clinical features
• Can cause mild disease (Gastritis) or severe
disease (peptic ulcer).
• Gastritis
• Peptic ulcer
• Recurrent pain in the upper abdomen
• Bleeding
•No bacteremia or disseminated disease (restricted
to GI tract).
• Gastric Carcinoma and Mucosal-associated
lymphoid tissue (MALT)

• Biopsy specimens (by endoscope), taking a sample from
stomach, then we do a culture on blood agar or MacConkey
agar(this is an invasive procedure)
• Culture
• Urea breath (noninvasive test)
• Antigen in the stool: Test for Helicobacter antigen in the
stool can be used for:
1. Diagnosis.
2. Confirmation that treatment has eliminated the organism.
• IgG antibodies: The presence of IgG antibodies in the patient’s
serum can also be used as evidence of infection.

• The gold standard investigation for confirmation of H.
pylori is esophagogastroduodenoscopy (EGD) with
histopathological examination of the biopsy.
• IgG antibodies: The presence of IgG antibodies in the patient’s serum can also be
used as evidence of infection.
 The antibodies against H. pylori persist for an indefinite period and does not differentiate
past from present infection.
 For the same reason, serological methods are not useful for evaluation of eradication after
completion of treatment.
• Urea breath (noninvasive test):
 Urease is not present in mammalian cell, hence its presence indicates urease containing
microbes.
 H. pylori utilize urease to breakdown urea into ammonia and carbon dioxide (CO2).
1. Radiolabeled urea is ingested
2. If the organism is present, urease will cleave the ingested urea.
3. Radiolabeled CO2 is evolved, goes to bloodstream and is exhaled by the lungs, and then the
radioactivity is quantified and measured in the breath for diagnosis of H.Pylori.

Treatment
• Triple therapy (two antibiotics+ Proton Pump
Inhibitors):
1. Amoxicillin, clarithromycin.
2. Amoxicillin, metronidazole.
• No vaccine
PPI: Omeprazole,
or other PPIs.
• The concept that underlies the choice of drugs is:
1. To use antibiotics to eliminate Helicobacter.
2. A drug to reduce gastric acidity.
• Why do we use two antibiotics?
Because of resistance.

H.Pylori Summary
• Quadruple therapy:
1. Bismuth Subsalicylate.
2. Metronidazole.
3. Tetracycline.
4. Proton Pump Inhibitor.

Bacterial Infections- Digestive
System Gram-Negative RodsRelated
tothe Enteric Tract
Modified by: Abdallah Dwayat
Resources used:
1.Dr.Murad Lecture.
2.Review of Medical microbiology and immunology.
3.First Aid.

Enterobacteriaceae
• Escherichia - Salmonella
• Shigella - Vibrio – Campylobacter –
Helicobacter
• Klebsiella - Enterobacter – Serratia - Proteus

Pathogens Outside the Enteric Tract
• These are enteric rods, but they produce their disease
and clinical manifestations outside the GI tract.
• Klebsiella can cause pneumonia, UTI.
• Pseudomonas: can cause cellulitis, one of the most
common causes of ventilator associated pneumonia.
• Klebsiella is present in large intestine.
• Proteus is one of the most common causes of UTI.

Pathogens outside the enteric tract
• Klebsiella – Enterobacter – Serratia
• Proteus - Providencia – Morganella
• Pseudomonas
• Bacteriodes – Prevotella
• Fusobacterium
• Bacteriodes is the most
common flora of the colon.
• Can cause peritonitis, in case
of ruptured appendix, or
diverticulitis.

Pathogens outside the enteric tract
• Klebsiella – Enterobacter – Serratia
•They are frequently found in the large intestine but
are also present in soil and water.
• Klebsiella pneumoniae has a very large
polysaccharide capsule, which gives its colonies a
striking mucoid appearance.
•Serratia marcescens produces red-pigmented
colonies.
•Klebsiella can cause community acquired and
hospital acquired diseases.
• Serratia and Enterobacter are only related to
hospital acquired diseases. [UTI, Endocarditis..]

K. pneumoniae
• Large intestine, soil and water
• Virulence Determinant:Large capsule (polysaccharide capsule, this gives it the ability
to be an obligatory pathogen, not an opportunistic one).
• Primary nonopportnistic pathogen.
• K.pneumoniae can cause:
1. Hospital-acquired pneumonia 2.Community Acquired pneumonia
• Community Acquired pneumonia especially in cases of:
1. Alcoholism 2.Old age 3.Chronic Respiratory Diseases 4.Diabetes.
• Pneumoniae (thick bloody sputum) necrosis and abscess
• UTI
• Capsule does two things for Klebsiella:
1. Gives it the ability to be an obligatory pathogen(the capsule is antiphagocytic).
2. Gives it the mucoid appearance(colonies) on bacteriological media.
In case of nosocomial infections, K.Pneumoniae can be highly resistant to antibiotics

Diagnosis and treatment
• Lactose fermenter
• EMB [colored
colonies]
• MacConkey [pink]
• Sensitivity test
• Empirical therapy
• It is highly resistant to antibiotics, especially in hospital-acquired
infections.
• Some of its strains produce extended spectrum Beta Lactamases.
Thus it needs longer duration to eradicate the bacteria.
• May require empirical therapy in some cases, until final diagnosis.
Resistant to
almost all known
antibiotics.
An aminoglycoside (e.g., gentamicin) and
a cephalosporin (e.g., cefotaxime) are used
empirically until the results of testing are known.

Proteus
• UTI [2nd most common cause of UTI]
Can cause:
1. Community Acquired infections
2. Hospital Acquired infections
• Gram negative rods
• Produces enzyme phenylalanine deaminase
• Urease positive
• Motile (swarming on blood agar)
• Based on DNA classification:
1. Proteus vulgaris 2.Proteus mirabilis
• Proteus mirabilis is
the species of
Proteus that causes
most community-
and hospital-
acquired infections.

• Human colon, soil and water
• Colonization of the urethra
• Production of enzymes
• Raised pH (stone formation)
• Effect of stone
• Alkaline media (favors growth of bacteria)
• Their tendency to cause urinary tract infections is probably due to their
presence in the colon and to colonization of the urethra, especially in
women.
• This bacteria is “NOH GUMP”:
 Non-lactose fermenter.
 Oxidase Negative.
 H2S production +
 Glucose Fermenter.
 Urease Positive.
 Motile on blood Agar.
 Phenylalanine deaminase +
• Urease Convert Urea into
ammonia and CO2.

Proteus
• Their motility does two things:
1. “swarming” overgrowth on blood agar.
2. may contribute to their ability to invade the urinary tract.
• Cause of stones due to Proteus:
 Proteus is urease +ve, it converts urea into Ammonia and CO2, ammonia elevates
urine PH [alkaline urine] which makes stones called “Struvites”.
• Struvites consist of “MAP”:
Magnesium Ammonium Phosphate.
• Alkaline urine causes two things:
1. Better growth for bacteria.
2. More extensive renal damage& precipitates for stones.
• Struvite Stones cause:
1. Obstruction of urine flow.
2. Damage urinary epithelium.
3. Recurrent infections due to trapping of bacteria within the stone.
treatment involves keeping the
urine at a low pH.

Diagnosis
• Blood agar : highly motile and
produce a “swarming” overgrowth
on blood agar.
• MacConkey or EMB: Colorless, non-
lactose fermenters
• H2S production (black butt) TSI :
Acid butt, alkaline slant due to glucose
fermentation, but also produces H2S, so
there will be black color in the butt.

Treatment
 Treatment should account for three things:
1. Infection.
2. Stones.
3. Urine
 Eradication of the infection:
• Aminoglycoside
• Trimethoprim-sulfamethoxazole
• Cephalosporins.
 Stones:
• Surgical removal of them.
 Urine:
• Acidification of it.
 To minimize renal damage, and bacterial growth.

Pseudomonas Aeruginosa
• Gram negative rods.
• Oxidase positive.
• Strict aerobic bacteria(They derive their energy only by oxidation of
sugars).
• Non-fermenters [Do not ferment Glucose].
• Can cause hospital-acquired or community acquired diseases.
• Infections are primarily in patients with lowered host defenses.
• One of the most common causes of Ventilator associated
pneumonia.[nosocomial infection]
• Sepsis, pneumonia, UTI
• Oxidation of sugar
• Causes infections on top of wounds, and burns.

• In order to cause Hospital-acquired infections,
it must persist in hospital environment.
Able to grow in water containing only
traces of nutreints.
• Prominent slime layer (mucoid appearance)
Item Pseudomonas Enterobacteriaceae
Gram +ve-ve Gram -ve Gram -ve
AerobicAnerobic Strict Aerobic Facultative Anaerobic
Glucose Fermentation Non-fermenters Fermenters
Oxidase +ve-ve Oxidase +ve Oxidase -ve

Pigments
• Two pigments
- Pyocyanin (blue color in
wounds)
- Pyoverdin (yellow-green)
 In the laboratory, these
pigments diffuse into the
agar, imparting a blue-
green color that is useful
in identification.

Clinical findings
• UTI
• Pneumonia (cystic fibrosis):
 Strains of P. aeruginosa isolated from cystic fibrosis patients
have a prominent slime layer (glycocalyx)
 Glycocalyx does two things:
1. Gives their colonies a very mucoid appearance.
2. Mediates adherence of the organism to mucous membranes of
the respiratory tract.
3. Prevents antibody from binding to the organism.
• Wound infections
• Severe external otitis (malignant otitis externa)

Diagnosis and Treatment
• Non-lactose fermenter
• Metallic sheen of the growth on TSI
• Blue-green pigment
• Resistant to many antibiotics
• Treatment of choice: Antipseudomonal penicillin
(ticarcillin, piperacillin) plus aminoglycoside.
• Resistant strains: colistin (polymyxin E) is useful.
• The drug of choice for urinary tract infections is
ciprofloxacin.

Viral Infections- Digestive System
Viruses thatInfect theEntericTract
Resources used:
1. Dr.Murad Lecture
2. Review of Medical Microbiology and Immunology.
3. First Aid.
4. CDC
+ Personal Interpretation.

Introduction
• Transmitted by the fecal-oral route
• Enter the body by via the enteric
tract
•Naked nucleocapsid viruses.
• Norovirus and Rotavirus can cause
diarrheal disease [Gastroenteritis].
• Poliovirus, Coxsackie virus and
Echovirus can cause diseases
outside the enteric tract.
• Hepatitis A, Poliovirus are from the
Picornaviruses family.
• Rotavirus is from the Reoviruses.
• Norovirus is from the Calicivirus.
 Virtually all viruses that are
transmitted by the fecal–oral
route (those that have to
survive in the environment) do
not have an envelope; that is,
they are naked nucleocapsid
viruses. These include viruses
such as: [ANCER P]
• Hepatitis A virus [Picorna]
• Noro virus [Calici]
• Coxsackie virus [Picorna]
• Echovirus [Picorna]
• Rotavirus [Reo]
• Poliovirus [Picorna]
 Poliovirus causes Poliomyelitis.
 Coxsackie virus causes
Myocarditis, meningitis,
(hand,foot,mouth) disease.
 Echovirus causes meningitis
and encephalitis.

General Characteristic for enteric viruses:
1. RNA viruses.
2. Non-enveloped icosahedral capsid.
3. Only Rotavirus has virion-encoded polymerase.
• Poliovirus, Echovirus, Coxsackie viruses are enteroviruses, The term “Enterovirus” refers to:
1. The enteric tract as an important site of viral replication.
2. And to the feces as a common source of infection and a common specimen from which
these viruses are isolated.

Remember that:
• The presence of an envelope confers instability on
the virus. Enveloped viruses are more sensitive to heat,
drying, detergents, and lipid solvents such as alcohol
and ether than are nonenveloped (nucleocapsid)
viruses, which are composed only of nucleic acid and
capsid proteins.
• Enteroviruses are part of the Picornavirus family.
 CDC:Rotavirus is very stable and may remain viable
in the environment for weeks or months if
disinfection does not occur.

• Rotavirus is from the reovirus family. It is a double-stranded RNA virus.
• Norwalk, Echovirus, Coxsackie, poliovirus: single stranded RNA viruses, with
+ve polarity.
• Double stranded RNA viruses, need special enzyme for replication: RNA
dependent RNA polymerase.
• Ss RNA with +ve polarity serves as mRNA no viral polymerase.

Rotavirus
• Rotavirus has a segmented double-stranded RNA genome surrounded by
a double-layered icosahedral Capsid without an envelope
• The rotavirus genome has RNA segmented into 11 segments.
 Segmented RNA Production of Functional polypeptide[structural or non-
structural].
 Non-segmented RNA: Production of large polypeptide that must be cleaved by
proteases.
• The virion contains an RNA-dependent RNA polymerase
• There are at least six serotypes of human rotavirus
• The outer surface protein (also known as the viral hemagglutinin) is the
type-specific antigen and elicits protective antibody.
• Rotavirus is a common cause of viral gastroenteritis, especially in young children.
Rotavirus reservoir: Transmission:
Human-GI tract and stool. Person-to-person [fecal-oral] or Fomites
[tools contaminated by stool]

Replicative Cycle
• Rotavirus replicates in the mucosal cells of small intestine.
• Receptors: Rotavirus attaches to the cell surface at the site of the β-adrenergic
receptor.
• After entry of the virion into the cell, the RNA-dependent RNA polymerase
synthesizes mRNA from each of the 11 segments within the cytoplasm.
• The 11 mRNAs are translated into the corresponding number of structural and
nonstructural proteins
• One of these, an RNA polymerase, synthesizes minus strands that will become
part of the genome of the progeny virus.
• Capsid proteins form an incomplete capsid around the minus strands, and then
the plus strands of the progeny genome segments are synthesized.
• The virus is released from the cytoplasm by lysis of the cell
 Nonenveloped viral particles are released from cells by cell lysis.
 Enveloped viruses are released by budding.
 Result of replicative cycle: Production of nonenveloped viruses, that lyse cells.
• Short incubation period (usually less than 48 hours).

Replicative Cycle
• After entry of the virion into the cell, the RNA-dependent RNA polymerase
synthesizes mRNA from each of the 11 segments within the cytoplasm.
• Remember that:
1. replication of RNA viruses occurs in the cytoplasm(except for two viruses)
Rotavirus replicates in the cytoplasm.
2. Rotavirus has segmented RNA (11 segments), each will produce a functional
polypeptide.
3. Segmented RNA viruses produce polypeptides that do not need to be
cleaved by proteases.
4. DsRNA virus needs RNA dependent RNA polymerase (host cells do not have
this enzyme).
5. Out of the eleven polypeptides, one of them produces mRNA strands with
negative polarity for the progeny. These strands are then converted into
positive polarity (intermediate form), after that the progeny will have
DsRNA.

Pathogenesis & Immunity
• Rotavirus enters through the oral route.
• Rotavirus replicates in the mucosal cells of the small intestine.
• Rotavirus-induced diarrhea is due to stimulation of enteric nervous system.
• Rotavirus infected enterocytes produce cytokines that stimulate enteric nervous
system.
• This stimulation causes excess secretion of fluids and electrolytes into bowel
lumen.
• The consequent loss of salt, glucose, and water leads to diarrhea. No
inflammation occurs, and the diarrhea is nonbloody.
• Immunity to rotavirus infection is unclear
• It is likely that intestinal IgA directed against specific serotypes protects against
reinfection and that colostrum[first milk] IgA protects newborns up to the age of
6 months.

Clinical Findings
• Rotavirus infection is characterized by:
1. Nausea & Vomiting
2. Watery, non bloody diarrhea
• Gastroenteritis is most serious in young children, in whom dehydration and
electrolyte imbalance are a major concern.
• Adults usually have minor symptoms.
Additional symptoms:
• Anorexia
• Abdominal cramps
• Rotavirus is one of the most common causes of mortality in developing
countries.

• Clinical
• Detection of rotavirus in the stool by using radioimmunoassay or enzyme-linked
immunosorbent assay (ELISA)
• PCR: The most sensitive method of diagnosis. Infection can be diagnosed by
testing the stool for rotaviral antigen or for rotavirus RNA using a PCR assay.
• The diagnosis can be made by observation of a fourfold or greater rise in
antibody titer.

Treatment & Prevention
• There is no antiviral agent.
• Fluid supplementation for dehydration and electrolyte imbalance.
• There are two rotavirus vaccines available. Both contain live virus and are given
orally
• One is a live, attenuated vaccine (Rotarix “RV1”), which contains the single most
common rotavirus serotype (G1) causing disease in the United States
• The other is a live reassortant vaccine (Rotateq “RV5”), which contains five
rotavirus strains. 5 strains: Human and Bovine, the bovine strain will not cause
disease to human.
Patients with a history of intussusception should
not receive either vaccines. Why?
increased risk of intussusception has been
reported with both vaccines.

Norovirus
• Norovirus is one of the most common causes of viral gastroenteritisin adults
• Norovirus is also the most common cause of viral gastroenteritis in children in
the United States because the rotavirus vaccine has lowered the incidence of
disease caused by that virus.
• Norwalk virus is an important norovirus and is named for an outbreak of
gastroenteritisin Norwalk.
• Important notes:
1. In the Palestinian vaccination system, we have a vaccine against Rotavirus.
2. There is no vaccine against Norovirus.
Enteric viruses are divided into:
1. Viruses that cause GI disease. [Norovirus, Rotavirus].
2. Viruses primarily outside the GI. [Polio, Echo, Coxsackie viruses].
Watery diarrhea

Important Properties
• Norovirus has a nonsegmented, single-stranded, positive polarity
• Nonenveloped virus with an icosahedral nucleocapsid [All of Enteric virus
are nonenveloped and their capsid shape is icosahedral].
• There is no polymerase within the virion [Because of the positive polarity].
• There are many serotypes
• Six genogroups have been identified (Most human infections are caused by
members of genogroupII)

Summary of Replicative Cycle
• The virion interacts with specific cell receptors on the cell membrane and then
enters the cell
• The capsid proteins are then removed
• After uncoating, the genome RNA functions as mRNA and is translated into one
very large polypeptide called noncapsid viral protein
• This polypeptide is cleaved by a virus-encoded protease to form both the capsid
proteins of the progeny virions and several noncapsid proteins
• Replication of the genome occurs by synthesis of a complementary negative
strand, which then serves as the template for the positive strands
• Virions accumulate in the cell cytoplasm and are released upon death
of the cell

Transmission & Epidemiology
• Norovirus is transmitted by the fecal–oral route, often involving the ingestion of
contaminated seafood or water.
• Outbreaks typically occur in group settings such as cruise ships (especially in the
Caribbean region), schools, camps
• Infection is enhanced by several features of the virus:
1. Low infectious dose
2. Excretion of virus in the stool both before the onset of symptoms and for several
weeks after recovery [similar to Rota virus: Infected persons shed large quantities
of virus in their stool beginning 2 days before the onset of diarrhea and for
several days after the onset of symptoms].
3. Resistance to inactivation by chlorination and to drying in the
environment.[Because it is nonenveloped].

Pathogenesis & Immunity
• Norovirus infection is typically limited to the mucosal cells of the intestinal tract
• Watery diarrhea without red cells or white cells occurs
• Many asymptomatic infections occur, as determined by the detection of
antibodies
• Immunity following infection appears to be brief[short term], and reinfection can
occur.
• New strains appear every 2 to 4 years and cause widespread infections.

Clinical Findings
• Disease is characterized by sudden onset of vomiting and diarrhea accompanied
by low-grade fever and abdominal cramping
• Neither the emesis nor the stool contains blood
• The illness typically lasts 2 to 3 days, and there are no long-term sequelae, except
in some immunocompromised patients in whom chronic gastroenteritis can
occur [typically it is not a chronic disease except in immunocompromised states,
where watery diarrhea develops to chronic gastroenteritis].
• In some outbreaks, certain patients manifest signs of central nervous system
Involvement [loss of consciousness, severe headache].

• A PCR-based test on the stool is performedwhen a specific diagnosis is required
• The diagnosis is often a clinical one.

Treatment & Prevention
• There is no antiviral therapy or vaccine available [in contrast to Rotavirus, where
there was two types of vaccines, but no antiviral agents].
• Dehydration and electrolyte imbalance caused by the vomiting and diarrhea may
require oral rehydration or intravenous fluids
• Personal hygiene, such as handwashing, and public health measures

Summary
 Both of Norovirus and Rotavirus are transmitted via the fecal oral route.
 Rotavirus: DsRNA, Norovirus: ssRNA +ve polarity.
 Both viruses have nonenveloped icosahedral capsid.
 Rotavirus has RNA dependent RNA polymerase, Norovirus doesn’t carry its own polymerase.
 Both of these viruses produce watery diarrhea.
 Norovirus is the most common cause of viral gastroenteritis in childhood and adulthood.
 Norovirus is from the calisivirus family, Rotavirus is from the reovirus family.
 There is no antiviral therapy for both viruses.
 There are two oral vaccines for Rotavirus, no vaccine against Norovirus.
 Rotavirus has segmented RNA, Norovirus has a nonsegmented RNA.
 Rotavirus produces 11 functional polypeptides, Norovirus produces a large polypeptide that
must be cleaved by viral-encoded protease.
 Both of Rotavirus and Norovirus can be transmitted through stool before onset of symptoms.

Viral Hepatitis
Resources used:
1. Dr.Murad Lecture.
2. Review of Medical Microbiology and Immunology.
3. First Aid
4. USMLE STEP 1: Hepatitis B lifecycle [youtube video]
+My interpretation.

Viral Hepatitis
• ThetermVIRALHEP
A
TITIS isusuallyusedto
describeinfectionscausedbyagentswhose
primary tissuetropismistheliver
• Acutehepatitismayalsooccuraspart ofthe clinical
courseof anumber of viral infections
- Humancytomegalovirus
- Epstein-Barr virus
- Herpessimplexvirus
- Y
ellowfever virus
- Rubella

Clinical Features
• Hepatitisduetoall theseviruses presentsclinicallyinavery similar
fashion,especiallyduring theacutephaseof theillness
• A specific diagnosis canonlybemadein thelaboratory
• Themajorityof infections aretotally Asymptomatic
butcommonclinical featuresinclude[foralltypes ofHepatitis]:
- Anorexia, Nausea,Vomiting,Right upperquadrantpain
- Raisedliver enzymesASTandAL
T
.[morethanthreefolds]
-Darkurine,palefeces.
Jaundiceis thehall markof infection,buttendstodevelop late

Viral Hepatitis
• Genetic Material:
• Hepatitis B: DNA virus.
• Other Hepatitis virus types: RNA viruses
• Hepatitis D [Delta agent]: defective viral particle, accompanies Hepatitis B.
• Mode of Transmission:
• Hepatitis A, Hepatitis E: Fecal-Oral transmission [contaminated food, water].
• Hepatitis B,C,D sexual activity causes transmission.
Is it Self limited or non-self limited? Does it produce chronic state or not?
• Hepatitis E is important in pregnancy, as severity of manifestations appear in pregnancy.
• Hepatitis A,E self-limiting diseases
[Resolving of signs and symptoms without chronic state]. [complete recovery]
• Hepatitis B,C,D can lead to chronic states.
Hepatitis B,C can precipitate to Hepatocellular carcinoma, i.e. they are carcinogenic viruses.
Hepatitis B can also lead to Liver Cirrhosis.
Vaccines are available for: Hepatitis A, Hepatitis B.
Vaccine for Hepatitis B is an obligatory vaccine in the Palestinian vaccination system.
Vaccine for Hepatitis A is optional.
Prepared immunoglobulins are found for Hepatitis B[Passive Immunization], and are important to be used
in special situations such as:
1. Needle-stick injury
2. Delivery of low birth weight newborn
3. Newborn for a surface antigen +ve mother.
There are several antigens for Hepatitis, especially with Hepatitis B, there are three different antigens :
1. Surface Antigen (HBsAg).
2. Core Antigen. (HBcAg). 3. E antigen (HBeAg) There is an Antibody for each of these antigens.

Questions:
• True or False:
1. Hepatitis A is an enveloped virus.
2. Hepatitis D is a carcinogenic virus.
3. Hepatitis A,C are transmitted through Fecal-Oral route.
4. Hepatitis B is a DsDNA virus.
5. Hepatitis B is an enveloped virus.
6. Hepatitis A,B are stable against heat, detergents.
7. Hepatitis E severe manifestations appear in pregnancy.
8. Passive immunization to Hepatitis B is given if there is a high birth weight
newborn.
9. Hepatitis B has three antigens: surface, core, E.
10. Hepatitis D infection can occur without being infected by Hepatitis B.
11. Hepatitis A,E are self limiting diseases.
12. There are no vaccines for Hepatitis C.
13. The genetic material of all types of Hepatitis are RNA except for Hepatitis B.
• How can we know the causative agent of Hepatitis, whether it is A,B…?
• How can all types of Hepatitis viruses cause Hepatitis?
• Numerate enveloped and nonenveloped Hepatitis virues.
• What is the mechanism of Hepatocytes injury in Hepatitis?
• What is the meaning of Delta agent being a defective virus?

Answers:
• How can we know the causative agent of Hepatitis, whether it is A,B…?
 By detection of antigens, or antibodies [laboratory diagnosis].
• How can all types of Hepatitis viruses cause Hepatitis?
 Their ability to infect hepatocytes is because they have proteins on their surface
that react with receptors on the surface of hepatocytes.
• Numerate enveloped and nonenveloped Hepatitis virues.
 Hepatitis A,E are nonenveloped, Hepatits B,C,D are enveloped,
• What is the mechanism of Hepatocytes injury in Hepatitis?
 All of Hepatitis viruses are noncytotoxic (i.e., they do not kill
hepatocytes directly). The death of hepatocytes is mediated by
cytotoxic T cells directed against viral antigen displayed on the
surface of the hepatocyte in association with class I major histocompatibility complex
(MHC) proteins.
• What is the meaning of Delta agent being a defective virus?
 It cannot replicate by itself because it does not have the genes for its envelope
protein). HDV can replicate only in cells also infected with HBV
because HDV uses the surface antigen of HBV (HBsAg) as its
envelope protein. HBV is therefore the helper virus for HDV.

Viral Hepatitis
A
“Infectious
Hepatitis”
“Serum Hepatitis”
Viral
hepatitis
Enterically
transmitted
Parenterally
transmitted
G
Other viruses
CMV, Arboviruses
etc.
E
Non A Non B
B D C

• Each type of Viral Hepatitis belongs to a different family:
Hapatitis A: Picornaviridae. Picornaviridae viruses: Rhinovirus, Coxsackie virus,
Poliovirus, Echovirus, Hepatitis A virus. [single stranded RNA with +ve polarity)
Hepatitis B: Double stranded DNA [RNA dependent DNA polymerase, as there is RNA
genome as intermediate genome “Reverse Transcriptase”]. Hepatitis B: Hepadnavirus.
Hepatitis C: single stranded RNA with +ve polarity, from Flavivirus family.
Hepatitis D: Viroid, Defective viral particle, from: Deltavirus. Usually associated with
Hepatitis B.
Hepatitis E: Single Stranded RNA with +ve polarity. From: Calicivirus family.
Calicivirus family includes: Noro Virus, Hepatitis E virus.
• Table 41-2 is important.
Genome and Virus Family

Transmission
• Signs and Symptoms are the same for all types of Hepatitis.
• Differentiation depends on specific antigens and antibodies.
• Hepatitis A,E Fecal Oral transmission (contaminated food, water) [Nonenveloped viral paticles, stable
viral particles].
• Hepatitis B, C, D through blood, sexual activity
• Hepatitis B can be transmitted at birth.
• Hepatitis B,C,D can produce chronic carrier state.
• Chronic Carrier state: Persistent presence in hepatocytes, either with minimal damage[minimal metaboli
activity], or with exacerbation[due to reduction of immune state for example].
• Chronic Carrier state can lead to several complications, such as:
1. Hepatocellular Carcinoma. [Hepatitis B,C]
2. Liver Cirrhosis.
3. Liver Failure.
• Hepatitis A,E don’t produce chronic carrier state.
• In Hepatitis A,E there is no need to use antiviral agents. In Hepatitis B,C,D there are several antiviral agents.
Chronic carrier state: The
organisms continue to grow with
or without producing symptoms
in the host.

Abbreviations:
• HAV, HCV, HEV… : Hepatitis (_) virus.
• HBsAg: Hepatitis B surface Antigen. HBsAb: Hepatitis B surface antibody.
• There are three different types of Hepatitis B antigens:
1. HbsAg 2.HBeAg 3.HbcAg [each antigen has a corresponding antibody.

• HA
Vis a typical enterovirusclassifiedin the
picornavirusfamily
• It has a single-stranded RNAgenome and a
nonenvelopedicosahedral nucleocapsidand
replicates in thecytoplasmofthecell
• It hasoneserotype

SummaryofReplicativeCycle
• HA
Vhasareplicative cyclesimilarto thatof other
enteroviruses

Transmission&Epidemiology
• HAV is transmitted by the fecal–oral route
• Increased incidence in low socio-economic
states.
• Humans are the reservoir for HAV
• Self-limiting disease
• Virus appears in the feces roughly 2 weeks
before the appearance of symptoms, so quarantine
of patients is ineffective
• Children are the most frequently infected
• Unlike HBV
, HAV is rarely transmitted via the
blood,

Pathogenesis&Immunity
• Thepathogenesisof HA
Vinfection is notcompletely understood
• Thevirusprobablyreplicatesinthegastrointestinal tractandspreads
totheliver viatheblood
• HA
Vinfection of culturedcells producesnocytopathiceffect.It is
likely that attackbycytotoxicTcells causesthedamageto the
hepatocytes
• Theinfectioniscleared, thedamageisrepaired, andnochronic
infectionensues
• Hepatitiscausedbythedifferent virusescannotbedistinguished
Pathologically[signsandsymptomsaresimilartoothertypes,butin
HBVtheseveritycanbehigher].
• Theimmuneresponseconsistsinitiallyof IgMantibody, which
is detectableat thetimejaundiceappears.

Clinical Findings
• Theclinical manifestationsof hepatitis are virtually thesame,
regardless ofwhichhepatitis virus is thecause
• Fever,anorexia,nausea,vomiting, andjaundice aretypical. Dark
urine, pale feces,andelevated transaminaselevels areseen.
Mostcasesresolve spontaneouslyin 2to 4weeks
• HepatitisAhasashortincubationperiod (3–4 weeks) in contrastto
that of hepatitis B,which is12weeks
• Most HA
Vinfectionsareasymptomatic
• Nochronichepatitis orchroniccarrier stateoccurs, andthereis no
predispositiontohepatocellularcarcinoma

• Thedetectionof IgMantibodyisthemost
important test
• fourfoldrisein IgGantibody titer canalsobeused
Timeline with HAV:
1. HAV starts to appear in feces 2 weeks before onset of symptoms.
2. Incubation period= 3-4 weeks
3. Most cases resolve spontaneously 2-4 weeks after infection.
4. The appearance of IgM is followed 1 to 3 weeks later by the production of IgG
antibody. [IgG production provides long life immunity].
Hepatitis A: Two mosts Most cases are asymptomatic
IgM detection is the most important test
Only detected by
presence of IgG
Self-limiting

• Third week after exposure: IgM production.
• Fifth week after exposure: IgG production.

Treatment &Prevention
• Noantiviral therapyisavailable.
• Active immunizationwith avaccine containinginactivated HA
Vis
available
• Acombinationvaccinethat immunizes againstbothHA
Vand
HBV calledT
winrixisavailable
• Passive immunizationwith immuneserumglobulin priorto infection
or within14daysafterexposure[forhighrisksituations,peoplewho
aretravellingtoendemicareas].

• HBVisamemberof thehepadnavirusfamily
• It isa42-nmenvelopedvirion,1 withanicosahedralnucleocapsid
corecontainingapartially double-strandedcircularDNAgenome
• The envelope contains a protein called the surface antigen
(HBsAg).
• There are three types of antigens for HBV:
1. HBsAg: Surface antigen is found in the envelope.
2. HBeAg: Soluble and released by the infected cells into the blood.
3. HBcAg: Found in the Nucleocapsid “Core of the virus”.
Surface
Core

• TheDNApolymerase hasbothRNA-dependent (reverse
transcriptase)andDNA-dependent activity.
• Electronmicroscopyof apatient’s serumrevealsthreedifferent types
ofparticles:
1. Few42-nmvirions
2. Many22-nmspheres
3. Long filaments22nmwide
• Bothofthemarecomposedofsurface antigen.
 HBV is the only human virus that produces these spheres and
filaments in such large numbers in the patient’s blood.
• The e antigen is an important indicator of transmissibility.

• Theenvelopecontains aprotein called the surfaceantigen
(HBsAg): important in diagnosis and vaccination system.
• Therearetwo otherimportant antigens bothlocatedinthecore of the
virus:
- Thecoreantigen(HBcAg)
- Theeantigen(HBeAg

ReplicativeCycle
• Goal of Replication:
 Partially DsDNA virus Partially DsDNA progeny.
• In order to start replication, the virion DNA should be
fixed, to become a fully double stranded DNA.
replication
DNA repair in Nucleus
Partially DsDNA Fully DsDNA
 This activity is done by virion DNA polymerase.
• This genetic material can be readily transcribed into RNA using cellular machinery [Cellular RNA
polymerase].
• The RNA polymerase activity produces mRNA with +ve polarity.
• This mRNA is used to synthesize DNA of the progeny, and for the synthesis of viral capsid.
• This RNA dependent DNA synthesis catalyzed by reverse transcriptase encoded by HBV takes place
within the newly assembled virion nucleocapsid core in the cytoplasm.

• After entryof thevirion into the cell andits uncoating,thenucleocapsid moves
tothe nucleus
• In thenucleus, the virion DNApolymerasesynthesizes themissingportionof DNA, anda
double-strandedcircular DNAisformed
• This DNAservesasatemplate for mRNAsynthesis bycellularRNApolymerase
• After the individual mRNAsaremade,afull-length positive-strandRNAis made,whichis the
template fortheminus strandof the progenyDNA
• Theminus strandthen servesasthetemplate fortheplus strand ofthegenomeDNA

• This RNA-dependentDNAsynthesis catalyzed by reverse
transcriptaseencodedbyHBVtakesplacewithinthenewly
assembledvirion nucleocapsidcore inthecytoplasm
• Hepadnavirusesaretheonlyvirusesthat producegenomeDNAby
reversetranscriptionwith viral RNAasthetemplate

• Thethreemainmodesof transmission are via blood,during sexual
intercourse,andperinatallyfrommothertoNewborn.
• Theobservationthat needle-stickinjuries cantransmit thevirus
indicatesthat onlyvery small amountsofbloodarenecessary
• Thereis noevidencethat transmission of HBVoccursduring breast
feeding.

• Afterenteringtheblood,thevirus infects hepatocytes, andviral
antigensaredisplayedonthesurfaceof thecells
• CytotoxicTcells mediateanimmuneattackagainsttheviral
antigens,andinflammationandnecrosis occur
• Immuneattack againstviral antigens oninfectedhepatocytesis
mediatedbycytotoxicTcells

• A chroniccarrier is: someonewhohasHBsAgpersistingin
their bloodfor 6monthsorlonger.
• Thechroniccarrier stateis attributed to apersistentinfection of the
hepatocytes, whichresults in theprolongedpresenceofHBVand
HBsAgintheblood
• Themaindeterminant of whetheraperson clears the infection or
becomes a chronic carrier is the adequacy of the cytotoxic T-cell
response
• Ahigh rateof hepatocellularcarcinoma(HCC)occursinchronic
carriers
• 90%ofAdultHepatitisBpatients completerecovery.
• 90%ofchildrenHepatitisBpatients chroniccarrierstate.

Clinical Findings
• ManyHBVinfectionsareasymptomaticandaredetectedonlybythe
presenceof antibodytoHBsAg
• Themeanincubationperiod forhepatitis Bis 10to12weeks,which
is muchlongerthanthat of hepatitisA(3–4weeks)
• Theclinical appearance of acutehepatitis Bis similar tothat of
hepatitisA.

• Thetwomostimportant serologictestsforthediagnosis of early
hepatitisBare thetestsfor
HBsAg
IgMantibodytothecoreantigen

• No chronic carrier state in
HAV.
• There is chronic carrier in
HBV, with production of
several antigens.
• HAV: Most important test
is IgM detection.
• In case of Hepatitis B,
there are several antigens
and antibodies.
• First antigen to appear is:
HBsAg
• Second antigen to appear
is: HBeAg
• First antibody to be
produced: HBcAb.
• Persistence of surface
antigen in the blood for
more than 6 months lead
to chronic carrier state.
• Diagnosis of acute
Hepatitis B:
1. HBsAg
2. HBeAg
3. Anti HBc

• In this figure: Persistence of HBsAg for more than 6 months Chronic state
• In chronic state: -ve HBeAg, +ve HBsAg, +ve IgG HBc
• In chronic state, ALT, AST levels are lower than in acute state

Prevention
• Preventioninvolvestheuseofeitherthevaccineorhyperimmune
globulinorboth
• Thevaccine(e.g.,Recombivax) containsHBsAgproducedinyeasts
byrecombinantDNAtechniques
• TwinrixthatcontainsbothHBsAgandinactivated HA
Vprovides
protectionagainst bothhepatitis BandhepatitisA
• Hepatitis Bimmuneglobulin (HBIG)containsahightiterofHBsAb
• Hepatitis B vaccine can be given as:
1. O,1,6: time of birth, 1st month, 6th month.
2. 2,4,6: 2nd month, 4th month, 6th month
3 doses of surface antigen.
• When do we give passive immunization against Hepatitis B?
1. Needle-stick injury.
2. Low birth weight newborn
3. Newborn for a +ve HBsAg mother.
Needle stick injury needs passive-active
immunization.
We give immunoglobulins, then the vaccine.
• There is no antiviral therapy in acute Hepatitis B.
• Chronic Hepatitis B therapy include entecevir, and tenofovir. [Drugs of choice],
they inhibit reverse transcriptase of HBV. Interferons are also used.

• HCVis amemberof theflavivirusfamily. It is anenveloped
virion containingagenomeofsingle-stranded,positive
polarity RNA
• It hasnovirion polymerase
• HCVhasat least six genotypesandmultiple subgenotypesbasedon
differencesin thegenesthatencodeoneof its twoenvelope
glycoproteins.

• Thereplication ofHCVis uncertainbecauseit hasnotbeengrown in
cell culture
• Otherflaviviruses replicate in thecytoplasmandtranslatetheir
genomeRNAintolargepolyproteins, fromwhich functionalviral
proteinsarecleaved byavirion-encoded protease
• Thisproteaseis thetarget of potentanti-HCV therapy.

• Humansare thereservoir forHCV
• It istransmittedprimarily via blood.At present, injectiondruguse
accountsforalmost all newHCVinfections
• Transmissionfrommotherto child duringbirthis
anotherverycommonmodeof transmission

• HCVinfectshepatocytesprimarily
, but thereisnoevidencefora
virus-inducedcytopathiceffectontheliver cells
• Death ofthehepatocytes is probably causedbyimmuneattackby
cytotoxicTcells
• HCVinfectionstronglypredisposestohepatocellularcarcinoma

LaboratoryDiagnosis
• HCVinfection is diagnosedbydetectingantibodiesto HCV
inanenzyme-linkedimmunosorbent assay(ELISA)
• HCVproteinsanddoesnotincludethehighly variable envelope
proteins
• Thetestdoesnotdistinguish between IgMandIgGanddoesnot
distinguishbetweenanacute,chronic,or resolved infection.
• If the result of ELISAantibody test is positive, a polymerase chain A
chronic infection is characterized byelevated transaminase levels, a
positive ELISAantibody test, and detectable viral RNAfor at least
6months

Prevention
• Thereisnovaccineandhyperimmuneglobulins
arenot available.
• Pooledimmune serumglobulins arenot useful.

Hepatitis E
• HEVisamajorcauseof hepatitistransmittedbythefecal–oralroute
• It is thought to bemorecommonthanHA
Vin manydeveloping
countries
• HEVis anonenveloped,single-strandedRNAvirus classified asa
memberof thehepevirusfamily
• ClinicallythediseaseresembleshepatitisA, withtheexception
ofahighmortalityrateinpregnant women
• NoeffectonFetus.
• Chronicinfection resulting inchronichepatitis andcirrhosis
butnothepatocellularcarcinoma,occurs in immunocompromised

• Thediagnosisistypically madebydetecting
IgMantibody toHEV[similartoHEV].
• APCRassaythat detectsHEVRNAinvaccine
patient specimensisavailable
• Thereisnoantiviral drugavailablefor acute
infectioninimmunocompetent patients.
• HAV, HEV: No antiviral therapy

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