Luminal Infections and Disorders Flashcards
What are the three main groups of microorganisms in the GI tract?
- Commensal
- Opportunistic
- Pathogenic
What are commensal organisms?
Commensals – normal inhabitant of the human body, living in communities – they form the microbiota
Colonize a lot of different environments on our body – hair, skin, oral cavity, colon, vagina, etc.
Neither the host or the microbe is harmed – both derive benefits from their relationship
What event has a big impact on the our microbiota early on in life?
Microbiota is largely established by the mother during birth
Passage through the birth canal, from the skin, breast-feeding and food
This then continues to develop throughout life
What benefits do microbiota provide the human host?
- Bacteria can help digest and process food which we can then absorb
- Promotes postnatal differentiation of the mucosal structures
- Physical barrier function
- Stimulates the immune system – allowing for immune system development
- Regulation of metabolism
- Colonization resistance against pathogens – fight off potential pathogenic bacteria
What benefits do humans provide to the commensal microbiota?
- Provide nutrients and growth factor
- Provide a protected habitat
- Means for dispersal – grow and thrive in gut and spread from there onwards
What are the main bacterial phyla represented in the colon?
Colon – main bacterial species represented – Bacteroidetes and firmicutes
What is an opportunistic pathogen?
Opportunistic pathogens - these are commensal microorganisms that can become pathogenic in specific situaitons.
- When a bacteria are housed in the GI tract – they are considered commensal
- Only when they cause disease do they become pathogens
- Opportunistic bacteria – sometimes cause disease in certain instances – note that disease is not required for survival but rather an accident e.g. When protective mechanisms are absent/reduced these bacteria can thrive causing disease
Examples in the gut:
* Escherichia coli
* Bacteriodes fragilis
* Enterococcus faecium/faecalis
What is a pathogenic microorganism?
Obligate pathogen - Need to cause disease to transmit between hosts (—> evolutionary survival)
Can produce asymptomatic infection (but ≠ commensal)
Infections are not necessarily more severe than with opportunistic pathogens
Examples:
* Escherichia coli – many different types
* Shigella dysenteriae
* Salmonella Typhi
* Campylobacter jejuni/coli
What is the difference between zoonotic and environmental microorganisms?
Two other categories to help us understand where pathogens come from…
What are the different factors in the gut that prevent infections from arising?
- Barrier function – epithelium – tight junction
- Intestinal microbiota – colonization resistance
- Mucus secreted through goblet cells – creates thick layer making it hard for the pathogen to pass through
- Local immune cells – Gut associated Lymphatic tissue – APCs, lymphocytes, Paneth cells, etc. – providing protection + secreting antimicrobial peptides
- Lumen pH
- Low oxygen tension – low amount of oxygen in the gut – most microbes are anaerobes
- Flow rate – peristalsis – wash out bacteria
- Bile salts/ digestive enzymes – toxic to bacteria
What are some different factors that could impact the normal protective factors, increasing the risk of opportunistic infection?
- Immunosuppression
- Disruption of barrier function – sepsis
- Antibiotic – disrupting normal microbiota
- Ileus – lack of motility/propulsion (appendicitis) - peristalsis is reduced – increased ability of the bacterial colonization
- Antacid drugs – disrupt pH
Do obligate pathogens require the normal protective factors to be disrupted in order to cause infection?
Obligate pathogen – don’t need the protective mechanisms to be disrupted in order to cause infections, rather it disrupts these protective factors by itself
What are some examples of how obligate pathogens disurpt the normal functioning of the GI tract?
- Toxin production – many different effects – attack the epithelium, disrupting it, causing inflammation, causing a perturbation in the environment
- Increase the flow rate – diarrhea
- Direct invasion properties – virulence ability – reaching and bypassing the epithelium
- Resistance to bile salts, enzymes and intestinal microbiotia
- Capsule/LPS – avoidance of the immune system
- Adherence and motility mechanisms
Some opportunistic pathogens can become obligate pathogen by picking up virulence factors
How do pathogens (opportunistic or obligate) cause diarrhea or vomiting (mechanism)?
Diarrhea
* 3x day, liquid more than 80% water and >300g per 24 hours
Two mechanisms:
* Secretory - microorganisms and toxin produced cause water loss from epithelium.
* Inflammatory diarrhea - direct damage to epithelium - release of proteins, blood, WBCs and inflammation of the epithelium
Vomiting
* Reflex
* Mechanisms of protection
* Stimulated by humoral and neuronal mechanism
* Obligate pathogens create toxins in the GI tract - sends a message to the brain – drives vomiting response – relaxation of the esophagus and contraction of the stomach – vagal nerve mediated
What are the four organisms that can cause GI infections that we’ll be focusing on?
- H. Pylori
- Vibrio Cholerae
- Shigella
- Clostridioides difficile
H. Pyrlori
* Gram-staining
* Is it common?
* How is it transmitted?
* What area of the body does it colonize?
- Gram-negative
- Widespread across the world – present in 50% of western adults
- Transmitted through food and water
- Colonizes the human stomach (little bit of duodenum) – able to…
1. Survive in acid environment – microaerophile - needs oxygen but not too much – matches stomach
2. Motility (able to move through mucus to get through to the wall of the stomach)
3. Urease activity (enzyme transforms urea into ammonia – which is alkali, creating a H+ buffer)
What are the clinical features, method of diagnosis and treatment for a H. pylori infection?
Main clinical features
* Gastritis – mucosa becomes inflamed
* Gastric and duodenal ulcers
* Increased risk of carcinoma
Diagnosis
* Gastroscopy with biopsy (invasive)
and/or
* urea breath test (give radioactive protein to eat – if H.P present – we get radioactive ammonia in the breath)
and/or
antigen in stools
Treatment - Three antibiotics
Vibrio Cholerae
* Gram-staining
* How is it transmitted?
* What is the bacteria sensitive to?
* What area of the body does it colonize?
* Virulence factor
- Gram-negative
- Transmission < contaminated water or food (seafood!)
- Sensitive to drying out, sunlight and acid – need high bacterial load to transfer as a result
- Colonizes - Mainly acting the jejunum and the ileum
- Virulence factors - Secretes toxin and adheres to mucosae (Pili)
What is the mechanism that drives diarrhea production in V. Cholera infection?
Not invasive pathogen – produces toxin - consisting of a A and B subunit
B subunit – binds to the GM1 receptor – A subunit enters the cell where it activates adenylate cyclase – increase cAMP – increasing Cl- secretion and reduced absorption of Na+ - resulting in a net flow of water out
V. Cholera
What are the clinical features?
How is a diagnosis made?
What is the treatment?
Clinical features
* Watery secretory diarrhea (Rice-water stools) – Water and mucus – no protein, blood, WBCs, etc.
* Causes severe dehydration
Diagnosis - Clinical aspects and stool culture
Main treatment – rehydrates (IV ideally) and potentially antibiotic
Shigella
* Gram-staining
* How is it transmitted?
* What area of the body does it colonize?
* How many species are there? Which is the main?
* How does it cause pathology?
- Gram-negative
- Transmission - contaminated water or food, very low infectious load - very communicable
- Site - Large Colon
- Four species - S. dysenteriae, S. flexneri, S. boydii and S. sonnei
- Invasive pathogen - invades the epithelium and causes Inflammation of the gut. Does produce toxin but not the main mechanism.
How does shigella cause infeciton?
- Enter gut epithelium through M-cells (responsible for presenting antigens to immune cells) – trojan horse - allowing them to spread through the epithelium.
- They become ingested by macrophage at the basal side – macrophage dies releasing a huge amounts of cytokines resulting in tissue destruction
Shigella
* What are the clinical features?
* What are the complicaitons?
* How is a diagnosis made?
* What is. the treatment?
Clinical Features
* Bacterial dysentery – bloody diarrhea (+pus/mucus) + abdominal cramps and fever – three main features
* Complications – toxic megacolon and systemic – autoimmune (guillain barre syndrome)
Diagnosis – Stool culture + PCR
Treatment – supportive and antibiotics (Ciprofloxacin and azithromycin)
Clostridioides Difficile
* Gram-staining
* How is it transmitted?
* What area of the body does it colonize?
* What promotes/increases risk of C. Difficile infection?
* How does it cause pathology?
- Gram-positive
- Transmission - Environmental pathogen - forms resistant spores - common in health care facilities
- Site - Colon
- Promoted by antibiotic use - disrupts normal microbiota
- A combination of direct cellular damage and immunopathology
What impact do C. Difficile toxins have on gut epithelial cells?
GTP binding proteins belong to the Rho family – cytoskeleton regulatory proteins
Toxin drives glucosylation of GTPases (like Rho) causes the collpase of the actin cytoskeleton
What is this diagram of C. Difficile infection showing?
C. Difficile mechanism of action - Cellular damage and immunopathology
- B toxin is more important in physiopathology – lead glucosylation of GTPase – cell will die
- Toxins can also pass through the tight junctions and interact with neutrophils which are then recruited driving a large immune response
What is a common histological feature observe din C. Difficile infeciton?
Exudate of dead epithelial cells, fibrin and inflammatory cells – forms pseudo membrane
Is C. Difficile infection common?
The most common cause of nosocomial (originating in hospitals) diarrhoea, with a severity spectrum ranging from asymptomatic carriage, mild to moderate diarrhoea, to life- threatening pseudomembranous colitis
It has been steadily increasing from the 1980s to the 2010s, now endemic in healthcare institutions and in the community, but slightly decreasing
C. Difficile
* What are the clinical features?
* How is it diagnosed
* How is it treated?
Clinical features
* Asymptomatic carriage
* Diarrhoea / simple colitis
* Pseudomembranous colitis
* Fulminant colitis
Diagnosis
* Clinical features
* Stool analyses: Antigen (Toxin or Bacteria (enzyme))
* Culture
Treated
* Antibiotics - Metronidazole or vancomycin?
Fidaxomicin - needs to be specific as killing normal microbiota could promote C. Difficle
* “Faecal transplants” - Prevent bacteria from colonizing by replacing the microbiome back following antibiotics (prevention)
* Immunotherapy - not much evidence
Note - Probiotics not succesful
What are 4 different ways we could use drugs to treat C. Difficile infection?
What role does prevention and control play in controlling C. Difficile outbreaks?
Very important!
Infection control – removal of spores of C. difficile – hospital environment cleaning – spores resistant to alcohol – need to use bleach
Antibiotic stewardship – avoid antibiotics that promote CD infections
What is special about the UK hyper-virulent strain of C. Difficile?
Hypervirulent strains – tcdC gene deletion - negative regulator of toxin release – deletion leads to increase levels
Resistant to quinolone antibiotics - not directly used to treat C. Difficile but when people were treated with quinolone C.Difficile was left behind whereas everything else was killed
What organism could be responsible for the infeciton in the following patient case?
H. Pylori Infection
What organism could be responsible for the infeciton in the following patient case?
Vibrio Cholerae
What organism could be responsible for the infeciton in the following patient case?
Shigella
What organism could be responsible for the infeciton in the following patient case?
Clostridioides difficile
What is the definition of gastroenteritis? What are the three main causes?
Gastro-enteritis = inflammation of the digestive tract, causing nausea, vomiting, abdominal pain, diarrhea, eventually fever.
Can be upper or lower digestive tract
Can be caused by:
* Viral – quite common – stomach flu
* Bacterial causes – main group – microbial food poisoning – two big types within this category – infection (viable microorganism was ingested) & intoxication (ingest the toxin but not the whole viable microorganism)
* Parasite causes – less common in the western world – more common in the developing world
What are some examples of bacterial species that cause infective and/or toxic gastro-enteritis
Infective - Campylobacter spp, Salmonella spp, shigella
Both - E. Coli
Toxic/intoxication - Clostridium perfringens, Bacillus cereus, Staphylococcus aureus Clostridium botulinum and Vibrio cholerae
Difference between mild, moderate and severe gastroenteritis?
What are the general differences between small bowel and large bowel gastroenteritis?
Blood in diarrhea is dependent on the degree of tissue invasion - e.g. shigella and salmonella travel quite deep causing bleeding.
Organism(s) that causes watery diarrhea with no fever?
Organism(s) that causes watery diarrhea with fever?
Organism(s) that causes bloody diarrhea with no fever?
Organism(s) that causes bloody diarrhea with fever?
What are the typical modes of transmission for organisms causing gastroenteritis?
Endogenou pathogens in food - no cooked thoroughly
Drinking water contaminated with feces
Human to human - faecal contamination
What is the definition of infective dose?
The number of pathogens needed to cause disease in the new host
Varies with the pathogen
Relatively high for all bacteria whereas viruses require a lower load
Foodborne Infections - Campylobacter species
* Does it infect the small or large bowel?
* Main species causing infection?
* Mechanism - infection or intoxication (toxin)?
* Symptoms?
* Associated with what type of food/liquid?
* Diagnosis and treatment?
* Complications?
Campylobacter species - Commonest cause of diarrhoea in the developed World
- Infects both the small and large bowel
- C. jejuni and C. coli
- Mechanism - infective
- Typically gives bloody and fever but can give bloody with no fever or watery with fever
- Associated with poultry (grows well in the gut of chicken), wild birds and other animals and in their milk and water – zoonotic
- Diagnosis - Clinical and stool culture
- Treatment - Antibiotics
- Complications - !! Guillain-Barré Syndrome!!
Foodborne Infections - Non-typhi Salmonella spp
* Does it infect the small or large bowel?
* Mechanism - infection or intoxication (toxin)?
* Symptoms?
* Associated with what type of food/liquid?
* Diagnosis and treatment?
Non-typhi Salmonella spp - Major cause of foodborne disease world-wide (2nd after Campylobacter)
- Small and large bowel
- Infective mechanism
- Very wide range of clinical manifestations - all four combinations of fever and diarrhea - Often serious: fever, diarrhoea, vomiting
- Associated with poultry/eggs (Typhi: Only human reservoir)
- Diagnosis - clinical symptoms and stool culture
- Treatment - Antibiotics - Be careful due to MDR
Foodborne Infections - Clostridium perfringens
* Does it infect the small or large bowel?
* Mechanism - infection or intoxication (toxin)?
* Symptoms?
* Associated with what type of food/liquid?
* Diagnosis and treatment?
Clostridium perfringens
- Small bowel
- Intoxication - toxin - Bacteria sporulate in small intestine and produce an enterotoxin - destruction of villus tips with resultant pain and diarrhoea
- Symptoms - Watery no fever or Watery with fever - can also lead to myonecrosis (necrosis of the skin up to th muscle).
- Associations - Warm food contamination with spores - bulk cooking of meat
- Diagnosis – stool and detection of toxin
- Treatment – supportive
Foodborne Infections - Clostridium botulinum
* Does it infect the small or large bowel?
* Mechanism - infection or intoxication (toxin)?
* Symptoms?
* Source?
* Diagnosis and treatment?
Clostridium botulinum
- Small bowel
- Mechanism - Intoxication
- Symptoms - Watery with no fever or watery with fever - can be absorbed into the blood stream resulting in neuro-Botulism (toxin mediated paralytic illness) + wound botulism – toxin on the skin – seen in heroin users
- Associated - Widely distributed in nature - soils, lake sediments, vegetables, GI tract of mammals, birds and fish. Home-canned or fermented foods.
- Diagnosis - Stool culture + Detection of toxin
- Treatment - Supportive + (Anti-Toxin)
Foodborne Infections - Staphylococcus aureus
* Does it infect the small or large bowel?
* Mechanism - infection or intoxication (toxin)?
* Symptoms?
* Source?
* Complications?
* Diagnosis and treatment?
Staphylococcus aureus
- Small bowel
- Mechanism - intoxication - heat stable toxin
- Symptoms - Very acute vomiting response often followed by diarrhoea - watery with or without fever
- Source - Contaminates salted foods and dairy produce
- Complication - sepsis
- Diagnosis - Not necessary
- Treatment - supportive
Foodborne Infections - Bacillus cereus
* Does it infect the small or large bowel?
* Mechanism - infection or intoxication (toxin)?
* Symptoms?
* Source?
* Diagnosis and treatment?
Bacillus cereus
- Small bowel
- Mechanism - Intoxicating - toxin
- Symptoms - Acute vomit response followed by diarrhoea - watery with or without fever
- Source - Spore germinate in warm cooked rice
- Diagnosis - Not necessary
- Treatment - supportive
Cool Fact - Separate toxins for vomiting and diarrhoea responses! (ingestion of toxin directly for vomiting response)
Foodborne Infections - Norovirus
* Does it infect the small or large bowel?
* Mechanism - infection or intoxication (toxin)?
* Symptoms?
* Source?
* Diagnosis and treatment?
Norovirus - Most common viral cause of epidemic gastroenteritis worldwide - Winter vomiting disease
- Small bowel and large bowel?
- Mechanism - infective and intoxication
- Symptoms - Vomiting, diarrhoea, low grade fever - watery with or without fever
- Source - Direct contact with fecal matter or vomit – direct contact but some outbreaks associated with shell-fish
- Diagnosis - Clinical and PCR
- Treatment - supportive
Foodborne - What are the four different strains of E. Coli that you should remember? Mechanism - infective or intoxication?
E. Coli – many different strains that result in different clinical manifestations - all the different types of diarrhea
Intoxication - Enterotoxigenic E. Coli
Three different invasive types:
EPEC – children – small intestine
EIEC – more like shigella
EHEC – more severe manifestations (colon)
How are the infective strains of E. Coli transmitted (EHEC, EPEC and EIEC)?
- Food-borne (faecal contamination)
- Faecal-oral transfer
- Environmental contamination by domestic animals
EHECs are highly infectious agents - Infectious dose c. 10 bacteria
How do EHECs and EPECs infect the GI tract - mechanism?
- Attachment to microvilli
- Use type III secretion system which will inject the toxin into the cell
- Results in the formation of its own gene – intimin
- Results in micro-villi destruction and pedestal formation due to the formation of polymerized actin
In what season are E. Coli, Salmonella, Campylobacter and Norovirus infections more common?
E. Coli - Summer
Salmonella - Summer
Campylobacter - Spring
Norovirus - Winter
What are the common oesophagal disorders that we are interested in?
GORD ( gastro-oesophageal reflux disease)
These are different ways GORD can manifest:
* Oesophagitis
* Barrett’s oesophagus
* Benign oesophageal stricture
Oesophageal Motility disorders ( e.g. Achalasia)
Eosinophilic oesophagitis
Oesophageal cancer
Outline how the oesophagus normally functions.
Deglutition (swallowing( is performed by striated muscle
- Bolus is formed
- The upper oesophageal sphincter relaxes
- Food enters the esophagus
- Primary peristaltic wave is triggered all the way down
- Lower oesophageal sphincter relaxes
- Food enters into stomach
What is high resolution manometry?
Allows us to track pressure changes in the oesophagus.
High pressure areas shown in red and low pressure in green/blue
What are some examples of common symptoms seen in oesophageal disease?
- Main symptoms is dysphagia – alarm symptom – manifestation of severe disease – inability/reduced ability to swallow
- Often if there is inflammation, it is accompanied by odynophagia (pain on swallowing)
- Heartburn – burn retrosternally – acid reflux into esophagus
- Acid regurgitation – acid is felt and tasted
- Waterbrash – characteristic symptom of increased saliva production due to the aforementioned symptoms
- Dental erosions
What are the two classifications for dysphagia?
Dysphagia - difficulty swallowing solids or liquids - alarm symptom – we want to exclude cancer
Can be…
1. Oropharyngeal - difficult bringing the bolus from the mouth to the oesophagus - usually neurological cases - stroke
2. Oesophageal
When someone presents with dysphagia, what hints can point us towards a diagnosis?
Elderly – think neurological causes if intermittent/long standing or sinister esophageal cancer if new, progressive with regurgitation and weight loss
Cancer – problems with solids first and then liquids – progressive dysphasia
Younger people – can’t swallow – same difficulty with solid and liquids – think about dysmotility – number one is achalasia but can also be secondary to acid reflux
Young patients – food bolus obstruction – think eosinophilic eosophagitis
Extra…
Hoarse voice – think of ENT causes (or advanced tumour left recurrent laryngeal nerve is infiltrated/impacted by advanced oesophageal cancer)
Pharyngeal pouch (posterior to the larynx) – pouch that accumulates and prevents food movement – think of this when people get regurgitation of food from previous days
What investigations do we use if someone presents with oesophageal disease?
Investigations
- Endoscopy and biopsy - gold standard
- Barium swallow – swallowing a barium meal – gives us a more dynamic information about the way esophagus contracts – can’t tell us about inflammation or potential cancers
- Oesophageal function test – manometry (measure pressure), pH (reflux) and impudence monitoring (looking for material refluxing that isn’t acidic) – look at motility and look at the exposure of acid
What are the two main reasons for GORD to arise?
- Transient lower oesophageal relaxations (sphincter becomes relaxed) – daytime reflux, small or no HH and often no esophagitis (no inflammation of the lining) – more common
- Reflux with low lower esophageal sphincter pressures – less common, nocturnal reflux – associate with the hiatus hernia (hernia slides up and down) – disrupts the lower esophageal sphincter function – causes esophagitis and much more likely to suffer Barret’s
Other mechanisms also potentially involved…
* Increased acid production by the stomach
What are the typical symptoms of GORD?
TYPICAL symptoms of GORD
* Heartburn – behind the sternum
* Acid regurgitation
* Waterbrash – excessive salivation
Precipitating factors - after a meal and postural (bending over, at night)
What does the treatment of GORD look like?
- Lifestyle measures – smoking, alcohol, diet (staying away from triggers - caffeine, high fat, carbonated drinks, etc. ) weight reduction
- Mechanical – posture, prevent lifting heavy weights, elevate head in bed
- Antacids are commonly used
- Acid suppression - Proton-pump inhibitors or H2 antagonists
- Complex GORD – particularly in young people – surgical operation – reconstruct the lower Oesophageal sphincter
What are the complications associated with GORD?
Complications of GORD
* Oesophagitis
* Oesophageal Stricture – narrowing of the esophagus in response to continuous inflammation
* Barret’s Oessophagus
* Adenocarcinoma (Most arise from Barrets)
What are some benign and malignant causes of oeophageal strictures?
OESOPHAGEAL STRICTURE= narrowing of Gullet
Benign
* GORD up to 10% - most common cause
* Barrett’s
* Extrinsic compression – tumours in the mediastinum or lung
* Post-radiotherapy
Malignant
* Oesophageal cancer
How is a benign oesophageal stricture treated?
Treatment
1. PPI – omeprazole
2. Dilate the narrowed oesophagus - Dilatation – opening up – stretch – push dilators - CRE balloons or push dilators
What is barret’s oesophagus?
Barret’s esophagus – growth of a stomach like epithelium up into the esophagus – gastric columnar epithelium growing into the esophagus (squamous epithelium replaced) – esophagus is made more robust
Problematic – prone to develop of dysplastic changes – adenocarcinoma – premalignant condition - increased risk.
Commonest in obese men >50
Often asymptomatic – symptoms of Acid reflux
How is barrett’s oesophagus treated?
- Ablation – stop the development of barrets – burn the area - especially if there is a high risk fo cancer.
- Long term treatment people with proton pump inhibitors
What are the two main types of oesophageal cancer?
Two cancer types
- Adenocarcinoma is becoming more common – more in younger (average age still 60) - found in the lower third of the esophagus – more associated with obesity and Barret’s.
- Squamous cell -– mid/upper eosophagus – more in the older population - associated with smoking and alcohol – becoming less common
How is a diagnosis of oesophageal cancer performed?
Gold standard - Upper endoscopy + biopsies used for diagnosis
TMN Staging…
* CT - metastases and lymph nodes
* Endoscopic ultrasound – used to stage the tumour – depth of invasion of the tumour
How can we help cancer patients if it is too advanced?
Oesophageal cancer – 2/3 of cases there isn’t much we can do about it
Palliation measures – relieve the difficulty swallowing – leads to ill-health due to malnutrition
Entermetal sheet/stent opening the esophagus – improves quality of life but doesn’t change the prognosis