What is the algorithm to determine the causative agent of acute gastroenteritis in a patient?

Algorithm to Determine the Causative Agent of Acute Gastroenteritis

Initial Clinical Assessment

The diagnosis of acute gastroenteritis is primarily clinical, and microbiological testing should be reserved for specific high-risk situations rather than routine cases. 1, 2, 3

Step 1: Establish Clinical Diagnosis

• Document acute onset of diarrhea (≥3 loose stools in 24 hours) with or without nausea, vomiting, fever, or abdominal pain 4
• Assess hydration status through skin turgor, mental status, mucous membrane moisture, capillary refill, and vital signs 2
• Obtain recent history of fluid intake/output, travel, antibiotic use, exposure to ill contacts, and immunocompromised status 1, 2

Step 2: Differentiate Viral from Bacterial Etiology Clinically

Viral gastroenteritis characteristics: 5

• Sudden onset with prominent vomiting as initial manifestation
• Watery, non-bloody diarrhea developing 24-48 hours after vomiting
• Low-grade fever (<39°C)
• Self-limited duration (12-60 hours for norovirus; 3-8 days for rotavirus)
• Exposure to others with similar symptoms in group settings

Bacterial gastroenteritis characteristics: 5

• High fever (>39°C)
• Bloody or mucoid stools
• Severe, localized abdominal pain
• Prolonged symptom duration (>7 days)
• Recent antibiotic use or foreign travel

Indications for Microbiological Testing

Do NOT routinely test when viral gastroenteritis is the likely diagnosis in immunocompetent patients with mild-moderate disease. 3, 4, 6

Test in These Specific Situations: 2, 5, 6

• Bloody diarrhea with fever and systemic toxicity
• Severe dehydration (≥10% fluid deficit) or signs of sepsis
• Immunocompromised patients (HIV, transplant recipients, immunosuppressive therapy, malignancy)
• Infants <3-6 months with suspected bacterial AGE
• Recent antibiotic use (suspect Clostridioides difficile)
• Recent foreign travel to developing countries
• Prolonged diarrhea (>7 days) or complicated cases
• Institutionalized patients or outbreak settings with risk of dissemination
• Severe or localized abdominal pain raising concern for surgical pathology

Diagnostic Testing Algorithm

Primary Microbiological Tests: 2, 5, 6

When testing is indicated, order multiplex gastrointestinal PCR panel (preferred over traditional stool culture) testing for: 7

• Bacterial pathogens: Salmonella, Shigella, Campylobacter, Yersinia, Shiga toxin-producing E. coli (STEC)
• Clostridioides difficile and its toxin (mandatory if recent antibiotic use or diarrhea with/without acute abdomen) 1
• Viral pathogens: Norovirus, rotavirus (if clinically indicated)
• Parasites: Giardia, Cryptosporidium, Entamoeba histolytica (if prolonged diarrhea or travel history)

Additional Laboratory Tests: 2, 5

• Complete blood count and acute phase reactants (CRP) if signs of severe disease or sepsis
• Basic metabolic panel if severe dehydration or altered mental status
• Blood cultures if febrile, toxic-appearing, or signs of bacteremia
• Urinalysis with culture if urinary symptoms present to rule out UTI/pyelonephritis 2

Specimen Collection Requirements: 3

• Collect stool specimens within first 48 hours of illness onset for outbreak investigations (viral shedding drops below detectable levels after 2-3 days)
• Bulk specimens (not rectal swabs) from at least 10 ill persons required for outbreak diagnosis
• Paired serum specimens for outbreak investigation: acute phase (first week) and convalescent phase (third to sixth week)

Special Populations and Pathogens

Immunocompromised Patients: 1

• Maintain high clinical suspicion as signs/symptoms may not be reliable
• Consider HIV-specific pathogens: abdominal tuberculosis, Mycobacterium avium complex
• Cytomegalovirus (CMV) colitis requires endoscopic biopsy for diagnosis (peripheral blood/stool testing insufficient) 3
• Test for Cryptosporidium, Microsporidium, Isospora in HIV patients

Post-Antibiotic Exposure: 1, 2

• Mandatory C. difficile testing with toxin assay
• C. difficile and norovirus are leading pathogens in hospitalized adults, detected year-round with fall/winter predominance 7

Emerging and Underrecognized Pathogens: 8, 6

• Campylobacter infections may be missed by culture-based methods; consider serological testing (serology alone diagnosed 46% of Campylobacter cases in one study) 8
• Viral-bacterial co-infections occur in 22% of hospitalized adults and are probably underrecognized 8
• Simultaneous infection significantly more likely with rotavirus and salmonella (RR 3.6 and 2.5 respectively) 8

Critical Red Flags Requiring Immediate Evaluation

These findings mandate urgent diagnostic workup and possible surgical consultation: 5

• Bilious vomiting (suspect malrotation with volvulus)
• Localized right lower quadrant pain with peritoneal signs (suspect appendicitis)
• Absent bowel sounds (absolute contraindication to oral rehydration) 2
• Altered mental status or severe lethargy (severe dehydration or sepsis)
• Prolonged skin tenting >2 seconds with cool extremities (severe dehydration requiring IV fluids)

Common Pitfalls to Avoid

• Do not delay rehydration therapy while awaiting diagnostic testing; begin oral rehydration solution immediately based on clinical assessment 2, 3
• Do not collect specimens after 48 hours of illness onset, as diagnostic yield becomes negligible 3
• Do not routinely test immunocompetent patients with typical viral gastroenteritis presentation 3, 4
• Do not underestimate dehydration in elderly patients who may not manifest classic signs and have higher mortality risk 2
• Do not use culture-based methods alone for Campylobacter detection; consider adding serology 8
• Do not overlook co-infections, particularly in patients with rotavirus or salmonella 8