GI infections Flashcards
Predisposing factors for GI infections (5)
- Travel to area with poor hygiene- direct exposure to sewerage
- Fecal contaminated food or water
- Food products not properly cleaned or cooked
- Previous, prolonged antimicrobial treatment
- Immunosuppressed patients suffer disseminated infections
Anatomy of the GI tract
Alimentary canal- includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, anus
Functions of the GI tract (2)
- Absorption of nutrients
- Excretion of waste products
GI host defense mechanisms (6)
- Peristalsis
- pH
- Mucus, lysozyme, proteases, lipases
- Secretory IgA
- Phagocytes
- Normal flora
Upper GI tract infections
Impact the stomach and duodenum. Infections include gastritis and peptic ulcerative disease
Lower GI tract infections
Impacts the small and large intestines. Symptoms- diarrhea, dysentery (purulent, mucous, bloody), cramping and abdominal pain
Normal flora of the upper small intestine (2)
- Streptococci
- Lactobacilli
10 - 1000 organisms/mL
Normal flora of the distal ileum (2)
- Enterobacterales
- Bacteroides sp.
106 - 107 organisms/mL
Normal flora of the large bowel (5)
Newborn: human epithelial flora, mostly gram-positive. Adult: mostly anaerobic (1000:1), approximately 1010-11 bugs/mL
1. Bacteroides sp.
2. Clostridium sp.
3. Peptostreptococcus sp.
4. Bifidobacterium sp.
5. Eubacterium sp., etc.
aerobe: Escherichia coli & other Enterobacterales, enterococci & other streptococci
Nosocomial pathogens (5)
- Staphylococcus aureus
- Pseudomonas aeruginosa
- Antimicrobial-resistant gram-negative rods
- Clostridioides difficile
- Candida albicans
Pathogenic mechanisms of enteric pathogens (3)
- Adherence to intestinal mucosa
- Toxigenic
- Invasion of the mucosal epithelium
Adherence to intestinal mucosa
Pathogens would have this mechanism prevent normal absorption and normal secretory function
Toxigenic infection mechanism
Intoxication- organisms growing in the GI tract produce toxins. Enterotoxins act primarily in the small intestine and produce a profuse and watery stool. WBCs and RBCs are not a prominent feature
Pathogenic invasion of mucosal epithelium
Cell destruction. There is occasional invasion of the bloodstream and systemic disease
Gram positive pathogens (5)
- S. aureus
- Bacillus cereus
- Clostridium perfringens Type A
- Clostridium botulinum
- Clostridioides difficile
S. aureus
Gram positive. Produces an enterotoxin. Severe nausea and vomiting begin 2 to 8 h after ingestion, typically followed by abdominal cramps and diarrhea, often lasting < 12 h.
Bacillus cereus
Gram positive. Produces an emetic toxin and an enterotoxin. The emetic toxin is heat and pH stable. Onset of symptoms takes 1-6 hours, and they last for less than 24 hours. There is nausea and vomiting but no fever, and diarrhea is rarely found. The toxin is pre-formed and is on food- found on contaminated rice, noodles, pasta, and cakes. The enterotoxin requires ingestion of 10^6 organisms/gram. Onset of symptoms takes 8-24 hours, and they last approximately 24 hours. Symptoms include abdominal pain and diarrheal disease. Found in cream sauces, cooked meat, poultry, vegetables, and desserts
Clostridium perfringens Type A
Gram positive. This is a common cause of food poisoning and causes mild, self limited disease. The bacteria produces a toxin after the organism is ingested. Symptom onset is 8-12 hours after ingestion. Includes large numbers of neutrophils, positive for occult blood. symptoms: pain, cramps, tenesmus. The organism is found in meats and gravies
Clostridium botulinum
Gram positive. Produces a neurotoxin that may cause death by respiratory paralysis. Adults experience intoxication, the microorganism is infrequently recovered from the stool. Infant botulism is not intoxication- the organism is ingested and multiplies, producing toxin
Clostridioides difficile
Gram positive. Antibiotic-associated pseudomembranous colitis, as the organism is usually suppressed by normal flora. There are hospital acquired and community acquired infections. Toxin mediated infection- toxin A is a tissue damaging enterotoxin, toxin B can be detected by CPE in cell culture
Gram negative pathogens
- Salmonella
- Shigella
- Yersinia species
- Escherichia coli
Salmonella species (3)
- Salmonella Typhi - serotype D1, typhoid (enteric fever)
- Salmonella Enteritidis - serotype group D
- Salmonella Typhimurium - serogroup B
Order Enterobacterales, more than 2400 serovars
Shigella species (4)
- S. dysenteriae, group A
- S. flexneri, group B
- S. boydii, group C
- S.sonnei, group D
Order Enterobacterales
Yersinia species (2)
- Y. enterocolitica
- Y. pseudotuberculosis
Motile at 22-30C, NON-MOTILE at 37C.
Escherichia coli
Gram negative. Enterotoxigenic (ETEC) - traveler’s diarrhea. Produces enterotoxins that result in severe epidemic diarrhea: heat-labile toxin (LT) - similar to cholera toxin & heat-stable toxin (ST). Invasion of intestinal wall results in inflammation and fluid loss. Symptoms: diarrhea, vomiting, chills, fever, and headache
Categories of Gram-negative pathogenic mechanisms (4)
- Enterohemorrhagic (EHEC/STEC)
- Enteroinvasive (EIEC)
- Enteropathogenic (EPEC)
- Enteroaggregative (EAEC)
Enterohemorrhagic
Verotoxin-producing E. coli O157:H7 & other strains. Comes from food sources, resembles Shiga toxin. Hemolytic uremic syndrome, abdominal cramps, watery diarrhea, lower GI hemorrhage. There is no fever and no cells in stool
Oxidase positive glucose fermenting pathogens (3)
Gram negative
1. Aeromonas hydrophila
2. Plesiomonas shigelloides
3. Vibrio sp.
Vibrio species (3)
- V. parahaemolyticus
- V. vulnificus
- V. cholerae
Vibrio cholerae
V. cholerae produces CT resulting in massive diarrhea and “rice water stools.” 2 biotypes of serotype O:1 (endemic in SE Asia): classical & El Tor. O139 is also an important serotype
Oxidase positive glucose non-fermenting pathogens (2)
- Campylobacter species
- Helicobacter pylori
Campylobacter species (3)
- C. jejuni
- C. coli
3, C. fetus
GI viruses (4)
- Hepatitis viruses
- Rotavirus
- Norwalk-like agents
- Adenovirus
GI parasites (6)
- Giardia sp.
- Cryptosporidium sp.
- Cyclospora sp.
- Entamoeba histolytica/dispar
- Balantidium coli
- Trichinella sp.
Diagnosis of gastritis and peptic ulcers
Specimen- gastric-antral biopsy, not stool. The etiological agent is Helicobacter pylori
Identification of Helicobacter pylori (4)
- Skirrow agar or Campylobacter agar with cefoperazone. Incubate microaerophilically at 35oC, urease – rapid positive
- Urea breath test
- ELISA antigen detectable in stool samples
- Serology – IgG for isolate
Gastritis and peptic ulcer treatment
3 used concurrently
1. Acid reducing agent: Omeprazole, prohibits last step of acid production
2. Antibiotic: Erythromycin, Amoxicillin, Metronidazole
3. Bismuth compounds: Pepto-bismol (bismuth sulfate) inhibits pepsin and increases mucous production
When is collection of a GI sample warranted?
Collection is warranted due to patient signs and symptoms. Around 95% of all stool cultures and negative for pathogen isolation. Criteria:
1. Immunocompromised
2. History of travel to geographically problematic area
3. Presences of bloody stools
4. Diarrhea for > 3 days
5. Diarrhea has required patient hydration therapy
6. Fever
Ideal GI sample collection
Before administration of pre-enema treatments and after administration of barium, oil, magnesium, or crystalline compound, wait >5 days to collect specimen. If first stool is negative, two more samples should be submitted over the following few days (every other day or every third day)- Rule out carrier state, must have 3 consecutive negative results
Types of GI specimens (5)
- Stool(fecal material) - specimen of choice- diarrheal samples are expected for those with infection
- Rectal swabs
- Duodenal aspirate
- Gastric aspirate
- Other: bile, colostomy, ileostomy
Rectal swabs
Acceptable for culture from infants or patients acutely ill with diarrhea. Not acceptable for detection of parasites, toxins, or viral antigens. Insert swab beyond anal sphincter, rotate the swab, remove it, place into transport medium. Fecal material must be on swab for acceptance
Duodenal aspirate
Specimen of choice for Giardia spp. Collection by intubation for aspiration or use of capsule technique called Entero-Test
Gelatin capsule with weighted coiled string, swallowed, recovered @ 4hr
Gastric aspirate
Specimen taken in early morning before food and water. For isolation of Mycobacterium sp. if sputum specimen not available. Children younger than 7 y.o.
Transport and storage of GI pathogens
Sample to lab within 2hrs of collection or fresh stool in transport medium can be refrigerated at 4C, plate within 24hr for best recovery.
Modified Cary-Blair or buffered glycerol transport medium.
Modified Cary-Blair for molecular multiplex panel processing. For proctitis suspected for Neisseria gonorrhoeae, do not refrigerate the specimen. For Clostridioides difficile toxin assay, immediately freeze specimen at -70oC or store at 4oC up to 48 hr. This is the only stool sample to be frozen
Modified Cary-Blair transport medium or buffered glycerol transport medium use
For Campylobacter sp., use Modified Cary-Blair medium, buffered glycerol can inhibit Campylobacter. For Shigella sp., organisms dies rapidly, can use either medium. Modified Cary-Blair is used for molecular multiplex panel processing- BioFire, BD MAX System, Verigene Luminex System
Methods for viral culture
Stool - refrigerate, do not freeze at -20oC. Rectal swab - use viral transport medium
No preservatives are used for which tests? (4)
- Direct wet mounts
- Clostridioides difficile toxin
- Virus detection by direct fluorescent antibody (DFA)
- ELISA/ Latex agglutination for Rotavirus
Reject samples if (6)
- Delay in transport >48hrs
- Multiple samples submitted on same day
- Dry swabs
- Hard, solid stools
- Stool with barium contamination
- Samples from patients hospitalized >3 days
Direct tests for detection of enteric pathogens (8)
- Gram stain
- Acid fast stain
- Trichrome stain
- Screen for oxidase positive organisms implicated in diarrheal disease
- Stool for fecal leukocytes
- Phase contrast or darkfield microscopy
- ELISA/latex agglutination
- Molecular testing
Possible Gram stain findings (4)
- Neutrophils or gram-positive cocci suggest staphylococcal infection.
- Gram-negative rods seen not helpful.
- Thin, comma-shaped gram-negative rod suggests Campylobacter or Vibrio
- Large, thin, parallel walls gram-positive rods suggests C. difficile
Which organisms is an acid fast stain used for? (3)
- Cryptosporidium sp.
- Isospora sp.
- Mycobacterium sp.
Screening for oxidase positive organisms implicated in diarrheal disease
SBA for oxidase +, -hemolytic organisms. Aeromonas sp., Plesiomonas sp., Vibrio sp. (will grow on SBA)
Fecal leukocytes in stool
Select bloody or mucus-containing areas of fecal material and mix with equal amounts of Loeffler’s methylene blue, or simply Gram stain
Phase contrast or darkfield microscopy
Darting motility and curved rods in warm specimen
Which pathogens does ELISA screen for? (6)
Giardia, Helicobacter, C. difficile, Cryptosporidium, Rotavirus, Entamoeba histolytica/dispar
Molecular testing
Biofire or Verigene- screens for Campylobacter, rotavirus, or C. diff
Processing stool specimens
Routine: look for SSC or SSYC- Salmonella, Shigella, Campylobacter spp. This is dictated by geographic location and seasons. If other pathogens suspected, physician should consult laboratory. Vibrio, E. coli O157:H7, Aeromonas, Plesiomonas, Yersinia. Anaerobic studies can be done, but not on species. STEC (EHEC) species: SMAC, SMAC-CT, CHROMagar media
Anaerobic studies
These are not done on feces. Small-bowel aspirates can be tested for Bacteroides and Bifidobacterium spp. These organisms can colonize small bowel. Cause malabsorption syndrome in the presence of obstruction
Routine culture media (10)
Inhibit some normal GI flora
1. BAP or BAP-A(ampicillin)
2. MAC- SMAC,CT-SMAC
3. HEA
4. XLD
5. SS agar
6. CAMPY-BAP & Skirrows
7. TCBS
8. CIN+Cold enrichment
9. CHROMagar
10. GN or Selenite enrichment broth (sub @ 24hr)
Reading Culture Plates
Look for non-lactose fermenting colonies. H2S positive (black centers) colonies suggest Salmonella sp. Examine special request media for suspicious colonies
Work-up of positive stool cultures
Salmonella or Shigella sp.- at 24 hr, set up gram-negative identification strip. At 48 hr, if identified as Salmonella or Shigella sp.- set up susceptibility tests. Serogroup Salmonella sp. or Shigella sp., subculture to two tryptic soy slants. Notify nursing unit or physician, infection control department, and state health department
Salmonella or Shigella slants
Use 24 hour incubation only
O157-STEC/EHEC,/VTEC or non-O157 STEC
NON-O157 STEC
O157 STEC
Culture-Independent Diagnostic Testing (CIDT)
Rapid but expensive compared to plated media and classical tube biochemicals. Includes MALDI-TOF and NAAT
MALDI-TOF
Colony ID from blood or MacConkey. Poor performance from SS and HE – only Genus ID
Genus and species ID for Salmonella and Campylobacter
Cannot differentiate E. coli, other STEC isolates or Shigella without IMVIC testing results
Cannot identify different serotypes of Salmonella
NAAT
BioFire, Verigene, Conventional PCR. Syndromic multiplex panels allow for rapid ID of multiple pathogens. More sensitive than culture methods, don’t have isolated organism for further testing
Policies- identification of C. diff (3)
- Only liquid or unformed stools tested
- Only test one specimen per patient every 24 hr.
- Up to 2 specimens tested within 7 days, 3-days apart
Toxin A&B, glutamate dehydrogenase (GDH)- C. diff
ELISA - alone not sensitive enough for ID - must be used with other testing. Need with positive GDH assay, GDH assay must also be in combination with another assay. NAAT - ALONE is enough for a definitive ID. Toxin assay – samples frozen at -70C
C. diff cultures
Within 2 hours of collection, cultures are stored under anaerobic conditions. Cycloserine-cefoxitin-fructose (CCFA) or cycloserine mannitol agar (CMA). Characteristics: fructose (+), mannitol (V+), nonhemolytic. Fluorescent pigment
