GI Infections





    • "Diarrhea"
      • Increase in water content, volume or frequency of stools.
      • Typically ≥3 stools/day (defined epidemiologically)
    • "Infectious Diarrhea"
      • Diarrhea due to infectious etiology.
      • Often accompanied by nausea, vomiting, abdo cramps. 
    • "Acute Diarrhea"
      • ≤14 days
    • "Chronic Diarrhea"
      • >14 days (Sometimes >30)

    Food-Related Diarrheal Illnesses



    • InfectiousDiarrheaApproach.png
    • Questions on history:
      • Characterize Symptoms:
        • Onset
          • abrupt? gradual? duration?)
        • Stool Characteristics
          • Watery, bloody, mucous, purulent, greasy etc..
        • Frequency of BM + quanity of stool
        • Dysenteric symptoms
          • fever, tenesmus (feeling need to passing stools, despite empty colon), blood and/or pus in stool
        • Volume Status
          • Thirst, tachycardia, orthostasis, decreased urination, lethargy, skin turgor
        • Associated Sx:
          • Nausea, vomiting, abdo pain, cramps, headache, myalgias, sensorium
      • Epidemiological Risk Factors
        • Travel to developing area
        • Day care
        • Unsafe foods (raw meats, eggs, shellfish, unpasteurized milk)
          • Swimming in or drinking untreated fresh surface water (lake/stream)
        • Sick contacts
        • Medications (antibiotics, antacids, anti-motility agents)
        • Medical Conditions (AIDS, immunosuppression)
        • Receptive anal intercourse

    Common Enteric Pathogens

    • Escherichia coli (STEC) (Shinga toxin-producing Escherichia coli)
      • Symptoms - Develop several days after exposure (toxin formed by growing bacterial contamination)
        • Bloody diarrhea (90% of pts) - hemorrhagic colitis.
        • Abdominal tenderness
        • Leukocytosis
        • Fever - uncommon (1/3 of pts)
      • Strain O157:H7 and O104:H4 is the most common in US.
      • Producing shinga toxin --> cause vascular damage --> Hemorrhagic colitis.
    • Bacillus cereus, Staphylococcus aureus
      • Also foodborne GI disease.
      • Symptom onset in <24hrs --> Caused by pre-formed toxin.
        • Nausea and vomiting (less commonly diarrhea).
    • Campylobacter jejuni and Yersinia enterocolitica
      • Also foodborne GI disease.
      • Bloody diarrhea UNCOMMON.
      • Fever in most patients.


    Overview Enteric Pathogens

    • Campylobacter jejuni

      • Raw or undercooked poultry, raw dairy products, and contaminated produce.

      • Sometimes bloody, usually not.

      • <1% get Guillain-Barre Syndrome

    • E.coli

      • Shinga Toxin-Producing E. coli (STEC) (aka. enterohemorrhagic E. coli infection - EHEC)

        • Classically R-sided abdo pain without high fever (bloody or non-bloody diarrhea).

        • Risk of hemolytic Uremic Syndrome, Renal Failure

      • Shunga Toxin-Producing E. coli O157 (STEC O157)

        • Test for shinga toxin and E.coli O157 strain analysis.

      • Enteroaggregative E.coli

        • Malnutrition with/without diarrhea.

    • Salmonella

      • Can cause aortitis --> bacteria bind to vessels with lots of atherosclerosis or grafts.

      • Reactive arthritis can occur. (if HLA-B27 positive)

    • Shigella

      • Reactive arthritis can occur. (if HLA-B27 positive)

    • Yersinia enterocolitica

      • Persistent abdo pain and fever in Asian-Americans in California and African-American infants

      • Perform cultures in fall/winter seasons.

      • Causes swelling of mesenteric lymph node, can mimic appendicitis.

      • Reactive arthritis can occur. (if HLA-B27 positive)

    • Cyclospora

    • Cryptosporidium

      • Malnutrition

    • Giardia

    • Vibrio

      • Seafood/sea coast exposure

      • Culture

    • Clostridium difficile

    • Caliciviruses

    • Other Enteric Viruses


      • Oral Glucose or Starch containing electrolyte solution.
      • (See WHO recommended rehydration solutions)
    • Report Suspected Outbreak
    • Stool culture (yield extremely low)
      • 5.8% positive for enteric pathogens:
      • Of all stool cultures: 1.4% Campylobacter, 0.9% salmonella, 0.6% shingella, 0.3%E.coli O157.
      • Recommendation: Test in all bloody diarrhea cases.  Other testing is controversial. 
    • Treatments:
      • Controversial
      • Risks: resistance, suprainfection, induction of disease-producing phage
      • Empiric Therapy Recommended in:
        • Traveller's diarrhea (ifETEC and other bacterial causes are likely)
          • Fluoroquinolone (Septra in children)
          • Reduces duration of illness from 3-5d to 1-2d.
        • Diarrhea >10-14d with suspected giardia (negative tests, hx of water exposure)
        • Moderate to severe invasive diarrhea (consider treating) - fluoroquinolone or TMP/SMZ in children.
      • Concern about resistant Campylobacter infections (10% in Minnesota)
        • Patients get worse as quinolones eradicate other flora.
    • If bloody diarrhea or HUS
      • Stool culture
      • Stool E.coli O157 detection
      • Stool Shinga toxin detection
    • Don'ts:
      • DO NOT send stool culture if diarrhea develops >3 days of hospitalization. (15-50% of all stool cultures)
        • Known as the "3-day-rule"
      • DO NOT repeat stool for Ova/Parasites.




    • Guerrant RL, Van Gilder T, Steiner TS, et al; Infectious Diseases Society of America. Practice guidelines for the management of infectious diarrhea. Clin Infect Dis. 2001;32(3):331-351. PMID: 11170940

    Clostridium Difficile

    Source: "A woman with community-acquired Clostridium difficile infection" by Christopher Kandel, et al (2012) CMAJ

    Source: Orange book

    source: NEJM+ Knowledge


    Click here for 2010 guidelines. 


    • Risk Factors
      • Antibiotic use in last 3 months (most modifiable)
        • Clindamycin
        • Fluoroquinolones
        • Broad-spectrum penicillins
        • Cephalosporins
      • PPIs
      • Previous abdo sugery
      • Age ≥65
      • IBD
      • Recent hospital stays
    • Symptoms:
      • ACUTE non-bloody watery diarrhea (occasionally bloody).
      • Lower abdominal pain
    • Clinical Features:
      • Fever, High WBC count
    • Complications:
      • Fulminant colitis (2-3%)
      • Toxic megacolon (triad: colon dilation ≥ 6cm on KUB, colonic atony, systemic toxicity)
      • Bowel Perforation
    • Diagnosis:
      • Stool PCR -many false negatives of colonization
      • (OR toxin assay EIA detects toxin B or A, fast, more specific)
    • Treatment
      • Stop offending abx (or shorten course)
      • Stop anti-motility agents
      • Determine if Severe or Non-Severe
        • Severe Vs. Non-Severe C.diff infection

          ANY of the following:


            1. Leukocytosis WBC ≥ 15,000 /uL

            2. Creat 1.5x patient's baseline


          For Severe, differentiate by:

          Complicated Vs. Uncomplicated

          ANY of following

           1. Hypotension

            2. Shock

            3. Ileus

            4. Megacolon

      • If NON-SEVERE (mild-to-mod)
        • Metronidazole 500mg po q8h  x10-14d
          • (new evidence, but not in guidelines, to start with OR Vancomycin 125mg PO q6h)
            • (NEJM paper: equal cure rates, MTZ less well tolerated)
        • Treat for 10-14d 
      • If SEVERE:
        • Vancomycin 125mg po q6h  x 10-14d (+/- Metronidazole)
        • Vancomycin 500mg QID PO/NG + metronidazole 500mg IV q8h
        • (If Ileus, add PR vanco)
      • If worsening  (ileus, rising WBC, rising lactate, shock, toxic megacolon, peritonitis)
        • Abdo CT
        • Urgent SURGERY CONSULT (subtotal colectomy (?diverting loop ileostomy or colonic lavage)
        • Consider PR vanco
      • NOTES
        • if cannot discontinue offending abx... continue C.diff therapy until ≥7d abx stopped. 
        • Stools may continue to be C.diff positive (do not retreat unless symptoms)
      • Recurrence:
        • 15-30% risk (usually in 2w of stopping abx therapy)
        • 1st Recurrence: Same as initial episode
        • 2nd Recurrence: Vancomycin PO pulse + taper.
          •  Consider ID, consider fecal transplant (NEJM 2013, JAMA 2016), or fidaxomicin 200mg BID x10d. 
      • Probiotics Saccharomyces boulardii - reduce recurrence risk. (avoid in immunosuppression).
        • Studies controversial.  
        • Most antibiotics not helpful (Lancet 2013)
      • CDiffRegimens.jpg
    • Monitor Treatment
      • Watch complications:   Ileus, Peritonitis
      • Typically diarrhea x3-4 days resolves by day 7.
      • Do not re-test stool (toxin persists for up to 6 weeks (40%))
    • Prevent Spread
      • Contact precautions!!
      • Two factors in prevention:
        • 1. Limiting Transmission
        • 2. Minimizing abx exposure 
      • Hand hygeine important!
        • Use Soap & Water.  C. diff spores are resistant to EtOH-based hand sanitizers.
        • All eqiupment wash with hypochloride-based solution.
    • Future Research:
      • Fidaxomicin vs. vancomycin --> similar cure rates.
        • Fidaxomicin had lower recurrence than vanco.
      • Monoclonal antibodies to C.diff toxin A and B reduce recurrence.
      • Rifaximin (minimally-absorbed macrolide) - given for two weeks after course of vanco decreased recurrence.
      • Fecal transplant - Observational studies --> effective to prevent recurrence.
        • No standardized regimens and no RCTs.

    Liver Abscesses / Cholangitis

    • Sources:
        1. Biliary tract infection
        2. Portal vein bacteremia  (Appendicitis, diverticulitis, IBD)
        3. Direct extension (perfed duodenal ulcer, perfed gall bladder, or perinephrin/pancreatic/subphrenic abscess).
        4. Skin (Penetrating wounds, surgical)
        5. Bactermia (any cause, via hepatic artery and multiple abscesses)
        6. Unidentified (25% of cases)

    • Organisms:
      • 1. Gram negatives + (Enterococcus) + anaerobes.!!!! (MOST COMMON)
      • 2. Skin organisms (S. aureus, GAS)
      • 3. Bacteremia (S.aureus, Strep angionus?, Klebsiella, Odd things)
    • Organisms (approach #2)
      • By site of primary infection
        • Peritonitis
          • Usually polymicrobial
            • Anaerobes (Bacteroides, Fusobacterium Peptostreptococcus, Actinomyces, and microaerophilic streptococci (S. milleri)
            • Gram-negatives (K. pneumoniae - esp the K1 serotype)
        • Candida (if immunocompromised)
        • Amoebic liver abscess 
    • Treat with Amox-Clav for 3-4-6 weeks (esp longer if cannot drain abscesses)
      • If allergic to amox clav then treat with Cipro-flagyl (ignore Enterococcus).
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