GI Infections Flashcards
What are the definitions of microbiome and microbiota? What are their functions?
Microbiome - refers to all the genome within the gut environment
Microbiota - refers to the organisms within the gut environment
Function: pathogen inhibition, immune protection, nutrient metabolism, drug metabolism, gut brain axis
Approach to history taking and examination for GI infections e.g. Questions you would ask and examination
Presenting compliant and history:
Diarrhoea - onset, duration, frequency, consistency (Bristol stool chart), mucous/ blood
Vomiting - onset, frequency
Pain - site, radiation, intermittent/ continuous
Travel history -
Where/ when/ how long, activities, food and drink, animals, travel companions and household contacts
Drug history - recent antibiotics, PPI, laxatives, immunosuppressant meds’
Occupation
Past medical history - immunodeficiency/ immunocompromised state, other Gi conditions
Volume status - mucous membranes, blood pressure, pulse, JVP
Abdo exam - ileus, peritonitis
What is the Bristol stool chart?
Type 1 - separate hard lumps, like nuts
Type 2 - sausage shaped but lumpy
Type 3 - like a sausage but with cracks
Type 4 - like a sausage or snake smooth and soft
Type 5 - soft blobs with clear cut edges (passed easily)
Type 6 - fluffy pieces with ragged edges a mushy stool
Type 7 - watery, no solid pieces, entirely liquid
Investigations of stool samples and what infections they would pick up
Stool culture - E. Coli, salmonella, shigella, campylobacter
Enzyme immunoassay - cryptosporidium, giardia, clostridioides difficile
PCR - clostridioides, entamoeba histolytica, norovirus, rotavirus, other bacterial
Microscopy - ova, cysts, parasites
Causes of watery diarrhoea and so what investigations you would do
Norovirus -PCR
Rotavirus - PCR
Clostridioides difficile - enzyme immunoassay
Enterotoxigenic E. Coli
Giardia lamblia - enzyme immunoassay
Cryptosporidium parvum - enzyme immunoassay
Causes of inflammatory diarrhoea
Non- typhoidal salmonella
Campylobacter - culture
Clostridioides difficile* - PCR
Shigella - culture
E.coli 0157 - culture
Entamoeba histolytica - PCR
What foods can give you slamonella?
Nit butter, eggs, beef, chicken, vegetables, chocolate, pork
Many foods
Whatinfections can salmonella cause and what two main categories can these be divided into?
Broad range of infections: gastroenteritis, enteric fever, bacteraemia, endovascular infections, osteomyelitis
Typhoidal salmonella (salmonella typhi/ paratyphi) -> enteric fever
Non-typhoidal salmonella (salmonella enteritidis/ Virchow etc) -> primary gastroenteritis
Describe non- typhoidal salmonella, incubation/ transmission/ features/ treatment/ complications
Incubation period - 8-72hrs
Transmission - food, Faeco-oral, animals
Features - diarrhoea, nausea, vomiting, abdo cramps
✅usually self limiting, ciprofloxacin, azithromycin, ceftriaxone. Sensitivity testing warranted if bacteraemia
Describe campylobacter - found, infection cause, symptoms, treatment , diagnosis, incubation, transmission , complications
Found in GI tract of animals especially poultry
Campylobacter jejunum/ Coli most common cause of infection
Incubation period 3 days
Transmission food/ water/ animal contact
Symptoms - abdo cramping, inflammatory diarrhoea, prodrome fever/ malaise, May transient bacteraemia
Stool culture
✅usually self limiting, immunocompromised/ elderly/ severe may need treatment e.g. macrolides or fluroquinolones
Complications - recapture arthritis, Guillain-Barré syndrome
Describe shigella - incubation, transmission, symptoms, treatment, complications, diagnosis
Spectrum of disease depends on infecting serotype
Shigella dysenteriae 1/ flexneri -> dysentery (bloody diarrhoea)
Incubation - 1-7days
Transmission - Faeco-oral, food, water, person to person
Symptoms - fevers, frequent low volume blood stools, tenesmus, inflammatory diarrhoea
✅usually self limiting, ciproflaxacin, azithromycin, ceftriaxone
Stool culture
Complications - intestinal rare: proctitis, rectal prolapse, toxic megacolon, perforation, obstruction. Systemic: bacteraemia, seizures children, reactive arthritis, haemolytic uraemia syndrome
Pathotypes of E.coli associated with diarrhoea
Enterotoxigenic E.coli
Enteropathogenic E.coli
Enterioinvasive e.coli
Enteroaggregative e.coli
Shiga toxin- producing E.coli
Symptoms of E.coli 0157 infection, who’s at risk, incubation, diagnosis
Symptoms: painful bloody diarrhoea, haemolytic uraemic syndrome (nonimmune- mediated haemolytic anaemia, thrombocytopenia, AKI), inflammatory diarrhoea
Stool culture
Children <10yrs, elderly, worsened by antibiotics
Incubation - 1-10days
What is clostridioides difficile, transmission, risk factors, complications, treatment, diagnosis
Anaerobic gram positive bacilli - one of the most common nosocomial infections, causes antibiotic associated colitis
Faecal- oral route
Produces spores v resistant and remain for long time
Produces both watery and inflammatory diarrhoea- enzyme immunoassay
Risks: >65yrs, antibiotic use, PPI therapy, prolonged hospitalisation
Complications: toxic megacolon, colitis, perforation
✅ metronidazole, oral vancomycin, fidaxomicin, faecal microbiota transplantation
What is norovirus, symptoms, incubation, transmission, diagnosis, treatment?
Winter vomiting bug
Causes profuse watery diarrhoea and vomiting
Incubation 12-48hrs
PCR
Transmission faecal-oral, direct contact, aerosol. Highly infectious
✅self-limiting, resolves 1-2days
What is rotavirus, what does it cause, incubation, transmission, symptoms, treatment, complications, prevention
Common cause gastroenteritis in young children
Incubation <48hrs
Transmission - faecal- oral, highly infective
Symptoms - diarrhoea, vomiting, fever, children more severe
Complications (rare) - seizures, encephalopathy, acute encephalitis
ORAL rotavirus VACCINE - 2 doses (8&12 weeks old)
✅usually self-limiting
What is cryptosporidium, transmission, treatment, incubation
Intracellular protozoan parasite -
Cryptosporidium parvum main species causing human infection
Watery diarrhoea
Associated with sporadic, water associated outbreaks (oocyst exits host, contaminated water, ingested)
✅usually self-limiting within 10-14 days, can be debilitating chronic illness in immunocompromised. Nitazoxanide
Most frequently affects children
Incubation 7-10days
Transmission - water, food, Faeco-oral, person to person, animals
What is giardia, who’s at risk, transmission, symptoms, treatment?
Caused by giardia duodenalis - protozoan parasite
Sporadic or epidemic infection linked to water/ food/ faeco-oral/ childcare settings/ international travel
Cysts & trophozoites passes in faeces -> matured cysts ingested
High risk groups: infants, children, immunocompromised, travellers, cystic fibrosis
Symptoms: malaise, steatorrhoea, abdo cramps, bloating, can be asymptomatic or can persist as chronic
-> malabsorption & weight loss
✅if symptomatic - metronidazole or nitazoxanide
What is entamoeba histolytica, symptoms, risks for severe disease, incubation, transmission, treatment?
Protozoan parasite can cause amoebic dysentery or infection at extra-intestinal sites e.g. amoebic liver disease, Abdo pain, fulminant colitis with necrosis and perforation, can mimic IBD, majority asymptomatic
Risks for severe disease: young age, corticosteroid therapy, pregnancy, malignancy, malnutrition, alcoholism
Incubation - 2weeks- years
Transmission: food, water, Faeco-oral, highly transmissible
✅high dose metronidazole and then intraluminal agent e.g. paromycin
