Microbiology of the Gastro-Intestinal System Flashcards
Normal flora of the GIT
The host’s normal gut flora is large
• Most of these bacteria are anaerobic
• They compete with potential pathogens for nutrients and
for places to attach to the colon wall
• The normal host flora can also produce substances toxic
to potential pathogens
• Microorganisms usually do not multiply in the esophagus
and stomach but are present in ingested food and as
transient flora
Normal flora (NF) of the GIT
• The stomach is usually sterile especially after a meal
– Gastric juices, acids, and enzymes, which help to protect
the stomach from microbial attack, are produced
– Most microorganisms are susceptible to the acid pH of the
stomach and are destroyed with exceptions of:
• Spore-forming bacterial species in their spore phase
• Cysts of parasites
• Helico bacter py lori
– Organisms that are pH-susceptible and survive are
generally protected by being enmeshed in food, and they
move to the small intestine
– Stomach acidity greatly reduces the number of organisms
that reach the small intestine
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Normal flora (NF) of the GIT
• The small intestine contains few microorganisms
– Obligate anaerobes far outnumber the facultative Gramnegative rods
• Make up more than 90% of the microbial flora of the large
intestine
– Gram-positive cocci, yeasts, and Pseudomonas
aerugi nosa are also usually present in the large
intestine
Normal flora (NF) of the GIT
• The GIT population may be altered by antibiotics
• In some cases, certain populations or organisms are
eradicated or suppressed, and other members of the
indigenous flora are able to proliferate
• This alteration can be the cause of a severe necrotizing
enterocolitis (C lostridium/Clostridioides
di fficile), diarrhea (S taphylococcus aureus), or
other superinfection
Microorganisms which are not susceptible to the acid pH of the stomach and are not destroyed
Spore forming bacterial species in their spore phase
Cysts of parasites
Helicobacter pylori
What can the alteration of the GIT population cause
Severe necrotizing enterocolitis-C./Clostridioides difficile
Diarrhoea-S. aureus
Other superinfections
Natural defences of the GIT
Gastric Acid
GUT associated lymphoid tissue(GALT)
Bowel normal flora(NF)
Bile Salts
Motility
Protection against toxins
Gastric acid
Major first defense
Decreases organisms that enter
intestine
People with less acid are
at increased risk of
infection
GUT Associated Lymphoid Tissue
Cellular: lymphocytes,
macrophages + lymphoid
tissue
Humoral: secretory- IgA
Bowel Normal Flora(NF)
Resistance to adhesion
by pathogens as receptor
site are blocked
Protection lost after
antibiotics -disturb NF
balance
Bile salts
Inhibit and may even kill
some organisms except
for enterobacteriaceae
and enterococci
Motility
Assists in clearing
pathogens
Prevent dehydration with
IV or oral rehydration
Protection against toxins
Microsomal enzymes of
hepatocytes
Detoxifies some drugs and
endotoxin
Gastroenteritis
A syndrome characterized by gastrointestinal symptoms including nausea, vomiting, diarrhoea and abdominal discomfort
Diarrhoea
Commonly defined as three or more loose stools in a 24-
hour period
– It is considered acute when the duration is 14 days or less
and persistent when the duration is 14 days or longer
– Usually resulting from disease of the small intestine and
involving increased fluid and electrolyte loss
– The most common outcome of GIT infection
Traveller’s diarrhoea
Any diarrhoeal illness associated with travelling
Enterotoxigenic Escherichia coli is the leading cause
Dysentery
Characterized by the presence of blood or mucus or both in stools
It is most often the result of inflammation of the small
bowel or colon in response to invasive bacterial infection
Enterocolitis
Inflammation involving the mucosa of both the small and large intestine
Cholera
An acute infection of the gastrointestinal tract caused by the comma shaped Gram negative bacterium, Vibrio
cholerae
Characterized by severe watery non bloody diarrhea-rice watery stools
Food poisoning
Food-borne outbreak
GIT and/or neurological symptoms
Two or more persons
– Exceptions: Botulism, chemical poisoning = 1 case
Within 72 hours
Common meal (same occasion)
NOTIFIABLE medical condition
Most common causes: Salmonella species,
Staphylococcus aureus, C. botulinum, C. perfringens
Bacteria, viruses & parasites causing GIT
infections:
Inflammatory Diarrhoea
Bacteria:
Shigella EHEC Salmonella enteritidis Campylobacter jejuni Vibrio parahaemolyticus Clostridium/ Clostridioides difficile
Viruses: None
Parasites:
Entamoeba histolytica
Infection is in the colon
Leucocytes and
sometimes blood = Dysentery
Bacteria, viruses & parasites causing GIT
infections:
Non inflammatory diarrhoea
Bacteria:
ETEC EAEC Vibrio cholerae Clostridium perfringens Bacillus cereus Staphylococcus aureus
Viruses:
Rota, Noro, Adeno &
Astrovirus
Parasites:
Giardia lamblia
Cryptosporidium parvum
Cyclospora cayetanensis
Microsporidia
Acute watery diarrhoea
Proximal small bowel
Seldom leucocytes
Bacteria, viruses & parasites causing GIT
infections
GIT and Systemic infection
Bacteria:
Salmonella enterica serovar Typhi Salmonella spp. (NTS) Yersinia enterocolitica Campylobacter spp.
Viruses:
Polio
Enteroviruses
Parasites: Entamoeba histolytica Echinococcus granulosis Strongyloides stercoralis
Generally involves
small bowel
Few leucocytes
The types of Diarrhoeal diseases
Enterotoxin-mediated
Invasive:
-Invasion of the Bowel mucosal surface
-Invasion of Full-Bowel thickness with lymphatic spread
Enterotoxin-mediated
Bacteria associated with enterotoxin production do not
invade the gut wall
The toxin does not elicit an inflammatory response
Patients usually do not have a fever
The pre-formed toxin is already present in the ingested
food- because toxin can act proximally in the bowel (the small intestine), the incubation period is relatively short, usually less than 12 hours
Rapid onset of symptoms following food ingestion
When patients present to a physician, they usually report an illness that started the day of or the day before presentation
They typically have a large number of non- bloody, watery stools and frequently have vomiting and abdominal cramping, particularly during defecation
Examples include:
-Enterotoxigenic Escherichia coli - accounts for the
largest percentage of cases of diarrhea in travelers to
underdeveloped areas
-Vibrio cholerae
-Staphy lococcus aureus
-Clostridium perfringens, and
-Bacillus cereus
I
Invasion of the Bowel Mucosal Surface
Organisms cause an inflammatory response
Characterized by the presence of fecal leukocytes, fever and leukocytosis
Organisms must first replicate in the colon, and then
invade the mucosal surface
Incubation period is usually longer than the enterotoxin -mediated diarrhea
Infections only involve the superficial mucosal surface of the bowel
Bacteremia or metastatic infection is infrequent
Patients may present with dysentery, characterized by
gross blood and pus in the stool
Examples:
- Salmonella spp.
- Campylobacter spp.
- Shigella spp.,
- Enterohaemorrhagic E. coli strains, and
- Entamoeba histolytica
Invasion of Full-Bowel Thickness with Lymphatic Spread
These organisms can invade the bowel wall, causing
bacteremia, and mesenteric lymphadenitis
Can be mistaken for appendicitis
Diarrhea may be absent at the onset of the disease
Red blood cells and fecal leukocytes are often present in the stool
Gross blood in the stool can occur in about 25% of
patients with Y. enterocolitica infection
Patients with Salmonella enterica ser Typhi infection may become chronic carriers and unknowingly spread the infection to others
Examples:
- Salmonella enterica ser Typhi and
- Yersinia enterocolitica
Specimen Collection and Handling
Stool specimens: transported to the laboratory shortly after
collection
– Preservatives (polyvinyl alcohol or formalin) must be
avoided if bacterial cultures are ordered
Microscopy, Culture and Sensitivity performed on same
specimen therefore, normal specimen container used
– If rectal swabs are to be processed, Cary- Blair or a similar
transport medium should be used
Biopsy specimens of mucosa
Rectal mucosa : scrapings, biopsies – parasites/ova excreted more direct specimens, e.g. schistosome ova; Ent. histolytica (trophozoites)
Gastric biopsies:
Helicobacter pylori take
specimens from edge of
ulcer, inflammationers to
Intestinal fluids
E.g. giardiasis, strongyloides
– Not readily detected in stools
– Duodenal aspirates/biopsies
required
Gastric Aspirates
TB esp. in children and
debilitated adults
Acute food poisoning-
toxins
Other: Blood cultures
NB in pts with fever e.g. Salmonella infections –
invasive infection
Direct Microscopic Examination
Stained or unstained slides, wet mount preparations
– Microscopic examination of the stool may reveal white blood
cells in cases of inflammatory diarrhea (e.g. Salmonella, Shigella, Y ersinia, Campy lobacter, EIEC, and various
Vibrio spp.)
– Red blood cells may be present because of intestinal wall
bleeding
– The bacteria may be visible on direct microscopic examination of
the stool
–
Culture
Selective and differential culture media are commonly
used to identify bacterial pathogens in stool
– Selective media contain antimicrobials or chemicals, which
limit the growth of normal bacterial flora and enhance thegrowth of pathogenic bacteria
– The differential aspect of the medium often allows
differentiation of bacterial species based on colony
morphology
• Differences in colony appearance are usually a result of
different biochemical characteristics of the organisms
Specific tests:
Antigen detection
Molecular methods
Antimicrobial susceptibility testing
Antibiotic associated/induced diarrhoea:
Etiology:
Antibiotic associated diarrhoea(AAD) refers to diarrhea
following antimicrobial administration
Clostridium difficile is the most common identifiable cause
Responsible for approximately 30% of cases
Although Clostridium/Clostridioides difficile Infection (CDI)is endogenous in most cases, hospital outbreaks have clearly established that the environment can be the source as well
Generation of spores from excretions promotes person-to person spread
Antibiotic associated/induced diarrhoea:
Pathogenesis:
When C. difficile becomes established in the colon of
individuals with normal gut microbiota, its numbers are
dwarfed by the other flora
Introduction of antibiotics reduces the number of
normal gut flora allowing growth of C. difficile
This is in particular: ampicillin, cephalosporins, and
clindamycin
Most strains produce both toxins, the TcdA and TcdB
Hypervirulent clones produce higher levels of both toxins and also secrete the C. difficile transferase (CDT)
Responsible for more cases and more deaths
In Pseudo membranous colitis (PMC):
Colonic mucosa is studded with inflammatory plaques
These may coalesce into an overlying “pseudomembrane”composed of fibrin, leukocytes, and necrotic colonic cells
Antibiotic Associated/Induced Diarrhoea
Selective media used
– However, direct detection of toxins in the stool has largely
replaced culture for diagnostic purposes
• Detection of its toxin has become routine
– Immunoassays are used to demonstrate toxin TcdA and/or
TcdB in stool
– Nucleic acid-based test have also been developed
Antibiotic associated/induced diarrhoea:
Treatment and prevention:
In AAD discontinuing the implicated antimicrobial often
results in the resolution of clinical symptoms
– Antibiotics for treatment: Metronidazole/vancomycin
/Fidaxomicin
• Fidaxomicin, achieves high levels in the bowel with results
comparable to vancomycin
– Fecal transplant
– With all regimens relapses are common presumably due to
the survival of the inert spores following a treatment course
Peptic ulcers
• Etiology:
– Helicobacter pylori is the etiologic agent
– The organism is found in the stomachs of 30% to 50% of
adults
– The exact mode of transmission is not known, but is
presumed to be person to person
• Fecal–oral route
• Contact with gastric secretions in some way
– Colonization increases progressively with age
– A declining prevalence in developed countries may be due
to decreased transmission because of
• Less crowding and frequent exposure to antimicrobial agents
Peptic ulcers
• Pathogenesis:
- Adherence to gastric mucosa
Multiple outer membrane proteins which bind to the surface
of gastric epithelial cells and certain erythrocyte antigens
- Motility
Flagella to swim to less acidic locale beneath the gastric mucus
- Persistence in the hostile environment of the stomach and
survival of the acid stomach: Urease
Protease damage the mucosa
– 70–80% of gastric ulcers – 90% of duodenal ulcers – Gastric carcinomas, intestinal lymphomas
Peptic ulcers:
Diagnosis
Specimen - Gastric mucosa biopsy
The most sensitive means of diagnosis is culture of the
gastric mucosa
Most sensitive indicator of cure following therapy
The H. pylori urease activity in biopsies
Noninvasive methods include serology and a urea breath test
For the breath test, the patient ingests 13C- or 14C-labeled urea, from which the urease in the stomach produces products that appear as labeled CO2
in the breath
Detection of antibody directed against H. pylori
Because IgG or IgA remains elevated as long as the infection persists, these tests are valuable both for screening and for evaluation of therapy
–
Peptic ulcer:
Treatment and prevention
Bismuth salts (e.g, Pepto-Bismol) has antimicrobial activity
Cure rates approaching 90% have been achieved with
various combinations of bismuth salts and/or a protein pump inhibitor plus two antibiotics
Clarithromycin plus either amoxicillin or metronidazole and metronidazole plus tetracycline have been effective
Relapse rates are low, particularly when acid secretion is also controlled with the use of a proton pump inhibitor
Prevention of H. pylori disease awaits further
understanding of transmission and immune mechanisms
Prophylactic treatment of asymptomatic persons colonized with H. pylori is not yet recommended
Diarrhoegenic E. coli:
Treatment
Most E. coli diarrhea are mild and self-limiting
– Rehydration and supportive measures are the mainstays
of therapy
– EHEC with hemorrhagic colitis and HUS- supportive
measures required, antimicrobials contraindicated
– TMP-SMX or fluoroquinolones reduces the duration of
diarrhea in ETEC, EIEC, and EPEC infection
– Antimotility agents are not helpful and are contraindicated
when EIEC or EHEC could be the etiologic agent
Diarrhoegenic E. coli
• Prevention:
Traveler’s diarrhea incidence can be greatly reduced by
- eating only cooked foods and peeled fruits
- drinking hot or carbonated beverages
Avoiding uncertain water, ice, salads, and raw vegetables is a wise precaution when traveling in developing countries
•
GIT infections caused by Campyl
GIT infections caused by Campylobacter
C. jejuni is by far the most common
– Primary reservoir is in animals
– Bacteria are transmitted to humans by ingestion of
contaminated food or by direct contact with pets • Mostly undercooked poultry, but outbreaks have been caused by
contaminated rural water supplies and unpasteurized milk
GIT infections caused by Campylobacter:
Pathogenesis
– Oral ingestion – Colonization of the intestinal mucosa – Adherence to enterocytes is facilitated by action of the flagellum – Entrance into cells in endocytotic vacuoles • Once inside, they move in association with the cell’s microtubule structure – Injury mechanisms include the • Cytotoxic cytolethal distending toxin (CDT) • Action of lipooligosaccharides (LOS) released in outer membrane vesicles – The intestinal pathology is that of an invasive pathogen with acute inflammation, crypt abscesses, and occasional seeding of the bloodstream GIT infections caused by Campylobacter • Diagnosis: – Stool samples – Buffered glycerol saline, is toxic to enteric campylobacters and should therefore be avoided – Incubate at 420C- C. fetus @ 370C • Enteric Campy lobacter require a microaerophilic and capnophilic environment
GIT infections caused by Campylobacter
• Diagnosis:
– Stool samples – Buffered glycerol saline, is toxic to enteric campylobacters and should therefore be avoided – Incubate at 420C- C. fetus @ 370C • Enteric Campy lobacter require a microaerophilic and capnophilic environment
Diagnosis – Microscopic Morphology • Campy lobacter spp. are motile, curved, non spore-forming, oxidase positive Gramnegative rods • May appear as long spirals or S’ or seagullwing shapes • On Gram-stained smears, these organisms stain poorly • They exhibit a characteristic darting motility – Colony Morphology • Moist, runny looking, and spreading • Usually nonhemolytic • Some are round and raised and others may be flat • C. fetus subsp. f etus produces smooth, convex, translucent colonies • Most do not produce pigment
GIT infections caused by Campylobacter
• Treatment
– Antimicrobial susceptibility testing not routinely performed
– Most patients recover without antimicrobial intervention
– Drugs of choice for treating intestinal campylobacteriosis
are azithromycin and erythromycin
– Ciprofloxacin and other quinolones can also be used
GIT infections caused by Clostridium
perfringens
• Outbreaks usually involve rich meat dishes such as stews, soups, or gravies that have been kept warm for a number of hours before consumption
Two types of food poisoning – Type A-relatively mild and self-limited GI illness – Type C- more serious but rarely seen disease • Follows the ingestion of enterotoxin-producing strains • Spores of some strains are heat-resistant and can convert to the vegetative form and multiply when food is not refrigerated or is rewarmed • After ingestion, the enterotoxin is released into the upper GIT, causing a fluid outpouring in which the ileum is most severely involved
GIT infections caused by Clostridium
perfringes:
Type A
caused by enterotoxin linked to sporulation • After an 8- to 30-hour incubation period, the patient experiences diarrhea and cramping abdominal pain for about 24 hours • Other than fluid replacement, therapy is usually unnecessary
GIT infections caused by Clostridium
perfringes:
Type C
Type C - enteritis necroticans is associated with strains that produce β-toxin – less comonly, α-toxin • After at least 5 to 6 hours, symptoms begin as acute onset of severe abdominal pain and diarrhea, which is often bloody, and may be accompanied by vomiting • Necrotic inflammation>>bowel perforation • Fatal, treatment is required
GIT infections caused by Bacillus cereus
• Gram-positive bacilli
• They are aerobic or
facultative anaerobic
bacilli that form
endospores
• Catalase positive
• B. cereus food poisoning
2 forms:
– Emetic (vomiting)
– Diarrhoeal
GIT infections caused by Bacillus cereus
• Culture of suspected food or stools may be done to
quantify and isolate B. cereus
• More than 105 cereus cells per gram of
food/stools with absence of other pathogens confirms
the diagnosis
• Most food poisoning cases caused by B. cereus
do not require antimicrobial treatment • B. cereus is resistant to penicillin and all of the other βlactam antibiotics except for the carbapenems
Clinical Syndrome caused by B. cereus:
Type:
- Incubation Period
- Diarrhoea
- Vomiting
- Duration of illness
- Foods implicated
Diarrheal: 8-16hrs Very common Ocassional 12-24 hrs Meat products
Emetic: 1-5hrs Fairly common Very common 6-24hrs Fried or boiled rice
GIT infections caused by Staphylococcus
aureus
Staphylococcal food poisoning is one of the most common foodborne illnesses in the world – Short incubation period – Characteristically, the food is moist and rich (e.g, red meat, poultry, creamy dishes) – Contaminated by a preparer who is a carrier – If the food is left unrefrigerated for hours between preparation and serving, the staphylococci are able to multiply and produce enterotoxin in the food – S. aureus enterotoxins stimulate gastrointestinal symptoms (primarily vomiting) – Once formed, these toxins are quite stable • They retain activity even after boiling or exposure to gastric and jejunal enzymes •
GIT infections caused by Staphylococcus aureus Dx Tx Px
Patients symptoms will guide
Supportive
Hand washing during, after and before eating
