Bacterial Gastroenteritis

Patient Population: Pediatric
Condition Major Pathogens  First-choice Therapy Alternative Therapy Comments

Bacterial gastroenteritis, community-onset 

Characterized by frequent, sometimes bloody, small-volume diarrhea associated with abdominal pain and cramping 

Escherichia coli 

Salmonella species 

Shigella species 

Campylobacter jejuni 

Yersinia enterocolitica 

Supportive care is the primary therapy for most patients 

Antibiotics can predispose to complications such as hemolytic uremic syndrome with Shiga-toxin producing E. coli infection 


Consider empiric therapy in toxic-appearing patients, young infants*, or immunocompromised hosts, or if recent international travel with diarrhea & fever:        

10  mg/kg/dose (max 500 mg/dose) enterally daily  


50 mg/kg/dose (max 1000 mg/dose) IV q24h  

*For infants 1-3 months of age and if needed for infections with other sites involved e.g. Salmonella gastroenteritis with bloodstream infection. For infant <1 month of age refer to Fever Without a Source - Young Infant section for initial empiric therapy 

Avoid empiric treatment if persistent diarrhea has lasted 14 days or more  


For traveler's diarrhea (enterotoxigenic E. coli)

Azithromycin 10 mg/kg/dose (max 500 mg/dose) enterally daily x 3 days - provide un-reconstituted powder for suspension to infants and children traveling in high-risk areas 


Send stool culture (BCH OAK) or bacterial panel (BCH SF) for diagnosis 

Consider testing for Clostridioides difficile if patient has recent hospital or antibiotic exposure 

Blood cultures should also be sent for patients who are hospitalized and/or toxic-appearing  with suspected bacterial gastroenteritis. If antibiotic therapy is given for Salmonella gastroenteritis, blood culture should be obtained prior to initiation of antibiotic.  

Directed therapy may be indicated early in the course for specific pathogens (such as Campylobacter, Shigella, Yersinia) but in most cases should be deferred until a positive stool culture result is obtained. For recommended therapies, refer to IDSA guidelines linked below or consult ID. 

Duration of therapy (if given) depends on the specific diagnosis 


Shane, AL, et al. Infectious Diseases Society of America clinical practice guidelines for the diagnosis and management of infectious diarrhea. Clinical Infectious Diseases, 2017: 65, e45-e80.  

American Academy of Pediatrics. In: Kimberlin DW, Barnett ED, Lynfield R, Sawyer MH, eds. Red Book: 2021 Report of the Committee on Infectious Diseases. 32nd ed. Elk Grove Village, IL: American Academy of Pediatrics; 2021.  

CDC Yellow Book 2020. Traveler's Diarrhea

Pediatric Empiric Antimicrobial Therapy Guidelines

This is a subsection of the UCSF Benioff Children’s Hospitals Empiric Antimicrobial Therapy Guidelines, developed by the Pediatric Antimicrobial Stewardship Programs at each campus to inform initial selection of empiric antimicrobial therapy for children at the UCSF Benioff Children’s Hospitals and affiliated outpatient sites. 

These are guidelines only and not intended to replace clinical judgment. Modification of therapy may be indicated based on patient comorbidities, previous antibiotic therapy or infection history. Doses provided are usual doses but may require modification based on patient age or comorbid conditions. Refer to Pediatric Antimicrobial Dosing Guideline for further guidance on dosing in children, and Neonatal Dosing Guideline for infants < 1 month of age. Consult a pediatric pharmacist for individualized renal or hepatic dose adjustment. Durations provided are usual recommendations for patients who are responding appropriately to therapy. For additional guidance, please contact Pediatric Infectious Diseases (ID) or the Pediatric Antimicrobial Stewardship Program (ASP) at the campus where your patient is receiving care.  

For questions or feedback about these guidelines, please email primary content owners, Rachel Wattier, Pediatric ASP Medical Director at BCH SF and Prachi Singh, Pediatric ASP Medical Director at BCH OAK. 

The content of these guidelines was updated in July 2021. See Summary and Rationale for Changes (password login to Box needed) for detailed explanations of the content changes.