Microbiology Flashcards
Is h.pylori acquired in infancy?
And how is it spread?
When do consequences arise?
Yes
is spread through oral-oral or faecal oral
consequences dont arise until later in life
What is h.pylori?
gram -ve microaerophillic flagellated bacillus
What can an H. pylori infection go on to produce?
No clinical disease in most cases
can go on to produce a gastric ulcer
or create a gastric Cancer
Where are the most bacteria in the ailementrary canal found?
mouth and large intestine - small bowel starts to increase the closer it gets to the large bowel
What is the sequence of pathogenic infection?
exposure, adhesion, invasion, colonisation- toxicity tissue damage or disease
What is the process of invasion of pathogen?
invasion - prodromal period, illness period, (convalescent period) starts to clear up then host might become a chronic carrier
What immune system component fights - bacteria
phagocytes, antibody and B lymphocytes, complement
What fights viruses (immune system)
T lymphocytes, antibody and B lymphocytes
What fights fungi?
Phagocytes, T lymphocytes and eosiniphils
What fights protozoa?
T lymphocytes and eosiniophils
What fights worms?
eosinophils and mast cells
How are enterbacteriacae classified in the GI tract?
Whether they are lactose fermenting or not
What turns pink in macConkey agar
lactose fermenters turn it pink
What method is used for rapid identification of bacteria?
MALDITOF - analyse composition of bacterial cell wall
How does 16s rRNA work?
Sequences whole genome
When is serology used?
differentiation between the same species
What is the normal flora of the bowel?
mouth - strep viridans, candida sp, staph
stomach/ duo - usually sterile due to low pH
jejunum - coliforms and anaerobes
coon - coliforms, enterococcus faecalis
define sepsis
systemic inflammatory response to infection
What is the disease continuum for sepsis?
Infection , systemic inflammatory response syndrome, sepsis, septic shock
What are some community sources of bacteremia
E coli(catheter related - can be in hospital), s. pneumoniae and staph aureus(Can be in hospital also) klebseilla (hospital), enterococci (hospital)
What are coliforms?
inhabit the colon - E.coli that inhibit large bowel
What are aerobic organisms?
Grow better in oxygen but can still grow without it - staph strep, enterococci and coliforms (majority of human pathogens)
What do bactera need in order to multiply?
Time, temperature, food source and moisture
What pathogen is assocated with antibiotics
C . diff
What pathogen is involved in daycare
rotavirus
What is the pathogen involved in anal sex? (men)
Shigella, camplyobacter and salmonella
What bacteria is related to HIV
mycobacterium, cytomegalovirus
What pathogens are generally involved in outbreaks on cruises
Norovirus
What is a microorganism with a short incubation period (1-6 hrs) (bacillus cereus - how can you get it what are the symptoms
and staph aureus - What are the symptoms
Bacillus cereus - heat resistant spores, profuse vomiting and reheated rice
Staph aureus - preformed toxin in food
rapid absorption
vomiting and abdominal pain
What is shigella?
Facultative anaerobe, gram neagive rod
What does a shigella infection lead to?
Invasion of colonic mucosal cells and induction of an intense inflammatory response
forms mucosal ulcers and abscesses
What does a shiga toxin do?
binds to receptors found on renal cells, RBC
inhibit protein syntheis = causes cell death
How so patients present with an ecoli infection?
Most common infections of ecoli is travellers diarrhoea
sometimes patients present with severe abdominal apin, diarrhoea which is bloody
What is the clinical indication for Ecoli -157
bloody diarrhoea - related to foods and is spread from person to person
Haemolytic ureamic syndrome
diarrhoea may have stopped so get help!
what is the incubation of Ecoli 0157
1-14 days
What is campylobacter?
Incubation?
How is it acquired?
Treatment?
gram negative enterobacyeriales
16 to 48 hrs incubation
usually passed around through poultry (raw milk)
water diahorrea - sometimes need admission
What are the most common type of campylobacter strain?
C jejuni
What are non typhoidal salmonella?
what is the incubation time
How is it transferred?
What is it found in?
Symptoms?
motile gram neg bacilli
8-72 hrs inucbation
fecal oral route
food - poultry, meat
cause d and vomiting (sometimes blood)
Where are H and O antigens found?
H = flagellum O = part of the Lipopolysaccharide
What is a useful test in salmonella for detecting outbreaks? - which groups are most common?
serotyping - help pinpoint the source of infection
Groups B, C and D and most common
How is salmonella diagnosed?
How is it treated?
blood cultures and stool samples
self limiting
suportive treatment - oral hydration
What are some key differences between typhoid and non-typhoidal salmonella
T = human NT = animals
incubation - T = 1-3 weeks NT= 8-72 hrs
T = typhoid fever NT= acute gastroenteritis
What is listeria monocytogene? - how is it acquired and was temp is good for it to grow?
non spore forming gram +ve rod, infection acquired form contaminated food - can grow at low temperature
What can listeria monocytogenes cause?
what are some complications?
Gastroenteritis - 9-48 hrs, fever muscle aches + diarrhoea
complications - meningitis/ bacteria, brain abscess
How is the diagnosis made in listeria monocytogenes ?
culture - CSF, in stool needs specific media
What are some risk factors of LM?
Iron overload (haemachromotosis)
Yersinia entercolitica?
appendicitis like symptoms: diarrhea vomiting, fever
caused by water or food contaminated with fecal matter
What are some casues of Acute travellers diahorrea?
Enterotoxigneic E coli
bacteri - camplyobacter, salmonella
virus - norovirus (cruise ships)
Cholera - big outbreaks in area of poor hygiene
What are the investigation of acute traveller’s diarrhoea?
stool culture
stool microscopy for cysts and parasites
Treatment for ATD?
Supportive - fluids
bloody diarrhoea may warrant treatment
What are the 2 types of enteric fever?
Typhoid or paratyphoid fever
What people usually get enteric fever?
Travelled to India or SE asia
What is the incubation period of enteric fever?
7-18 days
What are some symptoms of enteric fever?
fever, sweating, dry cough, chills, constipation/ diarrhoea
Complications of enteric fever?
GI bleeding GI perforation
What is the treatment for epirically for people with enteric fever?
IV Ceftriexone
What are the three different causes of jaundice?
Pre-heptatic - malaria, HUS
Hepatic - Acute viral hepatitis (Hep A and E)
leptospirosis - weils disease (acute liver failure and renal failure)
malaria, enteric fever
post hepatic - ascending cholangitis - and helminths
What are the investigations and treatment of jaundice (pathogen)
blood cultures
USS abdomen (obstruction)
serology for testing
supportive - then direct treatment for pathogen found if there has been one identified
What is amoebiasis? DP
What is it?
How is it spread?
symptoms?
investigation
treatment - metronidazole - luminal amoebicide
Entamoeba histolytica - a protoza
fecal oral spread
abdominal pain, fever, bloody diahorrea
toxic and unwell
investigation - stool microscopy for trophozoites or cysts
treatment - metronidazole followed by luminal amoebicide
What is amebic liver abcess? DP
What is it and what is the incubation period?
What are the symptoms?
Investigations?
treatment?
Entamoeba histolyica
incubation period - 8-20 weeks
sub acute over 2-4 weeks
fever, sweats, upper ab pain, hepatomegaly, tender over right lower ribs
investigations - Abnormal LFT’s USS or CT scan
metronidazole, - need to clear gut lumen of parasites with luminal amoebicide
Giardiasis - DP
What is it?
How is it spread?
What is the incubation period?
What are they symptoms?
What are the investigations?
What is the treatment?
Giarda intestinalis - flagellated protozoa
faecal oral spread (contaminated water)
incubation is around 7 days
presentation - watery, malodorous(foul smelling) diarrhoea, blaoting + cramps, weight loss
Investigations - stool microscopy for cysts (often difficult)
treatment - Metronidazole or tinidazole
Provide some characteristics of helminth infections:
Where are they found?
How are they diagnosed?
In the gut, in the tissue
associated with eosinophillia, often diagnosed by the adult worm passed or eggs in stool
What are intestinal nematodes?
round worms - ascariasis most common helminthic infection in the world affecting 25 % of the worlds population
What is the life cycle of parasite?
Egg ingested, hatch in small intestine, into venous system and via liver and heart to reach lungs
ascend tracheobronchial tree and then swallowed into the gut to develop into adult worm and start to produce eggs
What is schistomaiasis ? - what can this lead to?
infection from fresh water -
chronic infection, adult worms located in portal venules which can lead to hepatomegaly and liver fibrosis/ portal hypertension
What are cestodes? - how are they acquired?
tape worms - acquired by eating undercooked meat containing infectious larval cysts
Cysticercosis?
Tissue cyts muscle and brain that can lead to seizures
What is chagas disease?
Trypanasoma cruzi - transmitted by the kissing bug (triatome) - parasympathetic denerrvation affecting colon or Oesopahgus
What are the most common viruses that cause viral gastroenteritis?
rota virus, norovirus, sapovirus, adenovirus, astrovirus
When is rotavirus prevalent?
What can it cause
What are some clinical signs
how long does it last for
How is it diagnosed
What is the treatment
kids under 3 yrs - - repeat infection gets milder over time
can cause outbreaks
person to person
faecal oral - usually in winter
cincial effects - mild watery to perfuse diarrhoea causing shock
may have moderate fever first, vomiting then diarrhoea
NOT BLOODY
lasts about a week
Diagnosis is PCR on faeces
hydration is key management
How is rotavirus combatted?
The use of a vaccine - risk of intususseption increases as babies get older
When is norovirus prevalent?
winter vomiting disease - affects all ages
related to outbreaks - faecal oral or droplet spread
Survivial on fomites for days- weeks
Norovirus (most common adult GI viral infection)
What are the symptoms?
How is it diagnosed?
What is the treatment?
asymptomatic shedding - 48 hrs post stop of symptoms
D and V
short incubation - less than 24 hrs and lasts 2-4 days
diagnosed PCR stool
usually self limiting and hydration is key
How are infections tranmitted during sex?
Sexual/ genital secretions
direct innoculation
Fomites (inanimate object used as a vector for transmission - vibrator eg)
IVDU - Iv drug use (HIV, HCV)
How is syphilis spread?
Systemic/ haematogenous spread
Give an example of an infection spreading locally
herpes/ warts
What are some risk factors for STI’s
Under 25, change in sexual partner, non condom use
What can STI’s present with?
Peri anal pathology
Proctitis
Proctocolitis
Hepatobiliary problems
What does an HIV infection do?
Where are you more likely to get it?
Depletion of intestinal GALT (largest immune compartment in the body)
Rectum more likely to get the virus than through the oral route
Difference between antimicrobials and antibiotics
antimicrobial for all micro-organisms all agnets
Antibiotic is for bacteria - produced naturally by microorganisms and kill or inhbit the growth of other microorganisms
What is antibiotic resistance?
define multi drug resistant
Extensively drug resistant
Pan drug resistant
antibiotic will not inhibit bacterial growth at clinically achievable concentrations
Pumping it out of the bacterial cell or by producing molecules that can destory the antibiotic
Multi drug resistant - bacteria is non - susepctibale to at least 1 agent in 3 or more antimicrobial categories
XDR(extensive) - : non-susceptibility to at least 1 agent in all but 2 or fewer
antimicrobial categories
PDR - non sus to all agents in all antimicrobial categories
How is antibiotic resistance acquired?
Horizontal and vertical gene transfer
3 mechanisms - transformation, transduction, conjugation
In vertical transmission, a
bacterium accumulates
errors or mutations that cause antibiotic resistance during replication;
In horizontal transmission,
resistant genes are swapped
from one microbe to
another
This can occur via three mechanisms:
transformation, when bacteria scavenge resistance genes from dead bacterial cells and integrate
them into their own genomes;
transduction, when resistance genes are transferred by bacteriophages (viruses that infect bacteria); or
conjugation, when genes are transferred between bacterial cells through tubes called pilli.
What are some drivers of antibiotic resistance?
sicker inpatient population
increasing resistance in community
chronically ill
What is antimicrobial stewardship?
What is prudent prescribing?
Promoting and monitoring judicious use
of antimicrobials to preserve their future effectiveness’.
The optimal selection, dosage, and
duration of antimicrobial treatment that
results in the best clinical outcome for the
treatment with
minimal toxicity to the patient low risk of resistance
Antibiotic prescribing - What is the main thing to consider in antibiotic prescribing?
Constant review!
What does the HPV virus cause?
anal Warts that can extended rectum
How can Herpes simplex virus present?
How is spread?
1) Pain, ulcers, painful defection, bleeding,
spread through oral anal oral genital
What are the different types of syphilis(primary and secondary)
what symptoms does it present with?
What investigation is carried out?
Primary – solitary painless ulcer
Secondary – mucosal patches and ulcers
Multisystem disease!
Symptoms:
Pain of movement of bowels, blood in stool, crampy abdominal pains,
Colonsocpy – patchy mild congestion at rectum
Rectal biopsy
What are piles?
Piles – ulcers around the bottom
What can flare up a C. diff infection?
What are the main tests carried out for a Cdiff infection?
What is the main sign of C.diff infection?
Treatments before test comes back?
What are the complications?
What can cause a flare up of C.diff
What are the treatments for severe and non-severe?
Use of antibiotics
Stool C+S, FBC, U + E and abdominal x-ray is done for anyone with gastroenteritis
C.diff is detected with EIA toxin being positive then a C.diff infection is highly likely
IV fluids
Single side room
contact precautions
Sepsis
toxic megacolon
bowel perforation
Renal failure
Antibiotics - clindamycin, ciprofloxacin (+ other quinolones) cephalosporins and co-amoxiclav
(anti motility drugs, Age immunosuppression)
Severe = vancomycin
non severe = oral metronidazole
How is threadworm treated?
Strict hygiene measures and mebendazole for all of the household
What is the most likely organism for infective diarrhoea?
treatment?
Complications?
E Coli0157
Supportive treatment
Haemolytic urea syndrome - antibiotics can increase the risk of this happening
