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GI infections Flashcards

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1
Q

Predisposing factors for GI infections (5)

A
  1. Travel to area with poor hygiene- direct exposure to sewerage
  2. Fecal contaminated food or water
  3. Food products not properly cleaned or cooked
  4. Previous, prolonged antimicrobial treatment
  5. Immunosuppressed patients suffer disseminated infections
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2
Q

Anatomy of the GI tract

A

Alimentary canal- includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, anus

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3
Q

Functions of the GI tract (2)

A
  1. Absorption of nutrients
  2. Excretion of waste products
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4
Q

GI host defense mechanisms (6)

A
  1. Peristalsis
  2. pH
  3. Mucus, lysozyme, proteases, lipases
  4. Secretory IgA
  5. Phagocytes
  6. Normal flora
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5
Q

Upper GI tract infections

A

Impact the stomach and duodenum. Infections include gastritis and peptic ulcerative disease

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6
Q

Lower GI tract infections

A

Impacts the small and large intestines. Symptoms- diarrhea, dysentery (purulent, mucous, bloody), cramping and abdominal pain

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7
Q

Normal flora of the upper small intestine (2)

A
  1. Streptococci
  2. Lactobacilli
    10 - 1000 organisms/mL
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8
Q

Normal flora of the distal ileum (2)

A
  1. Enterobacterales
  2. Bacteroides sp.
    106 - 107 organisms/mL
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9
Q

Normal flora of the large bowel (5)

A

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

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10
Q

Nosocomial pathogens (5)

A
  1. Staphylococcus aureus
  2. Pseudomonas aeruginosa
  3. Antimicrobial-resistant gram-negative rods
  4. Clostridioides difficile
  5. Candida albicans
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11
Q

Pathogenic mechanisms of enteric pathogens (3)

A
  1. Adherence to intestinal mucosa
  2. Toxigenic
  3. Invasion of the mucosal epithelium
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12
Q

Adherence to intestinal mucosa

A

Pathogens would have this mechanism prevent normal absorption and normal secretory function

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13
Q

Toxigenic infection mechanism

A

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

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14
Q

Pathogenic invasion of mucosal epithelium

A

Cell destruction. There is occasional invasion of the bloodstream and systemic disease

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15
Q

Gram positive pathogens (5)

A
  1. S. aureus
  2. Bacillus cereus
  3. Clostridium perfringens Type A
  4. Clostridium botulinum
  5. Clostridioides difficile
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16
Q

S. aureus

A

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.

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17
Q

Bacillus cereus

A

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

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18
Q

Clostridium perfringens Type A

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

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19
Q

Clostridium botulinum

A

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

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20
Q

Clostridioides difficile

A

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

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21
Q

Gram negative pathogens

A
  1. Salmonella
  2. Shigella
  3. Yersinia species
  4. Escherichia coli
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22
Q

Salmonella species (3)

A
  1. Salmonella Typhi - serotype D1, typhoid (enteric fever)
  2. Salmonella Enteritidis - serotype group D
  3. Salmonella Typhimurium - serogroup B
    Order Enterobacterales, more than 2400 serovars
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23
Q

Shigella species (4)

A
  1. S. dysenteriae, group A
  2. S. flexneri, group B
  3. S. boydii, group C
  4. S.sonnei, group D
    Order Enterobacterales
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24
Q

Yersinia species (2)

A
  1. Y. enterocolitica
  2. Y. pseudotuberculosis
    Motile at 22-30C, NON-MOTILE at 37C.
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25
Q

Escherichia coli

A

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

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26
Q

Categories of Gram-negative pathogenic mechanisms (4)

A
  1. Enterohemorrhagic (EHEC/STEC)
  2. Enteroinvasive (EIEC)
  3. Enteropathogenic (EPEC)
  4. Enteroaggregative (EAEC)
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27
Q

Enterohemorrhagic

A

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

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28
Q

Oxidase positive glucose fermenting pathogens (3)

A

Gram negative
1. Aeromonas hydrophila
2. Plesiomonas shigelloides
3. Vibrio sp.

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29
Q

Vibrio species (3)

A
  1. V. parahaemolyticus
  2. V. vulnificus
  3. V. cholerae
30
Q

Vibrio cholerae

A

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

31
Q

Oxidase positive glucose non-fermenting pathogens (2)

A
  1. Campylobacter species
  2. Helicobacter pylori
32
Q

Campylobacter species (3)

A
  1. C. jejuni
  2. C. coli
    3, C. fetus
33
Q

GI viruses (4)

A
  1. Hepatitis viruses
  2. Rotavirus
  3. Norwalk-like agents
  4. Adenovirus
34
Q

GI parasites (6)

A
  1. Giardia sp.
  2. Cryptosporidium sp.
  3. Cyclospora sp.
  4. Entamoeba histolytica/dispar
  5. Balantidium coli
  6. Trichinella sp.
35
Q

Diagnosis of gastritis and peptic ulcers

A

Specimen- gastric-antral biopsy, not stool. The etiological agent is Helicobacter pylori

36
Q

Identification of Helicobacter pylori (4)

A
  1. Skirrow agar or Campylobacter agar with cefoperazone. Incubate microaerophilically at 35oC, urease – rapid positive
  2. Urea breath test
  3. ELISA antigen detectable in stool samples
  4. Serology – IgG for isolate
37
Q

Gastritis and peptic ulcer treatment

A

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

38
Q

When is collection of a GI sample warranted?

A

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

39
Q

Ideal GI sample collection

A

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

40
Q

Types of GI specimens (5)

A
  1. Stool(fecal material) - specimen of choice- diarrheal samples are expected for those with infection
  2. Rectal swabs
  3. Duodenal aspirate
  4. Gastric aspirate
  5. Other: bile, colostomy, ileostomy
41
Q

Rectal swabs

A

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

42
Q

Duodenal aspirate

A

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

43
Q

Gastric aspirate

A

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.

44
Q

Transport and storage of GI pathogens

A

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

45
Q

Modified Cary-Blair transport medium or buffered glycerol transport medium use

A

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

46
Q

Methods for viral culture

A

Stool - refrigerate, do not freeze at -20oC. Rectal swab - use viral transport medium

47
Q

No preservatives are used for which tests? (4)

A
  1. Direct wet mounts
  2. Clostridioides difficile toxin
  3. Virus detection by direct fluorescent antibody (DFA)
  4. ELISA/ Latex agglutination for Rotavirus
48
Q

Reject samples if (6)

A
  1. Delay in transport >48hrs
  2. Multiple samples submitted on same day
  3. Dry swabs
  4. Hard, solid stools
  5. Stool with barium contamination
  6. Samples from patients hospitalized >3 days
49
Q

Direct tests for detection of enteric pathogens (8)

A
  1. Gram stain
  2. Acid fast stain
  3. Trichrome stain
  4. Screen for oxidase positive organisms implicated in diarrheal disease
  5. Stool for fecal leukocytes
  6. Phase contrast or darkfield microscopy
  7. ELISA/latex agglutination
  8. Molecular testing
50
Q

Possible Gram stain findings (4)

A
  1. Neutrophils or gram-positive cocci suggest staphylococcal infection.
  2. Gram-negative rods seen not helpful.
  3. Thin, comma-shaped gram-negative rod suggests Campylobacter or Vibrio
  4. Large, thin, parallel walls gram-positive rods suggests C. difficile
51
Q

Which organisms is an acid fast stain used for? (3)

A
  1. Cryptosporidium sp.
  2. Isospora sp.
  3. Mycobacterium sp.
52
Q

Screening for oxidase positive organisms implicated in diarrheal disease

A

SBA for oxidase +, -hemolytic organisms. Aeromonas sp., Plesiomonas sp., Vibrio sp. (will grow on SBA)

53
Q

Fecal leukocytes in stool

A

Select bloody or mucus-containing areas of fecal material and mix with equal amounts of Loeffler’s methylene blue, or simply Gram stain

54
Q

Phase contrast or darkfield microscopy

A

Darting motility and curved rods in warm specimen

55
Q

Which pathogens does ELISA screen for? (6)

A

Giardia, Helicobacter, C. difficile, Cryptosporidium, Rotavirus, Entamoeba histolytica/dispar

56
Q

Molecular testing

A

Biofire or Verigene- screens for Campylobacter, rotavirus, or C. diff

57
Q

Processing stool specimens

A

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

58
Q

Anaerobic studies

A

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

59
Q

Routine culture media (10)

A

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)

60
Q

Reading Culture Plates

A

Look for non-lactose fermenting colonies. H2S positive (black centers) colonies suggest Salmonella sp. Examine special request media for suspicious colonies

61
Q

Work-up of positive stool cultures

A

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

62
Q

Salmonella or Shigella slants

A

Use 24 hour incubation only

63
Q

O157-STEC/EHEC,/VTEC or non-O157 STEC

A
64
Q

NON-O157 STEC

A
65
Q

O157 STEC

A
66
Q

Culture-Independent Diagnostic Testing (CIDT)

A

Rapid but expensive compared to plated media and classical tube biochemicals. Includes MALDI-TOF and NAAT

67
Q

MALDI-TOF

A

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

68
Q

NAAT

A

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

69
Q

Policies- identification of C. diff (3)

A
  1. Only liquid or unformed stools tested
  2. Only test one specimen per patient every 24 hr.
  3. Up to 2 specimens tested within 7 days, 3-days apart
70
Q

Toxin A&B, glutamate dehydrogenase (GDH)- C. diff

A

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

71
Q

C. diff cultures

A

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

Clinical Microbiology (19 decks)

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