Infectious Diarrhoea - Management of Infection Guidance for Primary Care

Publication: 30/09/2010  
Next review: 21/10/2023  
Clinical Guideline
ID: 2250 
Approved By: LAPC 
Copyright© Leeds Teaching Hospitals NHS Trust 2020  


This Clinical Guideline is intended for use by healthcare professionals within Leeds unless otherwise stated.
For healthcare professionals in other trusts, please ensure that you consult relevant local and national guidance.

Infectious Diarrhoea in Primary Care

Acute diarrhoea is usually defined as 3 or more episodes per day, <14 days duration. 
Infectious diarrhea is a self-limiting illness. Causes include a wide range of bacterial (e.g. Campylobacter spp., Salmonella spp., certain strains of Escherichia Coli), viral and protozoal pathogens.
For detailed information on sample collection and treating suspected infectious diarrhea in primary care, please see the Public Health England Quick reference guide.
A stool sample should be sent if there are symptoms / clinical indications or there are public health indications e.g. suspected food poisoning, diarrhoea in high risk situations or contact with other affected individual(s).
Send a single stool sample for bacterial cultures (MC&S) and (Rotavirus Antigen for children < 5 years).
Request Ova, Cysts and Parasites (OCP) if the patient is immunocompromised or there has been a history of foreign travel.
Request Viral PCR if institutional viral gastroenteritis outbreak suspected or if required on the basis of clinical history.


Antibiotics are NOT usually recommended for adults with diarrhoea of unknown pathology.3B
Antibiotic therapy is NOT indicated for Campylobacter unless the patient is systemically unwell. 2D Microbiology will be able to advise where considered in a specific cohort of patients e.g. the immunocompromised.
Ensure adequate rehydration using oral fluids.
Do not use anti-diarrhoeals as they may worsen acute gastroenteritis and its complications.

Arrange referral to hospital if:

  • The patient is vomiting and unable to retain oral fluids;
  • There are features of sepsis, dehydration or shock;
  • Previously healthy child with acute painful or bloody diarrhoea, to exclude E.Coli O157 infection.1D

PHE Managing infectious diarrhoea quick reference guide
PHE managing common infections guidance
LTHT Secondary care guideline

General Principles for Treating Infections
This summary table is based on the best available evidence, but use professional judgement and involve patients in management decisions.

  1. This summary table should not be used in isolation; it should be supported with patient information about safety netting, back-up antibiotics, self-care, infection severity and usual duration, clinical staff education, and audits. Materials are available on the RCGP TARGET website.
  2. Prescribe an antibiotic only when there is likely to be clear clinical benefit, giving alternative, non-antibiotic self-care advice, where appropriate.
  3. If person is systemically unwell with symptoms or signs of serious illness, or is at high risk of complications: give immediate antibiotic. Always consider possibility of sepsis, and refer to hospital if severe systemic infection.
  4. Use a lower threshold for antibiotics in immunocompromised, or in those with multiple morbidities; consider culture/specimens, and seek advice.
  5. In severe infection, or immunocompromised, it is important to initiate antibiotics as soon as possible, particularly if sepsis is suspected. If patient is not at moderate to high risk for sepsis, give information about symptom monitoring, and how to access medical care if they are concerned.
  6. Where an empirical therapy has failed or special circumstances exist, microbiological advice can be obtained from LTHT Microbiology (Mon-Fri 9am-5pm and Sat and Sun 9am-1pm: 07825 906030, 0113 39 23962/28580; Otherwise via LTHT switchboard - ask for the On call Microbiology Registrar)
  7. Limit prescribing over the telephone to exceptional cases.
  8. Use simple, generic antibiotics if possible. Avoid broad spectrum antibiotics (for example coamoxiclav, quinolones and cephalosporins) when narrow spectrum antibiotics remain effective, as they increase the risk of Clostridium difficile, MRSA and resistant UTIs.
  9. Avoid widespread use of topical antibiotics, especially in those agents also available systemically (for example fusidic acid); in most cases, topical use should be limited.
  10. Always check for antibiotic allergies. A dose and duration of treatment for adults is usually suggested, but may need modification for age, weight, renal function, or if immunocompromised. In severe or recurrent cases, consider a larger dose or longer course.
  11. Avoid use of quinolones unless benefits outweigh the risk as new 2018 evidence indicates that they may be rarely associated with long lasting disabling neuro-muscular and skeletal side effects.
  12. Refer to the BNF for further dosing and interaction information (for example the interaction between macrolides and statins), and check for hypersensitivity.

Note: Doses are oral and for adults unless otherwise stated. Please refer to BNF for further information.
Letters indicate strength of evidence:
A+ = systematic review: D = expert opinion


Record: 2250
Clinical condition:

Infectious Diarrhoea

Target patient group:
Target professional group(s): Primary Care Doctors
Adapted from:

Management of Infection guidance for primary care for consultation and local adaptation

Evidence base

Grading of guidance recommendations
The strength of each recommendation is qualified by a letter in parenthesis.

Study design


Good recent systematic review and meta-analysis of studies


One or more rigorous studies; randomised controlled trials


One or more prospective studies


One or more retrospective studies


Non-analytic studies, eg case reports or case series


Formal combination of expert opinion


Infectious diarrhoea

  1. Independent Investigation Committee. Review of the major outbreak of E. coli 0157 in Surrey, 2009: An evaluation of the outbreak and its management, with a consideration of the regulatory framework and control of risks relating to open farms. 2010 Jun. Available from:

    RATIONALE: An evaluation of the 2009 outbreak of E. coli 0157 and its management, with a consideration of the regulatory framework and control of risks relating to open farms. E. coli 0157 infection is relatively uncommon but, because the illness it causes can be severe or fatal, it remains a serious public health issue. E. coli 0157 should be suspected in any child presenting with bloody or painful diarrhoea.
  2. Farthing M, Feldman R, Finch R, Fox R, Leen C, Mandal B et al. The management of infective gastroenteritis in adults. A consensus statement by an expert panel convened by the British Society for the Study of Infection. J Infect. 1996 Nov; 33(3):143-152. Available from:  RATIONALE: An expert consensus statement suggesting that empirical treatment for patients well enough to be managed in primary care should not be recommended, as the majority of illnesses seen in the community do not have an identifiable bacterial cause. In addition, an RCT of quinolones as empiric therapy found no benefit in patients whose stool cultures were negative for bacterial infection.
  3. Public Health England (PHE). Managing suspected infectious diarrhoea. Quick reference guide for primary care: for consultation and local adaptation. 2015 Jan. Available from:
  4. CKS. Diarrhoea – adult’s assessment. Clinical Knowledge Summaries.  Accessed 09.08.2019

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