Gastrointestinal Infections

Michael Kaminski

Acute Diarrhea

Etiology & Pathogenesis 

  • ≥3 unformed stools/day or >250g/day; acute <14d, persistent 14–29d, chronic ≥30d 
    • Viral: Norovirus, rotavirus, adenovirus 
    • Bacterial: C diff > Salmonella > Campylobacter > Shigella > STEC 
    • Parasitic: Giardia, Cryptosporidium, E. histolytica (primarily persistent diarrhea) 
  • Host risk factors: infant/elderly, immunosuppressed, PPI, abx, abdominal surgery 
  • Low-dose pathogens (Shigella, norovirus, Giardia, Cryptosporidium, high person-to-person spread); moderate/high-dose pathogens (Salmonella, Campylobacter typically foodborne)

Clinical Presentation 

  • Vomiting-predominant: viral or preformed toxin (S. aureus, B. cereus); incubation 2–7h (toxin) vs. >14h (viral)
  • Colitis/dysentery (small-volume, bloody, tenesmus): Shigella, Campylobacter, STEC, C. difficile, invasive E. coli 
  • Red Flags: Febrile, grossly bloody stool, systemically ill, severe abd pain 
  • Sequelae: Reactive arthritis (Salmonella, Shigella, Yersinia); GBS (Campylobacter); postinfectious IBS

Diagnostics & Workup 

  • Send stool studies when febrile, hospitalized, persistent, at risk (elderly immunocompromised), “spreaders” (food handlers, daycare workers) 
  • Stool studies: GIPP, C diff, Stool OandP (if c/f parasitic) 
  • CT abd/pel only if other c/f intraabdominal pathology: intraabdominal complication, ischemic colitis, fulminant C. diff (decreased bowel sounds, peritonitic, distended), etc.

Treatment by Pathogen 

  • Supportive care: Fluids (PO preferred), replace electrolytes; loperamide if afebrile, no dysentery

Pathogen/Syndrome

First-Line Therapy
Norovirus, Rotavirus, etc. Supportive Care only
Shigella Cipro x3d OR Azithro x3d
Salmonella (nontyphoidal) No abx if mild/healthy;
Severe or bacteremia: FQ x/d or CTX 2g x/d
Typhoid/Enteric fever Uncomplicated: FQ or azithro
Complicated: FQ or IV CTX 7d (≥14d if immunosuppressed)
Campylobacter Azithro (500 mg qd x3d)
STEC (O157:H7) No abx (risk HUS)
Travelers' diarrhea No Fever/dysentery: Typically no abx, if treating: Cipro x1–3d
+Fever/dysentery: Azithro x1d
Giardia Tinidazole 2g single dose
Cryptosporidium Nitazoxanide x3–14d
Amebiasis Metro x5d + luminal agent (paromomycin or diloxanide)
C Diff See GI Section

Other GI Infections

Whipple Disease 

(T. whipplei)

  • Arthralgias, weight loss, chronic intermittent diarrhea, abdominal pain, +/- valvular disease 
  • Dx: Endoscopy/Bx with PAS and PCR for T. whipplei, +/- PCR from synovial fluid/lymph nodes 
  • Tx: CTX or PCN x2W, then Bactrim x 1Y, ID consult

Small Intestinal Bacterial Overgrowth 

(SIBO)

  • Bloating, abdominal pain, watery diarrhea 
  • A/w intestinal motility disorders, chronic pancreatitis, post-surgical changes (blind loops) 
  • Tx: Rifaximin x7-14d

H. pylori (see GI section) 

Acute cholangitis (see GI section)

Viral Hepatitis

Hepatitis A-E, HSV, VZV, EBV, CMV 

  • Evaluation: Liver enzymes (ALT>AST generally), elevated bili, HAV serology, HBV panel, HCV IgG w PCR. EBV/CMV/HSV/VZV PCRs. Consider testing for HDV (if HBV (+), from or travel to endemic area, cirrhosis, IVDU or other blood exposures), HEV (if pregnant, IVDU or other blood exposures, cirrhosis, undercooked meat exposure).

Hepatitis A 

  • ~4W incubation, fecal oral transmission. S/Sxs: N/V, anorexia, fever, malaise, abdominal pain, jaundice, dark urine. Dx: HAV IgM+, ALT>AST (1000s), elevated bili Tx: supportive care, vaccine available. Usually self-limiting but can cause fulminant liver failure. No chronic disease.

Hepatitis B

  • Transmission is bloodborne via perinatal, percutaneous, sexual. 2-3M incubation. Risk of chronicity inversely related to age at infection (90% neonates → <5% adults) 
  • Acute: jaundice, RUQ pain, fatigue, N/V, dark urine, arthralgias; majority clear spontaneously. 
  • Chronic: often asymptomatic, may progress to cirrhosis/HCC (ascites, varices, splenomegaly, jaundice, HE). Extrahepatic manifestations: PAN, membranous nephropathy, cryoglobulinemia 
  • Dx; LFTs, HBsAg, anti-HBs, anti-HBc, HBeAg, anti-HBe, HBV PCR, LFTs, INR, HIV/HCV/HDV screening, HAV immunity; HCC surveillance with ultrasound + AFP q6 months if indicated

HBV Phases

HBs

HBe

IgM anti-HBc

HBV DNA

ALT
Acute + + + High High
Window − − + Negative/Low Normal/Low
Resolved − − + Negative Normal
Immune Tolerant + + − Very High Normal
Immune Active (HBeAg+) + + − High High
Immune Active (HBeAg−) + − − Moderate High
Inactive Carrier + − − Negative/Low Normal
  • Tx: Discuss with Hepatology (no HIV) or ID (HIV+). Indications: Immune-active chronic hepB or cirrhosis with any detectable viremia. Preferred agents: Entecavir or tenofovir. Maybe IFNa. Depends on HBV viral load amongst other things.

Hepatitis C 

  • Transmitted via blood, sex, perinatal parenteral, incubation period 6-8 weeks, majority progress to chronic infection 
  • USPSTF recommends screening in all adults 18-79 with Hep C Ab, if + then PCR for viral load 
  • Dx: Ab +/RNA+ = current infxn, Ab+/RNA- = cleared or treated infxn. Check HCV genotype. Also check HIV, HepB. If cirrhosis then elastography+/-AFP. 
  • Acute: usually asymptomatic. Chronic: Nonspecific nausea, diarrhea, abdominal pain, anorexia, weakness, often progresses to cirrhosis and HCC. Extrahepatic: cryoglobulinemia, porphyria cutanea tarda, MPGN 
  • Tx: for chronic infections, consult ID (if HIV+) or GI (HIV-). Antivirals targeted to HCV genotype. Recheck viral load after 12W for SVR

Hepatitis D

  • Requires HBV for infection, consider screening with HBV

Hepatitis E

  • Rare in US but common worldwide. Self-limited acute infection with jaundice, malaise, anorexia, N/V, abd pain. Fecal oral transmission. Higher mortality in pregnant women
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