Version July 2025
INTRODUCTION —
The value of antibiotic prophylaxis for gastrointestinal (GI) procedures has been debated for many years. Previously, antibiotic prophylaxis was recommended for many GI procedures in patients with high-risk cardiac conditions to protect against infective endocarditis. However, practices have substantially changed, in part due to the low incidence of infective endocarditis following GI procedures and the lack of randomized trials supporting the benefit of antibiotic prophylaxis. Furthermore, the indiscriminate use of antibiotics can be associated with the development of resistant organisms, Clostridioides difficile colitis, unnecessary expense, and drug toxicity. (See "Clostridioides difficile infection in adults: Epidemiology, microbiology, and pathophysiology", section on 'Antibiotic use'.)
Recommendations for antibiotic prophylaxis prior to GI procedures will be reviewed here. General issues related to prophylaxis for bacterial endocarditis are discussed separately. (See "Prevention of endocarditis: Antibiotic prophylaxis and other measures".)
Several professional societies have published guidelines on antibiotic prophylaxis for GI procedures, and our approach is generally consistent with these guidelines [1-3].
PATHOGENESIS —
Infections following endoscopic procedures are rare and are presumably the result of bacteremia induced during the procedure or, in the case of procedures such as pancreatic cyst aspiration, the result of inoculation with bacteria during the procedure.
Bacteremia results from translocation of endogenous bacteria into the blood stream via mucosal trauma, whereas inoculation of sterile tissues or spaces (eg, cysts) occurs from direct contact with a contaminated endoscope or endoscopic accessory. Contrast injection may also result in bacteria being introduced into a previously sterile space (eg, the biliary tree during endoscopic retrograde cholangiopancreatography).
The concern with regard to bacteremia is that the bacteria may colonize a remote site, such as a diseased heart valve or a prosthetic joint, resulting in infection. However, it is likely that this is not a significant problem with regard to gastrointestinal (GI) procedures.
As an example, there is only a weak association of GI procedures with infective endocarditis, and data are lacking to support a causal link [1]. A literature review by the American Society for Gastrointestinal Endoscopy found only 25 cases of infective endocarditis following endoscopic procedures, which included esophageal dilation, sclerotherapy, gastroscopy, sigmoidoscopy, and colonoscopy [1]. In addition, antibiotic prophylaxis has not been shown to prevent endocarditis following GI procedures.
RATES OF BACTEREMIA AND INFECTION —
The rates of bacteremia following gastrointestinal (GI) procedures are generally lower than those seen following routine daily activities such as eating and defecating, and rarely result in clinically evident infection. Furthermore, bacteremia due to organisms capable of causing endocarditis occurs in less than 5 to 10 percent of cases [4-6].
Routine activities — Transient bacteremia is commonly seen following routine daily activities, with rates as high as 68 percent [1]. Some activities associated with bacteremia include:
●Brushing and flossing teeth: 20 to 68 percent
●Using toothpicks: 20 to 40 percent
●Chewing food: 7 to 51 percent
These observations should be considered when evaluating the incidence of transient bacteremia associated with GI endoscopic procedures.
High-risk procedures — The following endoscopic procedures are considered high risk for bacteremia:
●Dilation of an esophageal stricture – The risk of bacteremia with esophageal bougienage has been estimated to be 12 to 22 percent [7,8]. Factors that may increase the risk include multiple passes of the dilator and dilation of malignant strictures [8].
●Endoscopic sclerotherapy of varices – The mean reported rate of bacteremia is 15 percent (range 0 to 52 percent) with sclerotherapy [1]. Endoscopic variceal ligation is not considered high risk for bacteremia (risk estimated at 9 percent [range 1 to 25 percent]).
●Endoscopic retrograde cholangiopancreatography (ERCP) – The risk of bacteremia with ERCP depends upon whether the bile duct is obstructed [9,10]. In one review, the rate was 6 percent in the absence of obstruction and 18 percent in the presence of obstruction [9]. However, the risk of subsequent sepsis is uncertain. (See "Infectious adverse events related to endoscopic retrograde cholangiopancreatography (ERCP)".)
Other procedures are considered high risk for infection unrelated to bacteremia:
●Endoscopic ultrasound with fine-needle aspiration (EUS-FNA) – The reported rate of bacteremia associated with EUS-FNA ranges from 4 to 6 percent [1], making it a low-risk procedure with regard to bacteremia. However, the overall infection risk is probably higher. The risk of infection depends on the type of lesion being sampled. Limited data suggest that solid lesions are at low risk for infection (0.01 to 2 percent) [1,11]. The risk of infection following EUS-FNA of cystic lesions is less clear, with reported rates ranging from less than 1 percent to 14 percent [1,4]. Patients undergoing EUS-FNA of mediastinal cysts may be at higher risk for infection, with several case reports and case series reporting infection following EUS-FNA [12,13], some occurring despite the use of antibiotics [1]. (See 'Endoscopic ultrasound' below.)
●Percutaneous endoscopic gastrostomy (PEG) or jejunostomy (PEJ) tube placement – In a Cochrane analysis of 12 randomized trials of 1271 patients undergoing PEG tube placement, patients who received antibiotic prophylaxis had a significant reduction in peristomal infections compared with those who did not receive prophylactic antibiotics (pooled odds ratio 0.36) [14]. The procedure to place a PEJ tube is similar to PEG tube placement, though the use of prophylactic antibiotics in this setting has not been well studied.
Low-risk procedures — Routine upper endoscopy, colonoscopy, and flexible sigmoidoscopy are all considered to be low-risk procedures with regard to bacteremia and infection. This includes patients undergoing endoscopic biopsies or polypectomy. The mean reported rates of bacteremia have been estimated to be 4 percent for both gastroscopy without biopsy and colonoscopy, and 0 to 1 percent for flexible sigmoidoscopy [1]. (See 'Patient factors' below.)
WHEN TO USE ANTIBIOTIC PROPHYLAXIS —
Recommendations for antibiotic prophylaxis are based on the risks related to specific procedures, as well as patient factors that may predispose to infection (table 1 and table 2). Gastrointestinal (GI) procedures are low risk for bacterial endocarditis and therefore antibiotic prophylaxis to prevent endocarditis is not recommended, even in patients with the highest-risk cardiac conditions (such as prosthetic valves or prior endocarditis) [1]. Antibiotic prophylaxis is indicated in other settings, such as prior to percutaneous endoscopic gastrostomy (PEG) and jejunostomy (PEJ) tube placement.
Specific procedures
Routine upper endoscopy, colonoscopy, and flexible sigmoidoscopy — Antibiotic prophylaxis is not required for routine endoscopic procedures associated with a low risk of bacteremia. This includes patients undergoing endoscopic biopsies or polypectomy. In addition, antibiotic prophylaxis is not required for most patients undergoing high-risk procedures performed during routine endoscopy (eg, esophageal stricture dilation). (See 'Low-risk procedures' above and 'High-risk procedures' above.)
However, antibiotic prophylaxis is suggested for patients with severe neutropenia (absolute neutrophil count <500 cells/microL), advanced hematologic malignancies, or cirrhosis with ascites undergoing procedures such as esophageal dilation or endoscopic sclerotherapy, although data to support this recommendation are lacking. (See 'Immunocompromised states' below and 'Cirrhosis' below.)
Endoscopic retrograde cholangiopancreatography (ERCP) — Antibiotics are required for patients with cholangitis as part of their routine care, so additional prophylactic antibiotics are not needed.
We use antibiotic prophylaxis prior to ERCP for patients with any of the following risk factors (table 2):
●Biliary obstruction and risk for incomplete biliary drainage [1,15-18]. Conditions that make successful drainage less likely include malignant hilar obstruction, primary sclerosing cholangitis, and retained stone fragments. (See "Primary sclerosing cholangitis in adults: Management", section on 'Endoscopic therapy'.)
If biliary drainage is not successful, we continue antibiotics for three to five days, and we typically use an oral antibiotic regimen following the procedure (eg, ciprofloxacin 500 mg orally, once daily). For patients in whom drainage is established, we discontinue antibiotics if there is no evidence of cholangitis.
●History of liver transplantation.
●Other conditions associated with high infection risk (eg, severe neutropenia, advanced hematologic malignancy, cirrhosis with ascites). (See 'Immunocompromised states' below and 'Cirrhosis' below.)
For patients with biliary obstruction who are not at increased risk for incomplete biliary drainage, we do not routinely use antibiotic prophylaxis prior to ERCP. This approach is supported by consensus guidance and clinical experience, whereas data have been mixed [1,3,19,20]. In a meta-analysis of three trials comparing antibiotic prophylaxis with no prophylaxis in 309 patients who underwent ERCP with complete biliary drainage, there were no significant differences in rates of cholangitis between the groups (4 percent in both groups) [19]. In a subsequent trial comparing antibiotic prophylaxis with no prophylaxis in 378 patients with biliary obstruction undergoing ERCP, antibiotic prophylaxis resulted in lower risk of cholangitis (2 versus 6 percent, risk ratio [RR] 0.27, 95% CI 0.08-0.87) [20]. Additional studies are needed to confirm efficacy and lack of harm before routinely using antibiotic prophylaxis in all patients with biliary obstruction.
Endoscopic ultrasound — Antibiotic prophylaxis is not recommended for most patients undergoing endoscopic ultrasound with fine-needle aspiration (EUS-FNA) of solid lesions. However, it is suggested for patients with severe neutropenia, advanced hematologic malignancies, or cirrhosis with ascites. (See 'Immunocompromised states' below.)
The American Society of Gastrointestinal Endoscopy (ASGE) suggests antibiotic prophylaxis for EUS-FNA of cystic lesions, including pancreatic cysts [1]. However, with the exception of EUS-FNA of mediastinal cysts and EUS-FNA in patients at increased risk of infection, we do not agree with this recommendation. We support the use of antibiotic prophylaxis in patients with mediastinal cysts because these cysts seem to have a higher risk of infection, even when prophylactic antibiotics are used [1]. On the other hand, we believe there are insufficient data to support the routine use of prophylactic antibiotics for EUS-FNA of other cystic lesions [4,21,22]. For example, in a trial including 226 patients with pancreatic cysts who underwent EUS-FNA, postprocedure infection rates were not significantly different for patients given ciprofloxacin prophylaxis versus placebo (none versus one patient [0.9 percent]) [22]. In addition, rates of other adverse events (eg, fever) were not significantly different between groups. However, since data regarding the potential benefits and harms of antibiotics prior to EUS-FNA of pancreatic cysts are accumulating, prophylactic antibiotic therapy for some patients is a reasonable alternative (eg, patients with incomplete cyst aspiration, cysts associated with pancreatitis, and mucinous cysts) [23].
We give prophylactic antibiotics to all patients undergoing interventional EUS procedures, such as drainage of walled-off pancreatic necrosis, biliary drainage, and fine-needle injection of cysts/tumors. The antibiotic is given before the procedure and typically continued for three to five days after the procedure [1].
Percutaneous endoscopic gastrostomy or jejunostomy placement — Prophylactic antibiotics are recommended for all patients prior to placement of a PEG tube since meta-analyses of randomized trials have demonstrated that they substantially reduce the risk of peristomal wound infection [14,24]. Antibiotics are also recommended prior to PEJ tube placement.
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) as a major pathogen causing PEG-site infections in some centers has raised concerns about the effectiveness of prophylaxis with cephalosporins [25]. We agree with the ASGE guideline recommendation for preprocedural screening for MRSA in areas where MRSA is endemic and attempting decontamination before placing the feeding tube [1]. (See "Methicillin-resistant Staphylococcus aureus (MRSA) in adults: Prevention and control", section on 'Targeted decolonization'.)
Patient factors
Cardiac conditions — Certain cardiac lesions such as prosthetic valves or prior endocarditis have been classified as high risk for infective endocarditis for some procedures (eg, dental work). However, they are not considered indications for antibiotic prophylaxis for GI procedures [1,2]. In addition, antibiotic prophylaxis is not recommended for patients with nonvalvular cardiovascular devices such as pacemakers, defibrillators, and cardiac stents [1]. Patients with high-risk cardiac lesions who have active GI infections that are likely to be associated with enterococci (eg, cholangitis) should receive antibiotics active against enterococci. (See "Acute cholangitis: Clinical manifestations, diagnosis, and management", section on 'General measures'.)
The American Heart Association (AHA) guidelines recommend that antimicrobial prophylaxis be given to patients with high-risk heart valve lesions if they undergo procedures that are likely to result in bacteremia with a microorganism that has the potential ability to cause endocarditis [2]. They do not consider any GI procedure high risk for bacteremia with microorganisms that can cause endocarditis, and therefore do not recommend the routine use of antibiotic prophylaxis, even in patients with high-risk valvular lesions. However, they do note that it is reasonable to administer antibiotic therapy in high-risk patients with established GI tract infections, and the ASGE guidelines recommend that patients with high-risk cardiac lesions receive antibiotics that are active against enterococci if they have infections likely to be associated with enterococci [1].
A potential source of confusion and concern for some patients with cardiac lesions is that they may have been told in the past that they must have antibiotic prophylaxis for all procedures. We recommend that patients be reassured that the recommendations to not give antibiotic prophylaxis come from several professional societies, including the ASGE and the AHA [1,2].
For heart transplant recipients on immunosuppressive therapy who are undergoing endoscopy, we consult with the transplant team and infectious disease specialist for risk assessment and guidance on antibiotic prophylaxis prior to endoscopy.
Immunocompromised states — The use of prophylactic antibiotics in patients who are severely neutropenic (absolute neutrophil count <500 cells/microL) or who have advanced hematologic malignancies has not been well studied. However, these patients are at increased risk for infection after GI endoscopy [1]. We agree with the recommendation of the ASGE that antibiotic prophylaxis be given to patients with severe neutropenia or advanced hematologic malignancies who are undergoing procedures associated with a high risk of bacteremia. For patients undergoing low-risk procedures, we do not routinely give antibiotic prophylaxis. However, these patients should be under closer post-procedure surveillance for infection. (See 'High-risk procedures' above.)
Whether patients with other causes of immunocompromise (including those on high doses of glucocorticoids) benefit from antibiotic prophylaxis is unclear [26,27]. Routine administration of prophylactic antibiotics is not recommended for patients who are immunocompromised but do not have severe neutropenia or an advanced hematologic malignancy [1].
Cirrhosis — Patients with cirrhosis and acute GI bleeding should receive antibiotic prophylaxis. Antibiotic prophylaxis in this setting is discussed in detail elsewhere. (See "Overview of the management of patients with variceal bleeding".)
Limited data are available to guide recommendations on antibiotic prophylaxis for patients with cirrhosis and ascites who do not have acute GI bleeding. One study of 244 positive ascitic fluid cultures found that prior GI endoscopy was associated with spontaneous bacterial peritonitis on univariate but not multivariate analysis. Because patients may be at risk for bacterial translocation during endoscopic procedures, we suggest antibiotic prophylaxis for patients with cirrhosis and ascites who are undergoing procedures that are high risk for bacteremia, particularly if the patient is unlikely to tolerate an infection (eg, patients with decompensated cirrhosis). (See 'High-risk procedures' above and 'Low-risk procedures' above.)
Synthetic vascular grafts — We typically do not use antibiotic prophylaxis for patients with synthetic vascular grafts, and this approach is supported by society guidelines [1]. However, we suggest that elective procedures be performed before a synthetic graft is placed or delayed for six months following placement to permit time for endothelialization of the graft. If a procedure is necessary within six months of graft placement, we generally will give antibiotic prophylaxis for high-risk procedures. (See 'High-risk procedures' above.)
If the decision is made to give prophylactic antibiotics, the regimens recommended for patients who are immunocompromised are appropriate choices (table 2).
Prosthetic joints — Antibiotic prophylaxis is not recommended for patients with prosthetic joints because data supporting a benefit are limited. However, a case-control study suggested upper endoscopy may increase the risk of infection in patients undergoing upper endoscopy within two years of a joint replacement (adjusted odds ratio 4, 95% CI 1.5-10) [28]. Antibiotic prophylaxis is not recommended by the ASGE [1]. Our approach to a patient whose surgeon has recommended antibiotics is to discuss the issue with the patient. If the patient still wishes to receive antibiotics after the discussion, we will provide antibiotic prophylaxis [29]. This recommendation may change if more data become available suggesting an increased risk of infection following prosthetic joint placement.
Peritoneal dialysis — For peritoneal dialysis patients, we agree with a working group recommendation that the abdomen is emptied of fluid prior to any procedure (eg, upper endoscopy, colonoscopy) involving the abdomen or pelvis [30].
Whether to give antibiotic prophylaxis prior to endoscopic procedures for patients undergoing peritoneal dialysis is uncertain. There have been several case reports of peritonitis in patients undergoing peritoneal dialysis following colonoscopy, particularly after polypectomy (presumably because of bacterial translocation into the peritoneal cavity) [31-35], but there are no high-quality data to guide decision-making. Based on the available data, the International Society for Peritoneal Dialysis (ISPD) and ASGE recommend antibiotic prophylaxis for patients undergoing colonoscopy. We agree that this is a reasonable approach, while randomized trials are needed to further inform practice.
We do not use antibiotic prophylaxis prior to upper endoscopy because published evidence of a benefit is lacking. However, some experts use antibiotics prior to upper endoscopy. These issues and the choice of preprocedure antibiotic therapy are discussed separately [1,30]. (See "Risk factors and prevention of peritonitis in peritoneal dialysis", section on 'Management before procedures'.)
ANTIBIOTIC REGIMENS —
The choice of antibiotics will depend on the procedure being performed and patient factors such as allergies. Antibiotic regimens are presented in the table (table 2).
SOCIETY GUIDELINE LINKS —
Links to society and government-sponsored guidelines from selected countries and regions around the world are provided separately. (See "Society guideline links: Endoscopy preparation, sedation, and special considerations".)
SUMMARY AND RECOMMENDATIONS
●General principles – Recommendations for antibiotic prophylaxis for gastrointestinal (GI) procedures, as well as specific antibiotic regimens, are summarized in the tables (table 1 and table 2). (See 'When to use antibiotic prophylaxis' above.)
The majority of patients undergoing endoscopic procedures do not require antibiotic prophylaxis, including patients with valvular heart disease or prosthetic joints. (See 'Routine upper endoscopy, colonoscopy, and flexible sigmoidoscopy' above and 'Cardiac conditions' above and 'Prosthetic joints' above.)
Antibiotic prophylaxis is only required for procedures associated with a significant risk of infection, or in patients with conditions that make them more susceptible to infection who are undergoing procedures associated with a high risk of bacteremia. (See 'High-risk procedures' above.)
●Specific procedures
•Percutaneous endoscopic gastrostomy (PEG) or jejunostomy (PEJ) tube placement – We recommend antibiotic prophylaxis for all patients undergoing PEG or PEJ tube placement (Grade 1A). Prophylactic antibiotics given in this setting substantially reduce the risk of peristomal wound infection. (See 'Percutaneous endoscopic gastrostomy or jejunostomy placement' above.)
•Endoscopic retrograde cholangiopancreatography (ERCP) – For patients with biliary obstruction that is unlikely to be successfully drained endoscopically, we suggest antibiotic prophylaxis prior to ERCP (Grade 2C). (See 'Endoscopic retrograde cholangiopancreatography (ERCP)' above.)
We do not use antibiotic prophylaxis if the obstruction is likely to be drained during ERCP.
Patients with cholangitis should be receiving antibiotics as part of their routine treatment and do not require additional antibiotic prophylaxis.
•Endoscopic ultrasound with fine-needle aspiration (EUS-FNA) – For patients with pancreatic cysts undergoing EUS-FNA or ERCP, we suggest not giving prophylactic antibiotics (Grade 2C). We believe there are insufficient data to support their use in this setting. However, since the data regarding the potential benefits and harms of prophylactic antibiotics in such patients are accumulating, giving prophylactic antibiotics is a reasonable alternative (especially if the cyst is not fully aspirated) and is consistent with American Society of Gastrointestinal Endoscopy (ASGE) guidelines. (See 'Endoscopic ultrasound' above.)
For patients undergoing EUS-FNA of mediastinal cysts, we suggest giving antibiotic prophylaxis (Grade 2C). There are some data to suggest that mediastinal cysts have a greater risk of infection.
For patients undergoing EUS-FNA of other cystic lesions along the GI tract, we suggest not giving antibiotic prophylaxis (Grade 2C). We believe there are insufficient data to support the use of prophylactic antibiotics in this setting.
For patients undergoing EUS-FNA of solid lesions, we suggest not giving antibiotic prophylaxis (Grade 2C).
Antibiotics are typically given to all patients undergoing interventional EUS procedures such as drainage of walled-off pancreatic necrosis, biliary drainage, fine-needle injection of cysts/tumors, and fiducial placement.
●Patients who may require prophylaxis because of underlying medical conditions
•Patients who are immunocompromised – We suggest antibiotic prophylaxis be given to patients with severe neutropenia (absolute neutrophil count <500 cells/microL) or advanced hematologic malignancies who are undergoing procedures associated with a high risk of bacteremia (Grade 2C). (See 'Immunocompromised states' above and 'High-risk procedures' above.)
We do not routinely give antibiotic prophylaxis to patients who are immunocompromised but do not have severe neutropenia or an advanced hematologic malignancy.
•Patients with cirrhosis – We use antibiotics for patients with cirrhosis and acute GI bleeding, regardless of whether an endoscopy is performed. (See "Overview of the management of patients with variceal bleeding".)
For patients with cirrhosis who do not have acute GI bleeding, we suggest antibiotic prophylaxis if the patient has ascites and is undergoing a procedure associated with a high risk of bacteremia (Grade 2C). (See 'Cirrhosis' above and 'High-risk procedures' above.)
•Patients with synthetic vascular grafts – For most patients with synthetic vascular grafts, we suggest not giving antibiotic prophylaxis (Grade 2C). When possible, elective procedures should be performed before a synthetic graft is placed or delayed for six months following graft placement. If a procedure is necessary within six months of graft placement, we generally will give antibiotic prophylaxis for high-risk procedures. (See 'Synthetic vascular grafts' above.)
•Patients undergoing peritoneal dialysis – For patients undergoing peritoneal dialysis, the peritoneum should be empty prior to an endoscopic procedure. For patients who are undergoing upper endoscopy, we typically do not use antibiotic prophylaxis. For patients undergoing colonoscopy, society guidelines advise using antibiotic prophylaxis. We agree that this is a reasonable approach, while randomized trials are needed to further inform practice. (See 'Peritoneal dialysis' above.)
The choice of preprocedure antibiotic therapy in this setting is discussed separately. (See "Risk factors and prevention of peritonitis in peritoneal dialysis", section on 'Management before procedures'.)
