Bacterial and Fungal Infections of the Lower GI Tract – Part 2

Lower Gastrointestinal (GI) Tract – Overview

• Includes the small and large intestines (from jejunum to anus).

• Functions:

  • Digestion: Bile digests fats.

  • Absorption: Nutrients, water, electrolytes absorbed in small intestine.

  • Defecation: Waste is expelled via the anus.

  • Protection: Mucus, GALT (immune tissue), and microbiome protect from pathogens.

Gut Microbiome Basics

• 99% anaerobic bacteria.

• Ferment fibre to produce vitamins (e.g. B9/folic acid).

• Microbial numbers rise along the GI tract, peaking in the colon (~10¹⁴ cells).

Niche Microhabitats

• Bacteria exist in specific areas: lumen, mucosal layers, crypts.

• Affected by oxygen, pH, bile salts, nutrients.

Factors Affecting Microbiome

• Begins before birth, changes with age and environment.

• Firmicutes dominate early in life; Bacteroidetes later.

Role of Commensal Bacteria

• 500–1000 species.

• Compete with pathogens.

• Digest fibre, produce vitamins.

• Can exclude or inhibit harmful microbes.

Mucus & Antimicrobials

• Gut cells secrete antimicrobial peptides (AMPs):

  • Paneth cells (in crypts) produce:

    • Lysozyme (breaks bacterial walls),

    • Phospholipase (disrupts membranes),

    • Lectins (e.g. RegIII) and Defensins (kill pathogens).

Immune Defence (GALT)

• Gut = largest immune organ.

• Dendritic cells sample antigens → activate T & B cells.

• Work with mucus to create an “exclusion zone” to block bacteria.

Campylobacter jejuni

• Gram-negative, spiral, microaerophilic, thermophilic.

• Zoonotic: mainly from undercooked poultry.

• Infects mucosa, causes inflammatory diarrhoea (can be bloody), fever, cramps.

• Produces CDT toxin → DNA damage → cell death.

• Mimics nerve proteins → can trigger autoimmune paralysis (e.g. Guillain-Barré).

• Detection: Enrichment in special broths + ID by DNA tests.

• Treatment: Usually self-limiting. Erythromycin can help. Prevent dehydration.

Salmonella spp.

• Gram-negative rods, motile, facultative anaerobes.

• Main species: Salmonella enterica (many serotypes: e.g. Typhimurium, Enteritidis).

Typhoidal vs Non-Typhoidal

• Typhoidal (e.g. S. Typhi): Causes typhoid fever, spread human-to-human, vaccine available.

• Non-typhoidal: Foodborne illness, self-limiting diarrhoea, no vaccine.

Infection Mechanism

• Infects intestinal and immune cells.

• Uses Type III secretion system (“injectisome”) to insert toxins.

• Invades via Zipper (host receptor) or Trigger (cytoskeleton manipulation).

Detection & Treatment

• Enrichment in RVS broth, ID via PCR or antigen tests.

• Usually self-limiting. Ciprofloxacin, azithromycin for severe cases.

Clostridioides difficile (C. diff)

• Gram-positive, spore-forming, anaerobic rod.

• Found in 3% of adult guts.

• Spores survive stomach acid and hospital cleaning.

• Overgrowth often triggered by antibiotics disrupting gut flora.

Disease

• Produces toxins A & B → damages epithelium → severe diarrhoea.

• High mortality in severe cases.

• Biofilm + para-cresol helps it persist and outcompete other microbes.

Detection

• CCFA agar, toxin assays, and PCR for toxin genes.

• CCNA (cell rounding test) is the gold standard.

Treatment

• Stop original antibiotics.

• Use vancomycin or fidaxomicin.

• For recurrent cases: FMT (Faecal Microbiota Transplant) is highly effective.

Fungal Infections of the GI Tract

• Make up 1–2% of gut flora.

• Important for digestion and protection.

• Overgrowth happens in immunocompromised or post-antibiotics.

• Candida albicans can breach the gut barrier → sepsis, septic shock, death.

Listeria monocytogenes

• Gram-positive, facultative anaerobe, motile at low temps.

• Psychrophile – grows at fridge temps!

• Found in soil, water, animals.

• Infects 10% of human guts; can cross placenta, gut, and blood-brain barriers.

Key Takeaways

• Gut microbiome is critical for digestion, immune function, and protection.

• Pathogens like C. jejuni, Salmonella, C. difficile, and Listeria can cause serious GI infections.

• Good hygiene, proper cooking, and prudent antibiotic use are essential for prevention.

• FMT is a promising treatment for restoring healthy gut flora in resistant infections.