GI microbiology Flashcards by Jack Molyneux

What is gastroenteritis?

This is a brand term usually used to refer to an infective illness which causes diarrhoea, vomiting and often abdominal pain

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What are some characteristics that make a pathogen more likely to invade the normal GI microbiota?

High growth rates
High dispersal capability
Phenotype plasticity
High genetic diversity

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What are some examples of normal gut bacteria?

Enterobacteriacea sp
Enterococci sp
Milleri group streptococci
Anaerobic gram-positives
Anaerobic gram-negatives

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What are some risk factors for gastroenteritis?

Poor sanitation
Immunosuppression
Poor food preparation
Age (<5, not breast feeding, older age)
Malnutrition
Closed communities
Acid suppression (PPIs)

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What percentage of gastroenteritis has a viral aetiology?

~50%

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What are some common viral causes of gastroenteritis?

Adenovirus
Enterovirus
Norovirus
Rotavirus
Cytomegalovirus
Hepatitis A
SARS-CoV2

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What are the characteristics of norovirus gastroenteritis?

Highly infectious
Explosive D+V
Oral droplet spread
<24 hour incubation
Associated with cruise ships

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What are the characteristics of rotavirus gastroenteritis?

Commonest cause of D+V in children <3
Self-limiting
Associated with fever
Associated with cruise ships

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What are the characteristics of cytomegalovirus gastroenteritis?

Cause of colitis and bloody diarrhoea in the immunosuppressed
Associated with other invasive illnesses

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What is the average incubation period for viral gastroenteritis?

~24 hours

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What is the average incubation period for bacterial gastroenteritis?

A few hours to 4 days

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What is typhlitis?

Also known as neutropenic colitis
Typically a poly microbial inflammatory infection of the GI tract, post-chemotherapy or in HIV patients, causing high levels of mucosal damage and neutrophilic activation

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What are some bacteria that can cause secretory (Watery) diarrhoea in gastroenteritis?

Clostridioides difficile
Bacillus cereus
Listeria sp
Vibrio cholerae

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What are some bacteria that can cause inflammatory diarrhoea (Dysentery)?

Campylobacter jejuni
Salmonella (Non-typhoidal)
Shigella
E.coli 0157
Vibrio (Non-cholera)
Tropical sprue
Tropheryma whipplei (Whipple’s disease)

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What are some bacteria that can cause invasive diarrhoea in gastroenteritis?

Yersinia enterocolitica
Salmonella typhi/paratyphi

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What is the incubation period for parasitic gastrointestinal infection?

7-10 days

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What are some common GI parasites?

Entamoeba histolytic (Amoebiasis)
Giardia lamblia (Giardiasis)
Enterobius
Cryptosporidium
Hookworm

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What are some risk factors that can lead to clostridioides difficile infection?

4C antibiotics, extremes of age, PPI use, comirbidities

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What are the 4C antibiotics that can lead to clostridioides difficile infection?

Clindamycin
Co-amoxiclav
Cephalosporins
Ciprofloxacin (+ other fluoroquinolone)

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Describe the characteristics of the clostridioides difficile bacteria

Gram positive
Spore baring (Hand wash, not sanitise)
Bacillus
Part of normal gut flora
Produces enterotoxin (A) and cytotoxin (B), which can cause blood diarrhoea

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What are the treatment options for clostridioides difficile?

1st - Vancomycin
2nd - Fidaxomicin
3rd - Faecal transplant

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What is a possible complication of clostridioides difficile infection?

Post infection irritable bowel

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What are the characteristics of bacillus cereus gastroenteritis?

Toxin producing bacteria
Commonly associated with reheated rice
Can be found in any improperly reheated starchy food
Presents with profuse vomiting

What are the characteristics of listeria gastroenteritis?

Gram positive rod
Undergoes cold enrichment to survive in fridges
Associated with soft cheeses, raw milk, pre-cooked meats or pate
Carries high risk n pregnancy in immunosuppressed (Advise not to eat the above foods)
Can cause meningitis or bacteraemia

What are the characteristics of campylobacter jejuni gastroenteritis?

Most common cause of food born gastroenteritis Associated with poultry, raw milk and travel to SE Asia Self limiting Causes cramps and diarrhoea Fragile so easily destroyed by freezing or drying Can cause IBS, Gillian-Barré and reactive arthritis

What are some common reservoirs of non-typhoidal salmonella?

Eggs Dairy Pet food Turtle stomach Other reptiles

What are some conditions that can be caused by salmonella infection?

Endocarditis Aortitis Bone and joint infection Meningitis

What are some risk factors for salmonella infection?

Extremes of age HIV Chemotherapy Steroids Haemoglobinopathies Renal failure Low stomach acid (PPI, Infants, pernicious anaemia) Post-operation

How are the different serovars of salmonella identified?

O antigen - Lipopolysaccharide H antigen - Flagellar antigen Vi antigen - Capsular antigen

How is salmonella infection diagnosed?

Stool samples PCR

Salmonella is a gram ....

Negative rod

Describe the characteristics of shigella dysenteriae gastroenteritis

Produces a toxin which binds to receptors on renal cells or WBCs, inhibiting protein synthesis and causing cell death Causes blood diarrhoea Found in raw milk Second most common association with HUS

What is dysentery?

Bloody diarrhoea + Fever + Tenesmus

Describe the characteristics of E.coli 0157 gastroenteritis?

Produces a shigella-like toxin (STEC) Causes blood diarrhoea Associated with food (Beef), person to person and animal contact Most common association with HUS Most common cause of acute traveler's diarrhoea

What food is non-cholera vibrio bacteria most commonly associated with?

Seafood

What is meant by tropical sprue?

This is colonisation by a pathogen caused by alterations in intestinal bacteria flora in response to another environmental agent

Where is tropical sprue most commonly contracted?

Caribbean India South Africa South East Asia

How does tropical sprue present?

Diarrhoea Signs of malabsorption (Steatorrhoea, weight loss)

How is tropical sprue treated?

Metronidazole or tinidazole for parasitic IV ceftriaxone is severe sepsis

Describe the characteristics of Tropheryma whipplei gastroenteritis (Whipple's disease)

Increase risk if HLA-B27 antigen present Presents with diarrhoea Signs of malabsorption (Weight loss, steatorrhea) Other systemic involvement (Arthritis)

Describe the characteristics of Yersinia enterocolitica gastroenteritis

Common with travel to Asia Common with exposure to pigs May mimic appendicitis as it can invade mesenteric nodes

Describe the characteristics of salmonella typhi infection

Most common in those returning from Indian subcontinents and SE Asia Causes enteric fever (e.g. headache, constipation or diarrhoea, dry cough)

Describe the characteristics of emtamoeba histolytica infection

Amoebiasis 90% asymptomatic Can cause GI and hepatic conditions Bloody diarrhoea Weight loss Pain Toxic megacolon risk

How long after infection will symptoms of amoebiasis occur?

GI - 1-3 weeks Hepatic - Years

Describe the characteristics of giardia lamblia infection

Flagellated Protozoa Associated with swimming pools, lakes, rivers or untreated water Morning explosive diarrhoea Explosive, intermittent eggy burps Chronic malabsoprtive, malodorous diarrhoea Most common in SE Asia

Describe the characteristics of enterobius infection

Pinworm found mostly in children Lay eggs around the anus at night, causing itching Diagnosed using cellotape test

Describe the characteristics of cryptosoridium infection

Causes prolonged diarrhoea in immunosuppressed patients Spread via contaminated oocytes ingested in water Association with poorly treated swimming pools As few as 10 oocytes required to infect Can cause nutritional deficiency, weight loss and dehydration

What are the 2 main genuses of hookworm?

Ancylostoma Necator

How does hookworm enter the GI tract?

Through the skin

What are some parasites that enter the GI tract through the skin?

Hookworm Strongyloides Schistosoma

How is gastroenteritis usually managed?

Oral rehydration rarely antibiotics (Risk of HUS) Admit to hospital if signs of severe dehydration

What is haemolytic uraemic syndrome?

This is a group of blood disorders characterised by low RBCs, low platelets, high WBCs and acute kidney failure

What are the most common bacteria that can lead to haemolytic uraemic syndrome?

E.coli 0157 Shigella Salmonella

What are some signs of haemolytic uraemic syndrome?

Abdominal pain Fever Pallor Petechiae Oliguria

What bacteria can mimic Crohn's disease?

Lymphogranuloma venereum (Form of chlamydia)

What is the antibiotic treatment for infections of the GI tract (e.g. diverticulitis)?

IV Metronidazole (Covers anaerobes) IV amoxicillin (Covers enterococci) IV Gentamicin (Covers coliforms)

What are some bacteria that enter the body via the GI tract, but cause disease in other places?

Echinococcus (Hydatid disease) - Liver Trichinella spirali - Muscles Toxicara canis (Visceral lava migras) - Systemic Tinea solium (Crysticercosis) - Neurological Toxoplasma gondii - Febrile illness