Bacterial Overgrowth Syndrome

Small intestinal bacterial overgrowth (SIBO) is excessive proliferation of colonic-type bacteria within the small intestine, normally kept low by gastric acid, intestinal motility, and the ileocecal valve.

Predisposing factors include anatomical abnormalities (surgical blind loops, strictures, diverticula), motility disorders (diabetic autonomic neuropathy, scleroderma, opioid use), achlorhydria (PPI use, atrophic gastritis, prior gastric surgery), and immunodeficiency.

Bloating, abdominal distension and discomfort (often worse after meals), flatulence, diarrhea (from bacterial deconjugation of bile acids impairing fat absorption, causing steatorrhea in more significant cases), and, with chronic disease, malabsorption leading to weight loss and micronutrient deficiency, particularly vitamin B12 deficiency (paradoxically, folate can be normal or elevated, since colonic-type bacteria synthesize folate while consuming B12, a useful distinguishing biochemical pattern from simple dietary B12 deficiency).

Hydrogen/methane breath testing (glucose or lactulose substrate) is the standard non-invasive test, an early rise in breath hydrogen or methane after substrate ingestion supports the diagnosis, though sensitivity and specificity are imperfect
Small bowel aspirate and culture (quantitative bacterial count) is more invasive but more specific where available
B12, folate, and fat-soluble vitamin levels assess for malabsorptive consequences
Investigation for and correction of the underlying predisposing anatomical or motility abnormality

Antibiotic treatment: rifaximin 550 mg PO tds for 14 days is preferred given minimal systemic absorption and good efficacy against the typically anaerobic/coliform overgrowth flora; alternatives include a 10 to 14 day course of a combination or single systemic agent (e.g. ciprofloxacin, co-amoxiclav, or metronidazole) per local practice, particularly if methane-predominant (associated with Methanobrevibacter, sometimes treated with rifaximin plus neomycin)
Recurrence is common, particularly where the underlying predisposing factor (motility disorder, anatomical abnormality) cannot be corrected, and cyclical or recurrent antibiotic courses are often needed
Address the underlying cause where feasible (surgical correction of a blind loop, optimizing diabetic control, reviewing chronic PPI use)
Nutritional support and replacement of deficiencies (B12 IM as per standard protocol, fat-soluble vitamins as needed)
Dietary modification (low FODMAP approaches) may reduce symptom burden as an adjunct, though does not treat the underlying overgrowth itself

Referral: gastroenterology for breath testing, recurrent disease, or where an underlying anatomical/motility cause requires further workup.

Clinical toolsCalculators

BMI GCS EDD Parkland Formula

Corrected Sodium Corrected Calcium Anion Gap Creatinine Clearance Insulin Calculations qSOFA Wells PE Wells DVT CHA₂DS₂-VASc HAS-BLED CURB-65 Centor/McIsaac

Helicobacter Pylori Infection

Helicobacter pylori is a gram negative, urease-producing spiral bacterium colonizing the gastric mucosa, acquired predominantly in childhood via fecal-oral or oral-oral routes, with prevalence closely tied to socioeconomic conditions and sanitation.

It is the dominant cause of chronic gastritis (see that entry), a major cause of peptic ulcer disease (see that entry), and is classified as a Group 1 (definite) carcinogen given its causal role in gastric adenocarcinoma and MALT lymphoma.

Non-invasive "test and treat" testing (for dyspepsia without alarm features, or before eradication confirmation): urea breath test or stool antigen test, both requiring PPI cessation for 2 weeks and antibiotic cessation for 4 weeks before testing to avoid false negatives
Serology detects past exposure but cannot distinguish active from cleared infection and is not useful for confirming eradication
Where endoscopy is already indicated (alarm features, age above threshold): rapid urease test (CLO test), histology, or culture (culture allows susceptibility testing, increasingly valuable given rising resistance)

First line triple therapy: PPI (e.g. omeprazole 20 mg bd) + amoxicillin 1 g bd + clarithromycin 500 mg bd, for 7 to 14 days (14 days increasingly preferred given modestly higher eradication rates than 7 days)
Given rising clarithromycin resistance in many regions, quadruple bismuth-based therapy is increasingly used first line where local resistance exceeds roughly 15%: PPI + bismuth subsalicylate/subcitrate + metronidazole 400 mg bd + tetracycline 500 mg qds, for 10 to 14 days
Penicillin allergy: substitute metronidazole 400 mg bd for amoxicillin in the triple regimen, or use bismuth quadruple therapy
Second line (after triple therapy failure): bismuth quadruple therapy if not already used, or a levofloxacin-based regimen (PPI + amoxicillin + levofloxacin) guided by local resistance data
Confirm eradication with urea breath test or stool antigen at least 4 weeks after completing antibiotics and 2 weeks off PPI, in all cases given the public health and malignancy-prevention importance of confirmed cure, not just symptom resolution
MALT lymphoma localized to the stomach frequently regresses with eradication therapy alone if early stage (see Gastric Cancer entry for further management if it does not)

Referral: gastroenterology for endoscopy where indicated, treatment failure after two eradication attempts, or confirmed MALT lymphoma/malignancy.

Bacterial Overgrowth Syndrome

Overview

Clinical Features

Diagnosis

Management

Overview

Clinical Features

Diagnosis

Management