Microbiology in GI Flashcards
Is all colonisation permanent?
No some is transient
When does colonisation begin?
At birth: Differences in vaginal and C secion
Not all colonisation is normal
What are the host defences of the GI tract?
Acid in stomach
Normal gut flora
Peristlasis
Antimicrobial compounds
What are the 3 main groups of bacteria in the GI tract?
Enterobacteriaceae (gram negative bacilli)
Enterococcus (gram positive cocci)
Anaerobes
Give examples of enterobactericeae?
E coli
Klebsiella
Enterobacter
Proteus
Give examples of Enterococci?
Enterococcus faecalis (more common) Enterococcus Faecium
Give examples of anaerobes in the gut?
Gram negative baccilli- Bacteroides
Gram positive bacilli = C diff
What is colonisation?
The establishment of a micro organism on or within a host; may be short lived.
What is virulence?
Likelihood of causing disease
What is an oopportunistic pathogen?
Pathogen which would not normally cause an infection in a normal host but will in an immunocomprimised host
What tests can microbiology do to diagnose infection?
Microscopy: stool, urine, CSF, sputum, pus Culture Serology Antigen detection PCR/molecular studies
Which immune cells are commonly seen in bacterial infection?
Phagocytes
ANtibodys and B lymphocytes
Which immune cells are commonly seen in viral infection?
T lymphocytes
Which immune cells are commonly seen in Fungal infection?
Phagocytes, T lymphocytes and (eosinophils)
Which immune cells are commonly seen in helminth and parasitic infection?
Eosinophils and mast cells
What is primary peritonitis?
Transfer of bacteria from the gut to the peritoneum without perforation. Occurs in ascites and alcoholics
What is secondary peritonitis?
Where a perforation of the bowel causes bacteria in the bowel to spread to the peritoneum causing infection.
Post op or fistula
Give an example of Spirochete shaped bacteria?
H pylori
WHat are the 2 main groups of Enterobactericeae?
Lactose fermenting and non lactose fermenting.
What are the common lactose fermenting enterobactericeae?
E coli
Klebsiella
Enterobacter
Serratia
What are the common non lactose fermenting enterobactericeae?
Morganella Proteus Salmonalle Shingella Yersinis
What is another name for Enterobacteriaceae?
Coliforms
How long does it take for most microbiology results?
48 hours
What do lactose fermentors do to McConkey agar?
Turn it pink
CLED agar is used to identify microbes in GI infections. T or F?
True
What are the characteristics of enterobacteriaceae?
Gram negative bacilli Non spore forming Ferment sugars mostly Mostly motile Mostly facultative anaerobes Increasing resistance
Which enterobacteriaceae are not motile?
Shingella and Klebsiella- DO not have flagella
Enterobacteriaceae have fimbrae. What are fimbrae and what are they used for?
Filamentous appendages, shorter than flagella.
Help with binding and adhesion to tissues and enterocytes
What is a enterotoxin?
a toxin produced in or affecting the intestines, such as those causing food poisoning or cholera
eg Shiga toxin or shiga like toxin
What endotoxin do enterobacteriaceae have?
Lipopolysaccharide. When bacteria die the body is exposed to the LPS within the cell wall and this causes inflamation => gram negative sepsis
What causes oesophagitis in the immunosupressed?
Candida
If pancreatisis normally an infection problem?
No
Swarming on agar is characteristic of which bacteria?
Proteus sp
enterobacteriaceae, non lactose fermenting
Which organism is associated with petting zoos?
E coli 0157
What are the advantages and disadvantages of MALDI TOF?
+Analyse protein composition or bacterial cell wall
+ Quick
+ Discriminates between genetically similar organisms with identical 16s rRNA
- Low specificity- hard to differentiate between pathogenic and non pathogenic e coli or salmonella and e coli
- expensive
Many tests in reference labs
What is serotype?
A serotype is a distinct variation within a species of bacteria
What is serotyping?
Identifying a particular type of bacteria using O (body antigens) and H (Flagella antigens)
WHat are the normal colonisers of the mouth?
Strep viridans (+ cocci) , Neisseria (- cocci), Candida, Staphylococci, anaerobes
What are the colinisers of the small bowel?
Small numbers of coliforms and anaerobes
What are the colonisers of the colon?
Large numbers of coliforms, anaerobes and Enterococcus faecalis.
What are the normal colonisers of the bile ducts?
Usually sterile
What are the anaerobes which grow in the GI tract?
Clostridium
Bacteroides
Anaerobic cocci
What is cholangitis?
AN infection in the common bile duct usually resulting from a gallstone
What is charcot’s triad for cholangitis?
Fever
RUQ pain
Jaundice
When do you review empirical antibiotics?
After 48 hours at the latest. Should have the lab results.
When would OPHAT be considered in GI infection?
liver abscess as antibiotics for 6 weeks
What is used to treat an infection caused by enterococcus faecalis? What is the step down?
Amoxicillin
(Vancomycin if penicillin allergic)
Step down = oral switch to cotrimoxazole
Enterococcus faecium is more or less resistant and common than enterococcus faecalis?
Enterococcus faecium is more resistant and less common
Where do abscesses and infections i the liver come from?
Bile ducts- gallstones, malignancy, stricture
Hepatic artery- bacteraemia
Portal vein- bacteraemia, intra-abdominal infection, non metastatic colon cancer
What is the most important anaerobe in the gut?
Bacteriodes
What is sepsis?
Life threatening organ dysfunction caused by a dysregulated host response to infection
What is septic shock?
A subset of sepsis with circulatory and cellular metabolic dysfunction associated with a higher risk of mortality (essentially when fluid resuscitation does not work)
What are empirical antibiotics for peritonitis, bilary tract and intra-abdominal infection? and what is the step down?
IV ammoxicillin* (enterococci), metronidazole (anaerobes), gentamycin (enterobacteriaceae)
*Vancamycin if penicillin allergic
Step down = PO Cotrim and metronidazole
What gives a diagnosis of sepsis?
Infection with a NEWS score of 5+.
What are the components of Sepsis 6?
Give 3 take 3.
1) Blood cultures, other relevant cultures and U&Es.
2) Urine output- monitor hourly
3) Fluid resuscitation
4) Antibiotics IV
5) Lactate, FBC measurement
6) Oxygen- correct hypoxia
Why measure lactate in sepsis?
Measurement of tissue death. Raised lactate is a bad sign
How is a large abscess treated?
Surgery and drainage.
A large abscess has no blood supply and IV antibiotics will not penetrate it well.
What antibiotic is used if there are contraindications for gentamycin?
Aztreonam
