Investigation of Specific Infections Flashcards
How do investigations alter a clinical picture?
What questions do the tests ask?
Investigations ADD to a clinical picture and do not REPLACE it
each test asks a specific question:
- What is causing the infection and what can i use to treat it?
- Is the person at risk of developing an infection?
- Is this an infection?
Why is no test ‘infallible’?
Each test will have a positive and negative error rate
What is the difference between local and general sampling?
Local sampling:
- this is sampling from the source of infection
- it assists with diagnosis
- identifies bug causing the infection and what drug can be used to treat the patient
general sampling:
- involves blood cultures
- FBC, U&Es, LFTs, clotting CRP
- this is part of an investigation of sepsis
What are the 3 main central nervous system infections (CNS)?
- Meningitis
- Encephalitis
- Brain abscess
What is meningitis?
What causes it and how can it be diagnosed?
It is inflammation of the meninges
it is caused by viruses, bacteria, mycobacteria, fungi and parasites
it is diagnosed through lumbar puncture to collect cerebrospinal fluid
What tests are used in meningitis?
- 2 sets of blood cultures
- blood for bacterial PCR (S. Pneumoniae and N. Meningitidis)
- FBC, clotting, U&Es, LFTs, glucose, CRP
What is encephalitis and what is it caused by?
What test is used to diagnose it?
Inflammation of the brain that is usually viral
usually caused by Herpes viruses
Diagnosed with CSF requesting viral PCR specifically
What tends to cause a brain abscess?
They have a wide aetiology - bacterial, mycobacterial, fungal, parasitic
history (patient factors) can narrow down the cause
e.g. Ear, sinuses, blood, post-op etc.
What tests are used to identify a brain abscess?
Which test should be avoided and why?
LP should be discouraged as it is rarely positive and is high risk
Blood cultures are collected
Local sampling involves:
- Surgical biopsy / drainage of pus
- Gram stain, culture and sensitivity (PCR)
What are common ear, nose and throat infections?
Ear:
- acute otitis media
- otitis externa
Nose:
- sinusitis
Throat:
- pharyngitis - viral or bacterial
- diphtheria
What are the tests for acute otitis media and acute otitis externa?
Acute otitis media:
- clinical diagnosis - viral and bacterial
- send pus if the ear drum is perforated
Acute otitis externa:
- ear swab to determine the cause (bacterial, fungal, etc.)
- sensitivity
What is rhino-sinusitis caused by?
When should samples be taken?
- Majority viral
- can be a secondary bacterial infection
- caused by upper respiratory tract flora
a sample should be sent in all cases, but in severe cases it is unhelpful
What samples should be taken in severe cases of rhino-sinusitis?
- Pus from operative sinus lavage
- FBC, blood cultures
What are the majority of cases of pharyngitis (sore throat) caused by?
What tests should be sent and when?
Majority of cases are viral
a throat swab should be sent ONLY if there is evidence of bacterial infection
this involves looking for B-haem streps
What are the additional tests which may be used in pharyngitis (sore throat)?
- EBV serology
- swab for diphtheria
- pus if there is a Quinsy abscess
What are the 4 main respiratory infections?
- Influenza
- pneumonia
- pulmonary tuberculosis
- atypical infections in immunocompromised patients
What are the characteristics of influenza?
Which patients should be tested?
It is seasonal and highly transmissable
It can be sporadic or epidemic
It is not necessary to test everyone
Only those who may require treatment of those at risk of transmitting are tested
How is influenza tested for?
Through nose / throat swabs
These are analysed by PCR or immunofluorescence
PCR has sensitivity > 90% and specificity of 99%
How is pneumonia diagnosed?
The clinical diagnosis is based on respiratory symptoms, signs and chest X-ray changes
What severity assessment is used in diagnosing pneumonia?
CURB65 score
CRP may help guide diagnosis and antibiotic need
Low score:
- 0 - 1
- no investigations required
Moderate - severe score:
- 2 - 5
- sputum, blood cultures and atypical screen collected
What is involved in the atypical screen for pneumonia?
Urine for legionella antigen
nose / throat for mycoplasma PCR
this might include serum
What is required in order for someone to obtain pulmonary tuberculosis?
It is a disease which requires exposure and then reactivation at a later stage in life to produce pulmonary symptoms
What is involved in exposure testing for pulmonary tuberculosis?
- Mantoux
- IGRA (interferon G releasing assay)
These rely on an intact immune system
What are the tests for someone who has pulmonary symptoms and expected pulmonary tuberculosis?
3 sputum samples
microscopy and culture for 8 weeks
PCR
In what types of patients should atypical infections be considered in?
Immunosuppressed patients
haemato-oncology:
- solid organ transplant
- patients on chemotherapy
travel
other:
- diabetes
- chronic kidney disease
- underlying disease - e.g. HIV
What are the tests involved in looking for atypical respiratory infections?
Viral:
- e.g. RSV, CMV
- viral PCR performed
Fungal:
- e.g. aspergillus
- culture and aspergillus antigen test
Pneumocystis:
- PCP PCR
these are not looked for routinely
they are usually best investigated with deep respiratory samples
What are the most common skin and skin structure infections?
- Localised - impetigo, erysipelas, cellulitis
- severe/extensive - necrotising fasciitis
- diabetic foot infection
What tests are performed in localised skin and skin structure infections?
(impetigo, erysipelas, cellulitis)
Wound swabs:
- not helpful from intact skin
- send blister fluid or abscess pus
Needle aspirates from cellulitis:
- Poor as they only determine the pathogen in 10-30% of cases
Blood cultures:
- only positive in the most severe 5% of cases
- send in case of sepsis
What is necrotising fasciitis?
How is it treated and which tests are performed?
Rapidly spreading synergistic infection which is a surgical emergency as it has high mortality
2 sets of blood cultures are collected and FBC, U&Es, LFTs and CRP performed
What is a diabetic foot infection and what tests are performed?
Non-infected wounds or ulcers:
“smelly”, “weeping”, “exudate” are not evidence of infection
swabs are NOT sent
mild infection:
wound swabs are sent
moderate to severe (deep) infection:
debride the wound and then collect “clean” bone or tissue sample
What are the most common urinary tract infections?
- Lower UTI and upper UTI (pyelonephritis)
- prostatitis
- epididymo-orchitis
What should the clinical diagnosis and microbiology answer in an upper or lower UTI?
Lower UTI - cystitis
Upper UTI - pyelonephritis
clinical diagnosis supported by microbiology
answers the question “ what is causing this UTI and how should I treat it?”
But not “does this patient have a UTI?”
What is looked for in a urine sample for an upper or lower UTI?
If there is dysuria and frequency, then the probability of UTI > 90%
urine sample:
- WBC
- RBC
- epithelial cells
- bacterial growth
- sensitivities
What is used in the interpretation of a urine sample when diagnosing a UTI?
- Kass criteria give the threshold for “significant bacteriuria”
- automated analysers - microscopy to predict culture positivity
- think about how the urine was collected e.g. MSU, CSU, bag
What types of patients tend to get prostatitis?
What is the main focus of diagnosis?
50% of patients with recurrent UTIs and 90% of febrile UTIs have prostatitis
the main focus of infection is on the urine (post-prostatic massage)
What are the 2 main aetiologies of epididymo-orchitis?
How are they tested for?
Enteric/UTI or STI
urine is sent for cultures and chlamydia/gonorrhoea PCR
in severe cases, blood cultures, ultrasound screeening +/- drainage
What are the main gastrointestinal infections?
- Infectious diarrhoea
- Helicobacter pylori infection
- liver abscess
- cholangitis / cholecystitis
- diverticulitis
What types of pathogens cause infectious diarrhoea?
- Viruses - norovirus, rotavirus
- Bacteria - campylobacter, salmonella, shigella, E.coli, vibrio
- parasites - cryptosporidium, giardia, foreign travel
- C difficile infection
Why are samples for infectious diarrhoea conducted?
- Laboratory needs guiding with clinical details and risk factors
- majority of bacterial and viral diseases are self limiting
- a stool sample is used to guide treatment, public health and avoid transmission
What other investigations can be carried out for infectious diarrhoea?
- 3 stool samples to look for parasites
- bloods - FBC, clotting, U&Es, LFTs, CRP
- blood cultures
- abdominal imaging - plane film or CT
What are the tests for Helicobacter pylori that are used to guide antibiotic treatment?
H. Pylori antibody test:
- insensitive as it doesn’t distinguish active from past infection
H. Pylori stool antigen:
- simple, non-invasive and inexpensive
urea breath test:
- expensive
- gold standard for test of cure
biopsy urease test:
- invasive and possible cross reactions
STOP PPIs BEFORE TESTING
What are the causes of a liver abscess?
What types of tests should be performed?
Pyogenic (bacterial), hydatid or amoebic - history guides aetiology
- drain pus (if safe to do so)
- stool for OCP
- blood cultures
- FBC, U&Es, LFTs, CRP
- hydatid serology
- imaging - USS/CT
What tests are conducted for cholangitis / cholecystitis?
- Bloods - FBC, U&Es, LFTs, clotting, amylase
- blood cultures
- imaging - USS or CT
- bile fluid or pus if aspirated or drained
What are the 2 different types of diverticulitis?
Uncomplicated and complicated
complicated involves abscesses, fistula, perforation or obstruction
What tests are performed in diverticulitis?
- Pus from abscess
- blood cultures
- bloods - FBC, U&Es, LFTs, clotting, amylase
- imaging - CT
What are the 2 different categories of vascular infections?
Heart valves (endocarditis):
- native or prosthetic
Vessels:
- mycotic aneurysms
- prosthetic vascular graft infections (PVGI)
What is involved in the tests for endocarditis?
Blood cultures are fundamental to management as they have 96% positivity
three sets of blood cultures should be taken at different times during the first 24 hours in all patients with suspected endocarditis
What other investigations can be carried out in endocarditis?
- Echocardiography - transthoracic echo TTE or trans-oesophageal echo TOE
TOE should always be done for suspected PVE
- FBC, U&Es, LFTs, CRP
- serology for Bartonella, Chlamydia, Coxiella, Brucella
- valve tissue if valve replaced - culture, sensitivity and PCR
What are the initial tests involved in vascular graft infections?
Three sets of blood cultures should be taken at different times during the first 24 hours in all patients with suspected VGI
this has a lower culture positivity rate than endocarditis
What other infections are performed in vascular graft infections?
- Imaging - PET/CT, WBC scan from fluid around the graft
- tissue/fluid from around the graft for culture and PCR
What are the tests performed for viral hepatitis (hepatitis A, B and C) investigations?
Based on serology +/- PCR
Serology comprises ANTIGEN and ANTIBODY detection
PCR detects DNA or RNA from living or dead organisms, but usually presence of DNA/RNA suggests active infection
What are you looking for in serology for viral hepatitis infection?
Antigen - components of the organism
antibody - body’s immune response to organisms (acute IgM and chronic IgG)
What are the different types of syphylis that are investigated?
- Early (primary and secondary)
- latent
- late (tertiary-gummatous, neuro, cardiovascular)
- congenital
What is involved in syphilis investigation?
Detection by PCR (superseded dark ground microscopy)
Serology:
- screening test including IgM in primary infection
- treponemal specific antibody
- non-treponema specific antibody
