Session 11 Gut microbiota and infections

• The collection of bacteria, archaea and eukarya colonising the GI tract is termed the gut microbiota.
• When placenta harbors microbiome, colonization of gut begin in-utero -> In-utero colonization hypothesis
• When the placenta and fetus is considered to be sterile and the microbiome is acquired after birth -> sterile womb hypothesis
• Neonatal factors that affect fetus microbiota?

  • Gestational age
  • Mode of delivery
• Postnatal factors that affect gut microbiota?

  • Feeding (formula/breast)
  • maternal diet
  • Geographical location
• the composition of a ‘normal’ healthy gut microbiota?

  • Microbial communities from mother’s vagina - Lactobacillus
  • Microbial communities from mother’s skin: Staphylococcus spp, Corynebacterium
  • Facultative anaerobes: E. coli and other Enterobacteriaceae , Bacteroides fragilis
  • Breastfeeding/ Milk: Bifidobacterium sp
• Lactobacilli produce lactic acid which helps prevent harmful bacteria from colonising the gut.
• Bifidobacterium help digest fibre and complex carbs and produce SCFAs, aid in digestion of B vitamins and prevent infection.
• Microbiota: range of microorganisms found within an environment Microbiome: genomes found within the environment.
• Dysbiosis: disruption to the microbiota leading to an imbalance.
• Commensalism: microbiota colonise a host, co-exist without being harmful – referred to as ‘normal flora’ or ‘normal microbiota’.
• three significant categories of dysbiosis:?

  • Loss of beneficial organisms
  • Excessive growth of potentially harmful microorganisms
  • Loss of overall microbial diversity.
• Causes of dysbiosis?

  • Medications such as antibiotics
  • Increasing Age
  • Physical and psychological stress
  • Diet changes
  • Infections
• Clostridium difficile is a Gram positive, spore forming bacteria.
• C.diff associated antibiotics - clindamycin, cephalosporins, beta lactams, fluoroquinolones
• C.diff investigation?

  • First -> GDH antigen test and Toxin A and B test (EIA)
  • NAAT
• Treatment of C. difficile?

  • Vancomycin - 125mg x 4 times a day for 10 days
• Investigations for IBD?

  • Colonoscopy
  • Tissue biopsy
• Coeliac disease is a systemic autoimmune disorder triggered by gluten peptides from grains including wheat, rye, and barley.
• Diet high in red and processed meat is thought to increase the risk of colorectal cancer.
• Food poisoning: An illness caused by the consumption of food or water contaminated with bacteria and/or their toxins, or with parasites, viruses, or chemicals.
• Dysentery: an intestinal infection that causes diarrhoea containing blood or mucus
• Colitis: inflammation of the colon
• Enteritis: infleammation of the small intestin
• Gastroenteritis: stomach + small intestine inflammation.
• Non-inflammatory diarrhoea?

  • This is usually watery, large-volume, frequent stool
  • There is no tenesmus, blood in the stool, fever, or faecal leukocytes.
  • Histologically the GI architecture is preserved.
  • Can be subdivided into secretory and osmotic diarrhoea.
• Osmotic tends to be from maldigestion or malabsorption
• There is an altered transport of ions across the mucosa, which results in increased secretion and decreased absorption of fluids and electrolytes from the GI tract, especially in the small intestine. - Secretory diarrhoea
• Inflammatory diarrhoea?

  • It is usually associated with mucoid and bloody stool, tenesmus, fever, and severe crampy abdominal pain.
  • Histology of the GI tract is abnormal in inflammatory diarrhoea
• What information should I put on a stool sample?

  • Current or recent antibiotic therapy
  • Date of onset, length of history
  • Food history if relevant - e.g. shellfish consumption
  • Travel history - state countries and dates of travel and return
  • Association with known cases
  • Please state if from a suspected outbreak and give the HP zone number if known
  • Please state if sample is for clearance purposes
• Shigella dysenteriae is more common in low- and middle income countries and causes a more severe illness with dysentery.
• S dysenteriae type 1 is a cause of haemolytic uraemic syndrome owing to its production of Shiga toxin
• Treatment for H.pylori?

  Triple therapy regimen

  • A PPI
  • Two antibiotics
• Increased gastrin release resulting in gastric acid hypersecretion - Leads to severe inflammation and induction of gastric epithelial cell death - H. pylori infection(gastritis)
• Giardiasis is a parasitic infection that is caused by the protozoan Giardia lamblia.
• Treatment for giardiasis?

  Metronidazole
• Amoebiasis caused by entamoeba histolytica is treated with metronidazole.

  Associated with risk of liver abscess
• Cryptosporidiosis caused by cryptosporidium parvum is treated with nitazoxanide.

  Associated with HIV infection or other T-cell immune deficiences
• Cyclosporiasis is treated with trimethoprim-sulfamethoxazole.
• O&P tests?

  • Stool sample / worm sent in a sterilin 30ml universal, with quick-start cap and spoon.
  • Provide any recent travel history.
  • Ideally three stool specimens from three different days are recommended (clearly labelled with date and time) because of the intermittent shedding of cysts and ova.
  • A 'hot' stool (that must be examined within 30 minutes of being passed by the patient) may be provided for amoebae investigation.
  • Used for parasitic infections