Mednotes

L18 I&I GI tract Normal Flora

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tagsinfectionandimmunity, lecture
aliasesL18 I&I GI tract Normal Flora

15 min read

Overview

This lecture covers the gut microbiome: what it is, where it lives, what it normally does for the host, and how it goes wrong. It then works through the major disease consequences of the gut microbiome — polymicrobial anaerobic infections/abscesses, gas gangrene, necrotising enterocolitis (NEC), Helicobacter pylori infection, and Clostridioides difficile infection — covering pathogenesis, clinical spectrum, diagnosis and treatment for each.

The gut microbiome: composition and distribution

  • Microbiome = the microbes present at a body site plus their genomes (collectively ~1 x 10^14 cells, outnumbering human cells ~10:1, and >100x the number of genes in the human genome). Microflora/microbiota = just the microbes present.
  • Colonises body sites exposed to the environment: skin, mucous membranes (conjunctiva, oral cavity, upper respiratory tract, GI tract, genitourinary tract).
  • The gut holds ~95% of the total body microbiome.
  • Complex and diverse: hundreds to thousands of species/strains per person. About 1/3 of species are conserved between people (same 30-40 species); the other 2/3 are variable, contributing to high inter-individual variability (arguably making each person’s microbiome unique).
  • Colonisation begins soon after birth and is stable by 1-3 years old; composition is then relatively stable through life but can shift with diet or treatments (e.g. antibiotics).
  • Density and diversity increase down the tract, inversely related to pH:
    • Stomach/duodenum: ~10^3 organisms/g; low diversity; low pH (~1.5); genera include Lactobacilli, Streptococci, yeasts.
    • Jejunum/ileum: ~10^4-10^8 organisms/g; genera include Lactobacilli, coliform bacteria, streptococci, Bacteroides, Bifidobacteria, Fusobacteria.
    • Colon: ~10^10-10^12 organisms/g, making up ~55% of colon contents; near-neutral pH (5-7); most diverse site, containing Bacteroides, Bifidobacteria, Streptococci, Eubacteria, Fusobacteria, Clostridia, Veillonella, coliform bacteria, Lactobacilli, Proteus, Staphylococci, Pseudomonads, yeasts, protozoa.
  • The gut microbiome is predominantly anaerobic:
    • Obligate anaerobes: Lactobacillus and Bifidobacterium (commensal/probiotic); Clostridium and Bacteroides (opportunistic pathogens — these two cause most obligately anaerobic infections, e.g. Bacteroides fragilis).
    • Facultative anaerobes (all opportunistic pathogens): Enterobacterales (E. coli, Klebsiella, Enterobacter, Proteus), enterococci, streptococci, staphylococci, Pseudomonas.

Normal functions of the gut microbiome

  • Mutualistic relationship, important for overall health and development.
  • Developing and supporting immune function.
  • Colonisation resistance — inhibits colonisation by pathogens.
  • Metabolism of therapeutic drugs.
  • Bilirubin breakdown.
  • Immunological tolerance — helps the host differentiate commensals from pathogens, and generates tolerance to food antigens.
  • Supports normal gut function — supports the barrier effect of gut epithelium, stimulates mucus and antimicrobial peptide (AMP) production.
  • Energy salvage — ferments non-digestible carbohydrates (fibre) into short-chain fatty acids (SCFAs), providing energy for colonocytes.
  • Source of vitamins B12 and K, and amino acids.

Dysbiosis and disease

  • Dysbiosis = changes in the gut microbiome associated with disease. Three possible causal relationships, not fully resolved:
    1. Dysbiosis causes disease (microbiome changes → disease).
    2. Dysbiosis is caused by disease (disease → inflammation → microbiome changes).
    3. Dysbiosis does not initiate disease but perpetuates it (genetically susceptible host → disease → inflammation → microbiome changes → continuing inflammation, i.e. a self-sustaining loop).
  • Altering the microbiome (probiotics, prebiotics, faecal microbiota transplant) may help prevent or resolve dysbiosis and inflammation.
  • Dysbiosis is linked to a wide range of conditions, though mechanisms are poorly understood and are mostly based on comparing microbiomes of patients vs healthy controls: gut-brain axis (autism, psychiatric disorders, neurodegenerative disorders), gut-lung axis (asthma, obstructive pulmonary disease, lung cancer, pneumonia), metabolic disease (obesity, type 2 diabetes, mitochondrial dysfunction, cancer), cardiovascular disease (atherosclerosis, thrombosis, heart failure), gut-skin axis (psoriasis, acne vulgaris, skin cancer), and IBD/IBS/coeliac disease.
  • In IBD specifically, the gut microbiome is less diverse than in healthy controls, but it is unclear whether this is cause or effect.

Anaerobic infections, gas gangrene and necrotising enterocolitis

  • Occasional opportunistic pathogens: normally-commensal gut organisms cause disease when they cross the bowel epithelium (via perforation from surgery/trauma, or inflammation) into the blood, causing sepsis or infection of a distant site (e.g. a diabetic foot ulcer).
  • These infections are typically polymicrobial abscesses of abdominal organs/peritonitis: facultative anaerobes (Enterobacterales such as E. coli; staphylococci/streptococci/enterococci) use up available oxygen first, creating an anaerobic environment that then allows obligate anaerobes (Bacteroides, Clostridium) to grow — this can progress to liver abscesses.
  • Treatment requires antimicrobials active against obligate anaerobes: metronidazole, clindamycin, cephamycins, carbapenems, beta-lactam/beta-lactamase inhibitor combinations, quinolones (resistance to quinolones is an emerging issue). Polymicrobial infections (facultative + obligate anaerobes) may need combination or broad-spectrum therapy.
  • Gas gangrene (clostridial myonecrosis): caused by Clostridium perfringens, whose toxins cause necrosis of soft tissue and muscle plus gas production. Follows trauma or GI surgery. Rapidly progressive — can lead to sepsis, toxaemia, shock and multi-organ dysfunction syndrome (MODS); may require amputation/debridement; can be fatal. Treatment: IV penicillin +/- clindamycin.
  • Necrotising enterocolitis (NEC):
    • Occurs in pre-term, low-birth-weight, formula-fed infants, typically at 2-4 weeks of life; affects ~7% of premature infants and is a common cause of NICU admission.
    • Pathogenesis (dysbiosis-driven): normal colonisation builds the infant’s immune system and gut barrier function in a cycle from birth; antibiotics and formula feeding can disrupt correct colonisation, breaking this cycle. This is thought to allow bacterial translocation, causing intestinal inflammation, then ischaemia/necrosis of the gut wall with gas formation.
    • Presents on a spectrum of severity; difficult to diagnose as initial symptoms are non-specific, progressing to abdominal distension, poor feeding, blood in stools, vomiting. Imaging shows pneumatosis intestinalis (gas within the wall of the gut). Unrecognised/untreated cases can perforate, causing peritonitis/sepsis with high mortality (~50%).
    • Treatment: broad-spectrum antimicrobial combination (amoxicillin + gentamicin + metronidazole); surgical resection/repair if perforated. The microbiome’s exact role is unclear but thought important, so manipulation (probiotics, breast milk) is a potential treatment/prevention avenue.

Helicobacter pylori

  • Gram-negative, spiral (helical) rod; motile via a tuft of unipolar flagella; urease-positive, which allows it to survive in the acidic stomach.
  • Global carriage ~45%; acquired in childhood and persists for life. Prevalence linked to socioeconomic factors — higher in low/middle-income countries, lower in high-income countries; global rates falling overall but may be rising with increasing obesity. Example carriage rates: Shanghai adults 71.7%; healthy Koreans 50.8%; Australian adults 15.5%; Auckland high-schoolers — Pasifika 49%, Māori 27%, Asian 25%, NZ European 13.5%.
  • 80% of infections are asymptomatic; colonisation may even be protective against GERD, diarrhoea, allergy/asthma, IBD, TB and coeliac disease — possibly reflecting less virulent, toxin-negative strains in asymptomatic carriers vs more virulent, toxin-positive strains in the symptomatic 20%.
  • Virulence factors:
    • Urease: hydrolyses urea + H2O → CO2 + 2NH3, raising local gastric pH so the bacterium survives the acidic stomach.
    • Motility: allows penetration of the mucus layer.
    • Adhesins: bind gastric mucus and the Lewis blood group b antigen in gastric mucosa, possibly contributing to gastritis.
    • Toxins (more closely linked to disease): VacA causes gastritis by recruiting/activating immune cells and cytokines; CagA is oncogenic and promotes cancer.
  • Clinical spectrum: colonisation of gastric mucosa → superficial gastritis (weeks) → chronic inflammatory gastritis (months-years) → branches into atrophic gastritis (loss of glandular epithelium, no HCl/pepsin secretion), chronic active gastritis, or peptic/duodenal ulcer disease (over decades; ulcer disease in ~10% of infections). Atrophic gastritis (no HCl) further increases risk of progression to gastric adenocarcinoma (1-3% of infections); gastric MALToma is a rarer outcome (<0.1%).
  • Diagnosis:
    • Invasive (via endoscopy/biopsy): H&E stain (for gastritis/cancer), special stains, PCR, culture, rapid urease test (e.g. CLOtest).
    • Non-invasive: urea breath test (ingested labelled urea metabolised by gastric urease to CO2, exhaled and measured via the lungs; useful for monitoring treatment success/failure), faecal antigen test, serology (serum antibody).
  • Treatment: only symptomatic patients are treated, with triple therapy — a proton pump inhibitor plus two antimicrobials (e.g. clarithromycin + amoxicillin).

Clostridioides difficile

  • Obligately anaerobic, spore-forming, gram-positive rod (previously named Clostridium difficile). Infection = CDI (“C diff”).
  • Colonises 3-5% of adults but >20% of hospitalised patients.
  • Spores are key to transmission: they survive for extended periods in the environment, driving healthcare-associated infection (HAI); community-acquired infection (CAI) is an emerging issue.
  • Pathogenesis of infection: use of oral broad-spectrum antimicrobials (amoxicillin, co-amoxiclav, clindamycin, cephalosporins, carbapenems, fluoroquinolones) inhibits the normal gut microbiome, allowing rapid overgrowth of C. difficile and toxin production, leading to disease. Other risk factors: age >65, recent hospitalisation/residential care, immunocompromise, comorbidities, previous CDI.
  • Pathogenesis mechanism:
    1. Spores are ingested (mouth/oesophagus).
    2. In the intestine, exposure to primary bile acids triggers germination of spores into vegetative cells.
    3. In the colon, the organism colonises and produces toxins TcdA and TcdB (and, in some strains, additional toxins).
    4. Toxins inhibit Rho GTPases that control the actin cytoskeleton, disrupting epithelial tight junctions; this causes water loss (watery diarrhoea) and increased adherence of C. difficile to the epithelium.
    5. Toxins also activate macrophages and recruit neutrophils, generating cytokines and inflammation, and cause epithelial cell death/apoptosis, leading to mucosal ulceration and pseudomembrane formation (a pseudomembrane is composed of necrotic epithelial cells, neutrophils and fibrin).
    6. C. difficile then sporulates in the colon, completing the cycle.
  • Clinical spectrum (increasing severity, decreasing frequency):
    • Antibiotic-associated diarrhoea (AAD) — watery diarrhoea, abdominal pain, neutrophilia; more common, less severe.
    • Pseudomembranous colitis (PMC) — pseudomembrane overlying ulcerated, haemorrhagic, inflamed mucosa.
    • Toxic megacolon — pathological distension/dilation of the colon; less common, more severe.
    • Sepsis, multi-organ dysfunction syndrome (MODS), death.
  • Hypervirulent strains: can cause atypical infection with no usual risk factors (previously healthy, no prior antimicrobial history, community-acquired). These strains are more virulent — increased TcdA/TcdB production, additional toxins, increased sporulation, antimicrobial resistance — and cause higher mortality; uncommon in Aotearoa/NZ.
  • Diagnosis requires both a clinical and a microbiological component: a toxin-producing strain must be isolated from a loose stool sample from a symptomatic patient with risk factors. Toxin (TcdB) detection methods include PCR, LAMP, or EIA.
  • Treatment:
    • First step: stop the inciting antimicrobial therapy (diarrhoea may resolve on its own).
    • Oral antimicrobials (reach the site of infection): metronidazole (still first-choice in Aotearoa/NZ, but has no effect on spores, so relapse occurs in >25% of cases); vancomycin; fidaxomicin (does act on spores, so prevents relapse, but should be reserved for serious relapsing infection as resistance is emerging).
    • Faecal microbiota transplant (FMT) repopulates the gut and is under investigation/used to prevent relapse.
    • Avoid anti-motility agents — they increase contact time between toxins and the gut wall, worsening disease.
    • Infection control: isolate patients with CDI (standard precautions, ideally a negative-pressure room). Spores resist alcohol-based hand sanitiser, so hand washing with soap and water is required.

Antimicrobial choice must match both the organism and the site of infection: good choices for obligate anaerobes are clindamycin, metronidazole, beta-lactam/beta-lactamase inhibitor combinations, cephamycins, carbapenems, and quinolones; good choices for facultative anaerobes are third-generation cephalosporins, fluoroquinolones, and aminoglycosides.

The source slide deck has a text/image mismatch on one page (page 26): the visible slide image duplicates the "Clostridioides difficile" introduction slide, but the underlying extracted text for that same page is actually the deck's final "Additional resources" reference-link slide. Both pieces of content are captured above (the C. difficile content under its own section, the reference links noted below), but the user may want to check the original PDF/PowerPoint for a corrupted or misassembled page.

Self-test

  1. Define microbiome, distinguishing it from microbiota/microflora.
  2. Describe how bacterial density and diversity change from the stomach to the colon, and explain the relationship with pH.
  3. List the main obligate and facultative anaerobic genera/groups found in the gut microbiome, noting which are commensal/probiotic and which are opportunistic pathogens.
  4. List the normal functions of the gut microbiome.
  5. Describe the three proposed causal relationships between dysbiosis and disease.
  6. Explain the mechanism by which a polymicrobial intra-abdominal abscess develops after bowel perforation, and name the antimicrobials used to treat obligate anaerobic infections.
  7. Describe the pathogenesis and clinical course of gas gangrene, including its treatment.
  8. A premature, formula-fed infant develops abdominal distension and blood in the stools at 3 weeks of age, with gas visible in the bowel wall on x-ray. What is the diagnosis, what does the x-ray finding represent, and what is the treatment?
  9. Describe the virulence factors of Helicobacter pylori and how each contributes to survival or disease.
  10. Describe the clinical spectrum of H. pylori infection, from colonisation to gastric adenocarcinoma.
  11. List the methods used to diagnose H. pylori infection, distinguishing invasive from non-invasive tests, and state the treatment for symptomatic infection.
  12. Describe the mechanism by which broad-spectrum antimicrobial therapy leads to Clostridioides difficile infection.
  13. Describe the steps of C. difficile pathogenesis, from spore ingestion to pseudomembrane formation.
  14. Distinguish antibiotic-associated diarrhoea, pseudomembranous colitis and toxic megacolon in terms of frequency and severity.
  15. What distinguishes a hypervirulent C. difficile strain, and what diagnostic criteria confirm CDI?
  16. List the treatment options for CDI, noting which have activity against spores and which is reserved for relapsing disease, and explain why alcohol-based hand sanitiser is inadequate for infection control.
  17. Explain why treating a polymicrobial obligate/facultative anaerobic intra-abdominal infection requires different antimicrobial classes than treating a purely obligate anaerobic infection.

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