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GI Infections

Ahmed Samy, Lin Cao

Acute Diarrhea


  • ≥3 BMs/day or abnormally loose stools
  • Vast majority of infectious diarrhea cases are acute with more persistent diarrhea, consider additional workup for noninfectious etiologies as well
  • Can be watery or inflammatory (bloody stools, signs of sepsis, severe abdominal pain)
  • History: food hx (particularly undercooked meats or unpasteurized dairy), occupational exposures, recent travel, pet and animal exposures, immunocompromised


  • Exam: volume status, abdominal pain
  • Labs: CBC for leukocytosis/eosinophilia, BMP for electrolyte abnormalities, BCx if c/f systemic illness, consider GIPP or stool testing if severe illness or immunocompromise


  • Most cases are self-limited and resolve with just supportive care
  • Antimotility agents: bismuth subsalicylate, loperamide
    • Avoid antimotility agents with C. diff and inflammatory diarrhea
  • Avoid abx with Shigella and EHEC (can precipitate HUS), Salmonella (prolongs carrier time)
  • Antibiotics only indicated with severe illness or certain immunocompromised hosts:
    • Cipro 500mg bid or
    • Levofloxacin 500mg qd 3-5 days or
    • Azithro 500mg qd 3 days

Other GI Infections

Tropical Sprue

Background and Presentation

  • Common in native populations and visitors (one month) within the tropical area that involves the equator to 30° latitude.
  • Etiology is not entirely known, although infection and bacterial overgrowth are proposed mechanisms.
  • High-risk patients are those with endemic travel who present with chronic diarrhea (steatorrhea) and signs of malabsorption (glossitis, fatigue).


  • Labs: stool O&P, celiac serologies, CBC (megaloblastic anemia), folate, vitamin B12, niacin (less common)
  • Consider further workup for additional DDX depending on risk factors: opportunistic infections in the immunocompromised (HIV), idiopathic (tropical) pancreatitis, SIBO, intestinal lymphoma.
  • Best diagnostic test = endoscopy with mucosal biopsy of the small bowel. Findings (blunt villi, long crypts, increased inflammation) can be suggestive but are not specific to diagnosis (similar to celiac).


  • Antibiotics: 250mg tetracycline QID or 100mg doxycycline BID x 3-6 months, depending on resolution of symptoms and labs (CBC, vitamins).
  • Folate supplementation: 1-5mg daily for antibiotic duration. Helps mitigate symptoms and revert intestinal architecture. Can also be diagnostic based on response. Vitamin B12 supplementation if needed.

Whipple Disease

Background and Presentation

  • Infection of Tropheryma whipplei.
  • Combination of the classic four: migratory joint pains (early and preceding sign), abdominal pain, diarrhea, weight loss (later). Low threshold to evaluate CNS (cognitive dysfunction, cerebellar involvement) and cardiac (endocarditis) systems.


  • First consider overlapping syndromes that are more common (rheumatologic – seronegative polyarthritis, GI – IBD, infection – HIV).
  • Upper endoscopy, usually in the small bowel with biopsies for PAS-positive macrophage staining and PCR testing for T. whipplei.
  • If there is low suspicion of GI involvement, biopsy site should be reconsidered based on clinical presentation (joint fluid, lymph node).
  • If testing is positive, and even in the absence of neuro symptoms, must test CSF.


  • Initial therapy: CTX or penicillin G – dose/duration depends on system involved but likely minimum of two weeks.
  • Maintenance therapy: TMP-SMX 1 DS tablet BID x 1 year.

Small Intestinal Bacterial Overgrowth (SIBO)

Background and Presentation

  • Excess of organisms not usually present in small intestine (oropharynx, colon) -> inflammation -> intestinal maldigestion and malabsorption (carbohydrates, fats, protein, vitamins) with dysmotility. Escherichia coli and Klebsiella are commonly isolated.
  • Patients at risk: intestinal motility disorders (diabetes, opioid use, radiation enteritis), anatomical abnormalities (post-surgical strictures, diverticulosis), microbe immune system dysregulation (IgA deficiency, HIV), metabolic changes in digestion (liver and pancreatic disease).
  • Presents with bloating, abdominal discomfort, diarrhea (chronic watery more common).
  • Evaluation
  • Least invasive and most practical: positive carbohydrate breath test, which can identify SIBO variation types based on monitoring levels of hydrogen and methane.
  • Labs may show vitamin and mineral (fat-soluble, B12, iron, thiamine, niacin) deficiencies, macrocytic anemia, and high fecal fat.
  • Consider alternate DDX that may be interrelated: Crohn disease, celiac disease (serology, duodenal biopsy), IBS (abdominal pain associated with stool patterns).
  • If unclear or no risk obvious risk factors: upper endoscopy and colonoscopy.


  • Rifaximin (550mg TID x 14d) is first-line. Neomycin (500mg BID) may also be needed based on carbohydrate breath test (methanogen overgrowth). Cost may be a barrier, alternative antibiotics available.
  • Up to 40% recurrence and persistent symptom rate after initial antibiotic course. More likely in older age, appendectomy, and PPI use. Empirically treat with another course of antibiotics, preferably different from the initial course. Repeat carbohydrate breath test if symptomatic after > 3 months from therapy.
  • Failure after two trials of antibiotics should prompt reevaluation of diagnosis.
  • Repletion of vitamin and mineral deficiencies, as noted above.

Viral Hepatitis (A-E)

Also consider HSV (especially in pregnancy), VZV, EBV, CMV though less common and usually seen more in immunocompromised pts Evaluation - HAV, HBV, HCV IgG with PCR, HDV, HEV, EBV Qt, CMV Qt, HSV Qt, VZV IgM/IgG - LFTs: elevated AST/ALT (ALT>AST generally) that often precedes elevation of bilirubin - Can present on a spectrum of severity ranging from elevated LFTs to acute liver failure; get hepatology involved early for evaluation and monitoring

Hepatitis A

  • Presentation: self-limited, N/V, fever, malaise, abdominal pain, jaundice, dark urine
  • Transmission: Fecal oral transmission
  • Tx: supportive care, vaccine available

Hepatitis B

  • Transmission: perinatal, sexual contact, parenteral
  • Acute:
    • Presentation: Most pts have subclinical hepatitis but can present with serum sickness-like syndrome, anorexia, nausea, jaundice, RUQ pain, elevated LFTs
    • Tx: Generally supportive care unless severe illness, then generally treat with tenofovir/entecavir
    • HBV is less likely to become chronic than HCV
  • Chronic:
    • Presentation: Generally asymptomatic but can progress to cirrhosis and HCC
    • Extrahepatic manifestations 2/2 circulating immune complexes: polyarteritis nodosa, membranous nephropathy, aplastic anemia
    • Tx: entecavir/tenofovir, involve GI/ID, based on development of cirrhosis, ALT, HBV DNA level, immunosuppressed status.
    • Vaccine available

Hepatitis C

  • Transmission: parenteral, blood transfusion (prior to 1992), sexual, perinatal transmission
    • USPSTF recommends screening in all adults 18-79
  • Acute Presentation
    • Generally asymptomatic but may have jaundice, nausea, dark urine, RUQ pain, elevated LFTs
    • Majority of hep C cases progress to chronic infection
  • Chronic Presentation:
    • Nonspecific nausea, diarrhea, abdominal pain, anorexia, weakness but can progress to cirrhosis and HCC, LFTs not always elevated
    • Extrahepatic manifestations directly related to viral infection: essential mixed cryoglobulinemia, membranoproliferative glomerulonephritis, thyroiditis, porphyria cutanea tarda, lichen planus, etc
  • Tx: antivirals targeted to HCV genotype, however, there are pangenotypic regimens. Recheck viral load after 12 wks

Hepatitis D

  • Requires HBV for infection, consider screening with HBV

Hepatitis E

  • Presentation: self-limited acute infection with jaundice, malaise, anorexia, N/V, ab pain
  • Transmission: Fecal oral transmission
  • Significantly higher mortality in pregnant individuals

Other GI Infections

  • For reference, infections outlined elsewhere in the GI chapter: diarrheal-associated (including C. difficile), H. Pylori, biliary-related (cholecystitis, choledocholithiasis, cholangitis), diverticulitis, and esophageal (odynophagia).