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"Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea"

Published: Clinical Infectious Diseases ; 2017 ; 65 : e45 -e80


*Every 12 to 18 months following publication, IDSA reviews its guidelines to determine whether an update is required. This guideline was published in October 2017 and is the most current version.

The widening array of recognized enteric pathogens and the increasing demand for cost-containment sharpen the need for careful clinical and public health guidelines based on the best evidence currently available. Adequate fluid and electrolyte replacement and maintenance are key to managing diarrheal illnesses. Thorough clinical and epidemiological evaluation must define the severity and type of illness (e.g., febrile, hemorrhagic, nosocomial, persistent, or inflammatory), exposures (e.g., travel, ingestion of raw or undercooked meat, seafood, or milk products, contacts who are ill, day care or institutional exposure, recent antibiotic use), and whether the patient is immunocompromised, in order to direct the performance of selective diagnostic cultures, toxin testing, parasite studies, and the administration of antimicrobial therapy (the latter as for traveler's diarrhea, shigellosis, and possibly Campylobacter jejuni enteritis). Increasing numbers of isolates resistant to antimicrobial agents and the risk of worsened illness (such as hemolytic uremic syndrome with Shiga toxin-producing Escherichia coli O157:H7) further complicate antimicrobial and antimotility drug use. Thus, prevention by avoidance of undercooked meat or seafood, avoidance of unpasteurized milk or soft cheese, and selected use of available typhoid vaccines for travelers to areas where typhoid is endemic are key to the control of infectious diarrhea.

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Clinical, Demographic, and Epidemiologic Features

I. In people with diarrhea, which clinical, demographic, or epidemiologic features have diagnostic or management implications?


  1. A detailed clinical and exposure history should be obtained from people with diarrhea, under any circumstances, including when there is a history of similar illness in others (strong, moderate).
  2. People with diarrhea who attend or work in child care centers, long-term care facilities, patient care, food service, or recreational water venues (e.g., pools and lakes) should follow jurisdictional recommendations for outbreak reporting and infection control (strong, high).

II. In people with fever or bloody diarrhea, which clinical, demographic, or epidemiologic features have diagnostic or management implications?


  1. People with fever or bloody diarrhea should be evaluated for enteropathogens for which antimicrobial agents may confer clinical benefit, including Salmonella enterica subspecies, Shigella, and Campylobacter (strong, low).
  2. Enteric fever should be considered when a febrile person (with or without diarrhea) has a history of travel to areas in which causative agents are endemic, has had consumed foods prepared by people with recent endemic exposure, or has laboratory exposure to Salmonella enterica subspecies enterica serovar Typhi and Salmonella enterica subspecies enterica serovar Paratyphi (strong, moderate). In this document, Salmonella Typhi represents the more formal and detailed name Salmonella enterica subspecies enterica serovar Typhi, and Salmonella Paratyphi corresponds to the Paratyphi serovar.


III. What clinical, demographic, or epidemiologic features are associated with complications or severe disease?


  1. People of all ages with acute diarrhea should be evaluated for dehydration, which increases the risk of life-threatening illness and death, especially among the young and older adults (strong, high).
  2. When the clinical or epidemic history suggests a possible Shiga toxin–producing organism, diagnostic approaches should be applied that detect Shiga toxin (or the genes that encode them) and distinguish Escherichia coli O157:H7 from other Shiga toxin–producing E. coli (STEC) in stool (strong, moderate). If available, diagnostic approaches that can distinguish between Shiga toxin 1 and Shiga toxin 2, which is typically more potent, could be used (weak, moderate). In addition, Shigella dysenteriae type 1, and, rarely, other pathogens may produce Shiga toxin and should be considered as a cause of hemolytic uremic syndrome (HUS), especially in people with suggestive international travel or personal contact with a traveler (strong, moderate).
  3. Clinicians should evaluate people for postinfectious and extraintestinal manifestations associated with enteric infections (strong, moderate).



IV. Which pathogens should be considered in people presenting with diarrheal illnesses, and which diagnostic tests will aid in organism identification or outbreak investigation?


  1. Stool testing should be performed for Salmonella, Shigella, Campylobacter, Yersinia, C. difficile, and STEC in people with diarrhea accompanied by fever, bloody or mucoid stools, severe abdominal cramping or tenderness, or signs of sepsis (strong, moderate). Bloody stools are not an expected manifestation of infection with C. difficile. STEC O157 should be assessed by culture and non-O157 STEC should be detected by Shiga toxin or genomic assays (strong, low). Sorbitol-MacConkey agar or an appropriate chromogenic agar alternative is recommended to screen for O157:H7 STEC; detection of Shiga toxin is needed to detect other STEC serotype (strong, moderate).
  2. Blood cultures should be obtained from infants <3 months of age, people of any age with signs of septicemia or when enteric fever is suspected, people with systemic manifestations of infection, people who are immunocompromised, people with certain high-risk conditions such as hemolytic anemia, and people who traveled to or have had contact with travelers from enteric fever–endemic areas with a febrile illness of unknown etiology (strong, moderate).
  3. tool testing should be performed under clearly identified circumstances (Table 2) for Salmonella, Shigella, Campylobacter, Yersinia, C. difficile, and STEC in symptomatic hosts (strong, low). Specifically,
                a.) Test for Yersinia enterocolitica in people with persistent abdominal pain (especially school-aged children with right lower quadrant pain mimicking appendicitis who may have mesenteric adenitis), and in people with fever at epidemiologic risk for yersiniosis, including infants with direct or indirect exposures to raw or undercooked pork products.
                b.) In addition, test stool specimens for Vibriospecies in people with large volume rice water stools or either exposure to salty or brackish waters, consumption of raw or undercooked shellfish, or travel to cholera-endemic regions within 3 days prior to onset of diarrhea.
  1. A broader set of bacterial, viral, and parasitic agents should be considered regardless of the presence of fever, bloody or mucoid stools, or other markers of more severe illness in the context of a possible outbreak of diarrheal illness (e.g., multiple people with diarrhea who shared a common meal or a sudden rise in observed diarrheal cases). Selection of agents for testing should be based on a combination of host and epidemiologic risk factors and ideally in coordination with public health authorities (strong, moderate).
  2. A broad differential diagnosis is recommended in immunocompromised people with diarrhea, especially those with moderate and severe primary or secondary immune deficiencies, for evaluation of stool specimens by culture, viral studies, and examination for parasites (strong, moderate). People with acquired immune deficiency syndrome (AIDS) with persistent diarrhea should undergo additional testing for other organisms including, but not limited to, Cryptosporidium, Cyclospora, Cystoisospora, microsporidia, Mycobacterium avium complex, and cytomegalovirus (strong, moderate).
  3. Diagnostic testing is not recommended in most cases of uncomplicated traveler’s diarrhea unless treatment is indicated. Travelers with diarrhea lasting 14 days or longer should be evaluated for intestinal parasitic infections (strong, moderate). Testing for C. difficile should be performed in travelers treated with antimicrobial agent(s) within the preceding 8–12 weeks. In addition, gastrointestinal tract disease including inflammatory bowel disease (IBD) and postinfectious irritable bowel syndrome (IBS) should be considered for evaluation (strong, moderate).
  4. Clinical consideration should be included in the interpretation of results of multiple-pathogen nucleic acid amplification tests because these assays detect DNA and not necessarily viable organisms (strong, low).
  5. All specimens that test positive for bacterial pathogens by culture-independent diagnostic testing such as antigen-based molecular assays (gastrointestinal tract panels), and for which isolate submission is requested or required under public health reporting rules, should be cultured in the clinical laboratory or at a public health laboratory to ensure that outbreaks of similar organisms are detected and investigated (strong, low). Also, a culture may be required in situations where antimicrobial susceptibility testing results would affect care or public health responses (strong, low).
  6. Specimens from people involved in an outbreak of enteric disease should be tested for enteric pathogens per public health department guidance (strong, low).

V. Which diagnostic tests should be performed when enteric fever or bacteremia is suspected?


  1. Culture-independent, including panel-based multiplex molecular diagnostics from stool and blood specimens, and, when indicated, culture-dependent diagnostic testing should be performed when there is a clinical suspicion of enteric fever (diarrhea uncommon) or diarrhea with bacteremia (strong, moderate). Additionally, cultures of bone marrow (particularly valuable if antimicrobial agents have been administered), stool, duodenal fluid, and urine may be beneficial to detect enteric fever (weak, moderate). Serologic tests should not be used to diagnose enteric fever (strong, moderate).

VI. When should testing be performed for Clostridium difficile?


  1. Testing may be considered for C. difficile in people >2 years of age who have a history of diarrhea following antimicrobial use and in people with healthcare-associated diarrhea (weak, high). Testing for C. difficile may be considered in people who have persistent diarrhea without an etiology and without recognized risk factors (weak, low). A single diarrheal stool specimen is recommended for detection of toxin or a toxigenic C. difficile strain (e.g., nucleic acid amplification testing) (strong, low). Multiple specimens do not increase yield.

VII. What is the optimal specimen (e.g., stool, rectal swab, blood) for maximum yield of bacterial, viral, and protozoal organisms (for culture, immunoassay, and molecular testing)?


  1. The optimal specimen for laboratory diagnosis of infectious diarrhea is a diarrheal stool sample (i.e., a sample that takes the shape of the container). For detection of bacterial infections, if a timely diarrheal stool sample cannot be collected, a rectal swab may be used (weak, low). Molecular techniques generally are more sensitive and less dependent than culture on the quality of specimen. For identification of viral and protozoal agents, and C. difficile toxin, fresh stool is preferred (weak, low).

VIII. What is the clinical relevance of fecal leukocytes or lactoferrin or calprotectin in a person with acute diarrhea?


  1. Fecal leukocyte examination and stool lactoferrin detection should not be used to establish the cause of acute infectious diarrhea (strong, moderate). There are insufficient data available to make a recommendation on the value of fecal calprotectin measurement in people with acute infectious diarrhea.

IX. In which clinical scenarios should nonmicrobiologic diagnostic tests be performed (e.g., imaging, chemistries, complete blood count, and serology)?


  1. Serologic tests are not recommended to establish an etiology of infectious diarrhea or enteric fever (strong, low), but may be considered for people with postdiarrheal HUS in which a stool culture did not yield a Shiga toxin–producing organism (weak, low).
  2. A peripheral white blood cell count and differential and serologic assays should not be performed to establish an etiology of diarrhea (strong, low), but may be useful clinically (weak, low).
  3. Frequent monitoring of hemoglobin and platelet counts, electrolytes, and blood urea nitrogen and creatinine is recommended to detect hematologic and renal function abnormalities that are early manifestations of HUS and precede renal injury for people with diagnosed E. coli O157 or another STEC infection (especially STEC that produce Shiga toxin 2 or are associated with bloody diarrhea) (strong, high). Examining a peripheral blood smear for the presence of red blood cell fragments is necessary when HUS is suspected (strong, high).
  4. Endoscopy or proctoscopic examination should be considered in people with persistent, unexplained diarrhea who have AIDS, in people with certain underlying medical conditions as well as people with acute diarrhea with clinical colitis or proctitis and in people with persistent diarrhea who engage in anal intercourse (strong, low). Duodenal aspirate may be considered in select people for diagnosis of suspected Giardia, Strongyloides, Cystoisospora, or microsporidia infection (weak, low).
  5. Imaging (e.g., ultrasonography, computed tomography, or magnetic resonance imaging) may be considered to detect aortitis, mycotic aneurysms, signs and symptoms of peritonitis, intra-abdominal free air, toxic megacolon, or extravascular foci of infection in older people with invasive Salmonella enterica or Yersinia infections if there is sustained fever or bacteremia despite adequate antimicrobial therapy or if the patient has underlying atherosclerosis or has recent-onset chest, back, or abdominal pain (weak, low).

X. What follow-up evaluations of stool specimens and nonstool tests should be performed in people with laboratory-confirmed pathogen-specific diarrhea who improve or respond to treatment, and in people who fail to improve or who have persistent diarrhea?


  1. Follow-up testing is not recommended in most people for case management following resolution of diarrhea (strong, moderate). Collection and analysis of serial stool specimens using culture-dependent methods for Salmonella enterica subspecies enterica serovar Typhi or Salmonella enterica subspecies enterica serovar Paratyphi, STEC, Shigella, nontyphoidal Salmonella, and other bacterial pathogens are recommended in certain situations by local health authorities following cessation of diarrhea to enable return to child care, employment, or group social activities (strong, moderate). Practitioners should collaborate with local public health authorities to adhere to policies regarding return to settings in which transmission is a consideration (strong, high).
  2. A clinical and laboratory reevaluation may be indicated in people who do not respond to an initial course of therapy and should include consideration of noninfectious conditions including lactose intolerance (weak, low).
  3. Noninfectious conditions, including IBD and IBS, should be considered as underlying etiologies in people with symptoms lasting 14 or more days and unidentified sources (strong, moderate).
  4. Reassessment of fluid and electrolyte balance, nutritional status, and optimal dose and duration of antimicrobial therapy is recommended in people with persistent symptoms (strong, high).

Empiric Management of Infectious Diarrhea

XI. When is empiric antibacterial treatment indicated for children and adults with bloody diarrhea and, if inficated, with what agent?

         a.) What are modifying conditions that would support antimicrobial treatment of children and adults with bloody diarrhea?
         b.) In which instances should contacts be treated empirically if the agent is unknown?


  1. In immunocompetent children and adults, empiric antimicrobial therapy for bloody diarrhea while waiting for results of investigations is not recommended (strong, low), except for the following:
                a.) Infants <3 months of age with suspicion of a bacterial etiology.
                b.) Ill immunocompetent people with fever documented in a medical setting, abdominal pain, bloody diarrhea, and bacillary dysentery (frequent scant bloody stools, fever, abdominal cramps, tenesmus) presumptively due to Shigella.
                c.) People who have recently travelled internationally with body temperatures ≥38.5°C and/or signs of sepsis (weak, low). See here.
  1. The empiric antimicrobial therapy in adults should be either a fluoroquinolone such as ciprofloxacin, or azithromycin, depending on the local susceptibility patterns and travel history (strong, moderate). Empiric therapy for children includes a third-generation cephalosporin for infants <3 months of age and others with neurologic involvement, or azithromycin, depending on local susceptibility patterns and travel history (strong, moderate).
  2. Empiric antibacterial treatment should be considered in immunocompromised people with severe illness and bloody diarrhea (strong, low).
  3. Asymptomatic contacts of people with bloody diarrhea should not be offered empiric treatment, but should be advised to follow appropriate infection prevention and control measures (strong, moderate).
  4. People with clinical features of sepsis who are suspected of having enteric fever should be treated empirically with broad-spectrum antimicrobial therapy after blood, stool, and urine culture collection (strong, low). Antimicrobial therapy should be narrowed when antimicrobial susceptibility testing results become available (strong, high). If an isolate is unavailable and there is a clinical suspicion of enteric fever, antimicrobial choice may be tailored to susceptible patterns from the setting where acquisition occurred (weak, low).
  5. Antimicrobial therapy for people with infections attributed to STEC O157 and other STEC that produce Shiga toxin 2 (or if the toxin genotype is unknown) should be avoided (strong, moderate). Antimicrobial therapy for people with infections attributed to other STEC that do not produce Shiga toxin 2 (generally non-O157 STEC) is debatable due to insufficient evidence of benefit or the potential harm associated with some classes of antimicrobial agents (strong, low).

XII. When is empiric treatment indicated for children and adults with acute, prolonged, or persistent watery diarrhea and, if indicated, with what agent?

         a.) What are modifying conditions that would support empiric antimicrobial treatment of children and adults with watery diarrhea?

         b.) In which instances, if any, should contacts be treated empirically if the agent is unknown?


  1. In most people with acute watery diarrhea and without recent international travel, empiric antimicrobial therapy is not recommended (strong, low). An exception may be made in people who are immunocompromised or young infants who are ill-appearing. Empiric treatment should be avoided in people with persistent watery diarrhea lasting 14 days or more (strong, low).
  2. Asymptomatic contacts of people with acute or persistent watery diarrhea should not be offered empiric or preventive therapy, but should be advised to follow appropriate infection prevention and control measures (strong, moderate).

Directed Management of Infectious Diarrhea


XIII. How should treatment be modified when a clinically plausible organism is identified from a diagnostic test?


  1. Antimicrobial treatment should be modified or discontinued when a clinically plausible organism is identified (strong, high).

Supportive Treatment

XIV. How should rehydration therapy be administered?


  1. Reduced osmolarity oral rehydration solution (ORS) is recommended as the first-line therapy of mild to moderate dehydration in infants, children, and adults with acute diarrhea from any cause (strong, moderate), and in people with mild to moderate dehydration associated with vomiting or severe diarrhea.
  2. Nasogastric administration of ORS may be considered in infants, children, and adults with moderate dehydration, who cannot tolerate oral intake, or in children with normal mental status who are too weak or refuse to drink adequately (weak, low).
  3. Isotonic intravenous fluids such as lactated Ringer’s and normal saline solution should be administered when there is severe dehydration, shock, or altered mental status and failure of ORS therapy (strong, high) or ileus (strong, moderate). In people with ketonemia, an initial course of intravenous hydration may be needed to enable tolerance of oral rehydration (weak, low).
  4. In severe dehydration, intravenous rehydration should be continued until pulse, perfusion, and mental status normalize and the patient awakens, has no risk factors for aspiration, and has no evidence of ileus (strong, low). The remaining deficit can be replaced by using ORS (weak, low). Infants, children, and adults with mild to moderate dehydration should receive ORS until clinical dehydration is corrected (strong, low).
  5. Once the patient is rehydrated, maintenance fluids should be administered. Replace ongoing losses in stools from infants, children, and adults with ORS, until diarrhea and vomiting are resolved (strong, low).

XV. When should feeding be initiated following rehydration?


  1. Human milk feeding should be continued in infants and children throughout the diarrheal episode (strong, low).
  2. Resumption of an age-appropriate usual diet is recommended during or immediately after the rehydration process is completed (strong, low).

Ancillary Management

XVI. What options are available for symptomatic relief, and when should they be offered?


  1. Ancillary treatment with antimotility, antinausea, or antiemetic agents can be considered once the patient is adequately hydrated, but their use is not a substitute for fluid and electrolyte therapy (weak, low).
  2. Antimotility drugs (e.g., loperamide) should not be given to children <18 years of age with acute diarrhea (strong, moderate). Loperamide may be given to immunocompetent adults with acute watery diarrhea (weak, moderate), but should be avoided at any age in suspected or proven cases where toxic megacolon may result in inflammatory diarrhea or diarrhea with fever (strong, low).
  3. Antinausea and antiemetic (e.g., ondansetron) may be given to facilitate tolerance of oral rehydration in children >4 years of age and in adolescents with acute gastroenteritis associated with vomiting (weak, moderate).

XVII. What is the role of a probiotic or zinc in treatment or prevention of infectious diarrhea in children and adults?


  1. Probiotic preparations may be offered to reduce the symptom severity and duration in immunocompetent adults and children with infectious or antimicrobial-associated diarrhea (weak, moderate). Specific recommendations regarding selection of probiotic organism(s), route of delivery, and dosage may be found through literature searches of studies and through guidance from manufacturers.
  2. Oral zinc supplementation reduces the duration of diarrhea in children 6 months to 5 years of age who reside in countries with a high prevalence of zinc deficiency or who have signs of malnutrition (strong, moderate).

XVIII. Which asymptomatic people with an identified bacterial organism from stool culture or molecular testing should be treated with an antimicrobial agent?


  1. Asymptomatic people who practice hand hygiene and live and work in low-risk settings (do not provide healthcare or child or elderly adult care and are not food service employees) do not need treatment, except asymptomatic people with Salmonella enterica subspecies enterica serovar Typhi in their stool who may be treated empirically to reduce potential for transmission (weak, low). Asymptomatic people who practice hand hygiene and live and work in high-risk settings (provide healthcare or child or elderly adult care and are food service employees) should be treated according to local public health guidance (strong, high).


XIX. What strategies, including public health measures, are beneficial in preventing transmission of pathogens associated with infectious diarrhea?


  1. Hand hygiene should be performed after using the toilet, changing diapers, before and after preparing food, before eating, after handling garbage or soiled laundry items, and after touching animals or their feces or environments, especially in public settings such as petting zoos (strong, moderate).
  2. Infection control measures including use of gloves and gowns, hand hygiene with soap and water, or alcohol-based sanitizers should be followed in the care of people with diarrhea (strong, high). The selection of a hand hygiene product should be based upon a known or suspected pathogen and the environment in which the organism may be transmitted (strong, low). See here.
  3. Appropriate food safety practices are recommended to avoid cross-contamination of other foods or cooking surfaces and utensils during grocery shopping, food preparation, and storage; ensure that foods containing meats and eggs are cooked and maintained at proper temperatures (strong, moderate).
  4. Healthcare providers should direct educational efforts toward all people with diarrhea, but particularly to people with primary and secondary immune deficiencies, pregnant women, parents of young children, and the elderly as they have increased risk of complications from diarrheal disease (strong, low).
  5. Ill people with diarrhea should avoid swimming, water-related activities, and sexual contact with other people when symptomatic while adhering to meticulous hand hygiene (strong, low).

XX. What are the relative efficacies and effectiveness of vaccines (rotavirus, typhoid, and cholera) to reduce and prevent transmission of pathogens associated with infectious diarrhea, and when should they be used?


  1. Rotavirus vaccine should be administered to all infants without a known contraindication (strong, high).
  2. Two typhoid vaccines (oral and injectable) are licensed in the United States but are not recommended routinely. Typhoid vaccination is recommended as an adjunct to hand hygiene and the avoidance of high-risk foods and beverages, for travelers to areas where there is moderate to high risk for exposure to Salmonella enterica subspecies enterica serovar Typhi, people with intimate exposure (e.g., household contact) to a documented Salmonella enterica subspecies enterica serovar Typhi chronic carrier, and microbiologists and other laboratory personnel routinely exposed to cultures of Salmonella enterica subspecies enterica serovar Typhi (strong, high). Booster doses are recommended for people who remain at risk (strong, high).
  3. A live attenuated cholera vaccine, which is available as a single-dose oral vaccine in the United States, is recommended for adults 18–64 years of age who travel to cholera-affected areas (strong, high). See here.

XXI. How does reporting of nationally notifiable organisms identified from stool specimens impact the control and prevention of diarrheal disease in the United States?


  1. All diseases listed in the table of National Notifiable Diseases Surveillance System at the national level, including those that cause diarrhea, should be reported to the appropriate state, territorial, or local health department with submission of isolates of certain pathogens (e.g., Salmonella, STEC, Shigella, and Listeria) to ensure that control and prevention practices may be implemented (strong, high).

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