Gastrointestinal Endoscopy and Gastroenterology in Adults - Antimicrobial prophylaxis

Publication: 19/11/2009  --
Last review: 03/02/2020  
Next review: 03/02/2023  
Clinical Guideline
ID: 1744 
Approved By: Improving Antimicrobial Prescribing Group 
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.

Guideline for antimicrobial prophylaxis in gastrointestinal endoscopy and gastroenterology in adults

Summary table of routine recommendations


Prophylaxis recommended?

Evidence level

Prophylaxis intended to reduce


Antimicrobial dose/route
Administered ≤1 hour before procedure


MRSA risk#/penicillin allergy

1) Patients with endocarditis risk undergoing any gastrointestinal endoscopy.

No, unless clinical evidence of infection


risk of infective endocarditis.




2) ERCP for following patient groups:

a) ongoing cholangitis or sepsis elsewhere

Be guided by recent culture results. Patients should already be on antimicrobials.


procedure-related bacteraemia


Contact microbiologist if required


b) biliary obstruction and/or common bile duct stones and/or straightforward stent change

NO –but start prophylaxis if cannulation achieved but biliary decompression not achieved




Co-amoxiclav electronic Medicines Compendium information on Co-amoxiclav 1.2g iv or 625mg po 8-hourly until decompression achieved.

Ciprofloxacin electronic Medicines Compendium information on Ciprofloxacin 500mg 12-h po until decompression achieved.

c) ERCP when complete biliary drainage unlikely to be achieved (e.g. sclerosing cholangitis and/or hilar cholangiocarcinoma)
see full guideline.





Ciprofloxacin electronic Medicines Compendium information on Ciprofloxacin 750mg po single dose
OR Gentamicin 2mg/kg i.v single dose

Gentamicin 2mg/kg i.v single dose

d) communicating pancreatic cyst or pseudocyst



risk of cyst infection


Ciprofloxacin electronic Medicines Compendium information on Ciprofloxacin 750mg po single dose
OR Gentamicin 2mg/kg iv single dose

Gentamicin 2mg/kg iv single dose

e) biliary complications post liver transplant





As c) plus Amoxicillin electronic Medicines Compendium information on Amoxicillin 1g iv

As c) plus Teicoplanin electronic Medicines Compendium information on Teicoplanin 400mg iv single dose

3)ENDOSCOPIC ULTRASOUND FOR: a) fine needle aspiration solid lesions



local infection


b) fine needle aspiration of cystic lesions in or near pancreas, or drainage of cystic cavity



cyst infection


Co-amoxiclav electronic Medicines Compendium information on Co-amoxiclav 1.2g iv single dose

Teicoplanin electronic Medicines Compendium information on Teicoplanin 400mg iv single dose




peristomal infection


Teicoplanin electronic Medicines Compendium information on Teicoplanin 400mg iv single dose

Teicoplanin electronic Medicines Compendium information on Teicoplanin 400mg iv single dose




peristomal infection


Teicoplanin electronic Medicines Compendium information on Teicoplanin 400mg iv single dose

Teicoplanin electronic Medicines Compendium information on Teicoplanin 400mg iv single dose

NNT =Number needed to treat

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2. Background information

Antimicrobial prophylaxis is indicated for gastrointestinal endoscopy in some situations to prevent infective complications. Current practise has been reviewed in light of publication of new guidance from the National Institute for Health and Clinical Excellence (NICE ) on endocarditis prophylaxis 3 and the imminent publication of updated prophylaxis recommendations from the British Society for Gastroenterology Endoscopy Working Party 2.

In addition, on-going problems with Clostridium difficile infection, meticillin-resistant Staphylococcus aureus (MRSA) infection and increasing concerns about community-acquired MRSA have been taken into consideration. Reducing the risk of acquisition of these pathogens by avoiding unnecessary antimicrobial exposure is a pressing concern.

For many gastrointestinal endoscopic procedures there is no evidence that antimicrobial prophylaxis is of benefit to patients and its use is therefore not recommended. These guidelines should be applicable to the majority of patients but where the recommendations in these guidelines do not seem appropriate for a particular patient, the endoscopist is advised to discuss the case with a microbiologist.

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3. Special antimicrobial prophylaxis recommendations

3.1 Antibiotic prophylaxis is no longer recommended for the prevention of infective endocarditis in patients with cardiac risk factors who undergo diagnostic or therapeutic endoscopy. Evidence Level B.

3.2 The possibility of infective endocarditis should be considered in patients with known cardiac risk factors who develop symptoms and signs of infection during the weeks following an endoscopic procedure. Such patients should undergo prompt investigation and appropriate treatment. Evidence Level C.

3.3 Patients with ongoing cholangitis (or other infections for which therapeutic endoscopy is indicated as part of their management plan) should be established on appropriate antimicrobial therapy prior to any interventional procedures (Those with risk factors for endocarditis should be treated with regimens active against enterococci until the results of any operative sampling is available). Evidence Level A.

3.4 Additional single dose ERCP prophylaxis is not normally recommended for those already established on antimicrobial treatment for cholangitis. Evidence Level A.

3.5 Routine prophylaxis for ERCP is no longer considered appropriate, but, if it proves impossible to achieve adequate biliary decompression, a full antibiotic course is indicated while arrangements are being made to achieve this goal by repeat ERCP or some other means. Evidence Level B.

3.6 There are specific circumstances where antibiotic prophylaxis should be given routinely to cover ERCP. These include:

  • patients with biliary disorders, such as primary sclerosing cholangitis or hilar cholangiocarcinoma in whom it can be anticipated that complete biliary drainage will be difficult or impossible to achieve during one procedure
  • patients with a history of liver transplantation
  • patients with pancreatic pseudocyst
  • patients with severe neutropenia (<0.5x109/l) and/or advanced haematological malignancy.
    Evidence Level B.

3.7 When prophylaxis for ERCP is given, oral Ciprofloxacin electronic Medicines Compendium information on Ciprofloxacin or intravenous Gentamicin is recommended. Evidence Level B.

3.8 The recommended antibiotic regimen for ERCP prophylaxis and/or persisting biliary obstruction following attempted decompression at ERCP may need to be altered locally in the light of epidemiological patterns in isolates of micro-organisms resistant to these agents. Evidence Level C.

3.9 Indications for prophylaxis for percutaneous endoscopic gastrostomy (PEG) or jejunostomy (PEJ) should receive a single dose of Teicoplanin electronic Medicines Compendium information on Teicoplanin 400mg in the hour prior to the procedure. We regard all patients as high risk for MRSA infection. BSG guidelines state that antibiotic prophylaxis has been shown to lower the risk of skin site infection. However the increasing recognition of MRSA has led to an appraisal of protocols at a local level. Evidence Level C.

3.10 Patients already receiving broad spectrum antibiotics do not require additional prophylaxis for PEG. Evidence Level B.

3.11 Antibiotic prophylaxis is indicated for the fine needle aspiration of cystic lesions in or adjacent to the pancreas, and for endoscopic transgastric or transenteric drainage of pancreatic pseudocysts. Evidence Level B.

3.12 Antibiotic prophylaxis is recommended for patients with severe neutropenia (<0.5 x109 /litre) and/or profound immunocompromise (e.g. advanced haematological malignancy) who undergo procedures that are known to be associated with a high risk of bacteraemia (Table 1). Evidence Level C.

3.13 Recent positive culture results should be taken into account when deciding on antibiotic prophylaxis regimens, and microbiological advice sought if required. Evidence Level C.

3.14 Given that endocarditis prophylaxis will no longer be routinely given, professional bodies and specialist societies should work towards establishing national prospective registries of patients with endocarditis to enable analysis of the temporal relationship to any preceding endoscopic procedure. Likewise cholangitis complicating ERCP may become more common now that prophylaxis for patients with biliary obstruction will no longer be routine, and consideration should be given to establishing national registries of post-ERCP cholangitis.


Record: 1744
Clinical condition:

Gastrointestinal endoscopy and gastroenterology surgery in adults

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

Evidence base

Evidence level.
A. Meta-analyses, randomised controlled trials/systematic reviews of RCTs
B. Robust experimental or observational studies
C. Expert consensus.
D. LTHT Consensus [no national guidelines exist, or guidelines from different learned bodies contradict each other, or no evidence exists]


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Approved By

Improving Antimicrobial Prescribing Group

Document history

LHP version 1.0

Related information

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