Investigation of Specific Infections Flashcards
Why are most laboratory tests are used to confirm suspected clinical diagnosis (signs and symptoms) and not all the time?
Prevents over diagnosis which prevents over use of antibiotics - no point treating infection if no symptoms
What is a:
a) true positive?
b) true negative?
c) false positive?
d) false negative?
a) patient with disease tests positive
b) patient without the disease tests negative
c) patient without disease tests positive
d) patient with disease tests negative
What is ‘sensitivity’ of a test?
The proportion of people WITH the disease who test POSITIVE
True positive / (true positive + false negative)
What is ‘specificity’ of a test?
The proportion of people WITHOUT the disease who test NEGATIVE
True negative / (false positive + true negative)
If a test has a low specificity, what does this mean?
False positives are identified who do not have disease
What is ‘M, C and S’?
Microscopy, culture and sensitivity
What does microscopy involve?
- Looking at specimen under microscope –> direct visualisation of organisms
- Usually STERILE samples e.g. spinal fluid
- Cell count (e.g. white cells - infection?)
- Gram stain
What does culture involve?
Plated out using swabs onto different types of cultural media (e.g. for anaerobes)
What does sensitivity involve?
Antibiotic sensitivity testing (EUCAST disc testing)
What are examples of a sterile sample?
CSF, abscess, pus, synovial fluid, tissue biopsies
What are examples of non-sterile samples?
Sputum
What is seen in culture of sputum samples?
Lot of growth of lots of different respiratory organisms - only pick out the important ones
Blood tests can also be used for specific infections.
When detecting immunity, what would:
- IgG
- IgM
be looking for?
- IgG: previous infection
- IgM: current infection (or reactivation)
What is a complement fixation test?
A blood test in which a sample of serum is exposed to a particular antigen and complement in order to determine whether or not antibodies to that particular antigen are present. The nature of complement is to react in combination with antigen–antibody complexes.
N.B. these are being phased out
How can pathogens be detected in blood tests?
Blood culture - M,C & S
Polymerase chain reaction (PCR)
Microscopy (malaria)
If an unwell patient presents at the hospital, what are the generic tests that are done (e.g. for patients with sepsis)?
- Blood cultures
- FBC
- U&E
- LFT
- CRP
- Clotting
- Procalcitonin
What does procalcitonin indicate?
A biomarker that exhibits greater specificity than other proinflammatory markers (eg, cytokines) in identifying patients with sepsis and can be used in the diagnosis of bacterial infections.
Examples of more specific tests:
Pus from abscess – culture and sensitivity results
Hepatitis B serology
Meningococcal PCR on CSF
What are the symptoms of meningitis?
Fever, headache, neck stiffness. Sometimes meningococcal or viral rash
What are the symptoms of a brain abscess?
Fever, headache, neurological impact depending on anatomical location, can lead to ventriculitis
What is meningitis?
Inflammation of the meninges.
There are many different causes: viruses, bacteria, mycobacteria, fungi and parasites
What is encephalitis?
Inflammation of the brain parenchyma
Which organism is the most common cause of bacterial meningitis?
Streptococcus pneumoniae
Which organism is the most common cause of viral meningitis?
Enteroviruses
Also herpes viruses
What imaging would be done in meningitis/encephalitis?
- CT head
- MRI head
Then a lumbar puncture
What is a lumbar puncture?
Draw CSF and analyse
As soon as a patient presents with meningitis, what are they given?
Broad spectrum antibiotics
Results from lumbar puncture are then used for more specific treatments
What is the dominant white cell type in:
a) viral
b) bacterial
c) fungal
d) TB
meningitis?
a) lymphocytes
b) neutrophils
c) lymphocytes
d) lymphocytes
N.B. there are exceptions to this:
- A late presentation of meningitis can present with more lymphocytes
- Listeria monocytogenes (causes bacterial meningitis) can present with more lymphocytes
Which mycobacteria causes meningitis?
Mycobacterium tuberculosis
Who is Listeria monocytogenes meningitis more common in?
Neonates and eldery
What is the CSF sample in meningitis/encephalitis tested for?
- Cell count, protein, glucose
- Culture plate - look for common pathogens seen in meningitis e.g. Streptococcus pneumoniae
- PCR for viruses e.g. enterovirus, adeno, VZV, HSV, parechovirus
If the patient history is suggestive, also test CSF for:
- Cryptococcal antigen
- Toxoplasma PCR
- TB culture
What are the common causes of neonatal meningitis?
- Bacteraemia
- Group B strep
- E. coli
- Listeria monocytogenes
What non-CSF tests should be done in suspected meningitis/encephalitis?
Blood cultures (2 sets)
Bacterial throat swab
Blood for HIV and blood PCR (S. pneumoniae, N. meningitidis)
What is a brain abscess? What can lead to one?
A brain abscess is a collection of pus enclosed in the brain tissue
It usually occurs when bacteria or fungi enter the brain tissue after an infection or severe head injury.
What are examples of mechanisms of infection in brain abscesses?
- Severe ENT infection e.g. sinusitis
2. Infective endocarditis, infection of heart valves, can spread to the brain
How are brain abscesses investigated? How does this differ from meningitis?
NOT lumbar puncture or CSF
Brain abscesses instead are usually aspirated or excised in theatre –> then blood culture done
Why is lumbar puncture/CSF not recommended in brain abscesses?
High risk of ‘coning’ where the brain is forced through the foramen magnum - this is due to high pressure on the brain
Is pneumonia an URTI or a LRTI?
Lower
What is the most common cause of bacterial pneumonia?
Streptococcus pneumoniae
What is the most common cause of viral pneumonia?
Haemophilus influenzae
What is community acquired pneumonia?
develops in people outside a hospital
Which respiratory disease is often misdiagnosed as pneumonia?
pulmonary tuberculosis (TB)
Which organism causes pulmonary TB?
Mycobacterium tuberculosis
Common symptoms of ‘typical’ pneumonia?
Cough, sputum, fever, SOB, pleuritic chest pain
What investigations are done when a patient presents with ‘typical’ pneumonia?
- Chest x-ray
- Blood cultures
- Sputum (for MC&S)
What is an ‘atypical’ pneumonia screen?
- Sputum for MC&S
- Viral PCR
- Mycoplasma (serology/PCR)
- Chlamydia (PCR)
- Legionella antigen in urine
How can ‘atypical’ pneumonia present?
Unusual symptoms - arthralgia, myalgia, rashes
What is ‘atypical’ pneumonia?
- Tends to be caused by different organisms
- Tends to have milder symptoms
- Need alternative treatments
What atypical organism can cause pnuemonia?
Mycobacteria, chlamydia pneumoniae
What would indicate the need for an atypical pneumonia screen?
If not getting better after antibiotics
Unusual chest xray
Unusual clinical features
Pulmonary tuberculosis requires exposure to M. tuberculosis and then reactivation.
What exposure tests can be done?
- Mantoux
- IGRA’s (interferon gamma release assay)
What is the purpose of exposure tests for M. tuberculosis?
See if people have had exposure to M. tuberculosis in past, even if they are not displaying symptoms
Why would you do exposure tests for M. tuberculosis before putting patients on immunosuppressants e.g. before a bone marrow transplant?
To double check they don’t have latent TB that could cause severe symptoms once they are immunosuppressed
How is active pulmonary TB investigated?
- Chest xray
- 3 sputum samples
- 8+ weeks culture
- Whole-genome sequencing
- PCR
What fungal pathogens are immunocompromised patients particularly susceptible to that can cause respiratory tract infections?
- Aspergillus fumigatus infection
- Cryptococcosis
- Mucormycosis
What bacterial pathogens are immunocompromised patients particularly susceptible to that can cause respiratory tract infections?
- Nocardia sp.
- Gram-negatives – resistant
What tests are used to diagnose respiratory tract infections in immunocompromised hosts?
- Bronchoscopy
- Aspergillus/CMV blood tests
What are 3 examples of localised skin and soft tissue infections?
- Impetigo
- Erysipelas
- Cellulitis
What is an example of a severe/extensive skin and soft tissue infection?
Necrotising fascitis
How are localised SSTIs tested for?
Wound swabs unhelpful from intact skin
Blister fluid/pus is better
How can severe/necrotising fasciitis be tested for?
Blood cultures are positive in only 5% severe cases
Tissue results from nec. fasciitis can be helpful
The Wagner Ulcer Classification System is used to identify the seriousness of diabetic foot ulcers.
What is each stage? (1-5)
0: no open lesions; may have healed lesion
1: superficial ulcer without penetration to deeper layers
2: deeper ulcer, reaching tendon, bone, or joint capsule
3: deeper tissues involved, with abscess, osteomyelitis, or tendonitis
4: gangrene in a portion of forefoot or heel
5: extensive gangrenous involvement of the entire foot
What are the causes of diabetic foot ulcers?
Poor circulation:
- A form of vascular disease
- Makes it more difficult for ulcers to heal.
High blood sugar (hyperglycemia):
- Can slow the healing process of an infected foot ulcer
Nerve damage:
- Reduces sensitivity to foot pain and results in painless wounds that can cause ulcers.
Irritated or wounded feet
Why are urine tract infections only tested for when absolutely necessary?
Due to overuse and resistance of antibiotics
Patients are only encouraged to use antibiotics if symptoms are severe
Many patients have positive samples but no symptoms - don’t need treatment
Which bacteria are UTIs usually caused by?
Bacteria from the gastrointestinal tract entering the urinary tract, with Escherichia coli being the most common cause
Which organism can cause UTIs in hospitalised patients who are immunocompromised or have an indwelling catheter?
Candida albicans
How do lower UTIs typically present?
Inflammation of the bladder (cystitis) and urethra (urethritis).
N.B. this can ascend and lead to upper UTI
How do upper UTIs typically present?
- Dysuria
- increased urinary frequency and urgency
- urine that is strong smelling, cloudy or contains blood,
- persistent lower abdominal pain.
Asymptomatic bacteriuria is not routinely treated with antibacterials.
What is the exception to this?
Pregnant women
What is the choice of antibacterial therapy for lower UTIs?
Nitrofurantoin, or trimethoprim
What category of bacteria (gram stain) is a UTI typically caused by?
Gram-negative bacteria
How should urine samples be collected?
Mid stream
What should be suspected in men with recurrent UTIs?
- Prostatitis
2. Epididymo-orchitis
What is prostatitis?
Inflammation of the prostate gland - Acute prostatitis is usually caused when bacteria in the urinary tract enter the prostate.
What is epididymo-orchitis?
Inflammation of the epididymis - normally caused by STI or UTI or enteric bacteria
How effective are antibiotics in treating epididymo-orchitis and prostatitis?
Very effective
When testing for prostatitis/epididymo-orchitis or recurrent UTIs, what should also be tested for?
Urine/swab for chlamydia/Gonorrhoea NAAT (PCR)
What are examples of intra-vascular infections?
Endocarditis – native/prosthetic valve
Pacemaker infection
Vascular graft infection
Catheter
How should intra-vascular infections be diagnosed?
Three sets of blood cultures should be taken at different times during the first 24 hours in all patients with suspected endocarditis (can be same arm)
What history is key to gain from the patient when diagnosing GI tract infections?
- Returning traveller
- Hospital long stay patient with recent course of antibiotics
Which 5 bacteria are responsible for community acquired gastroenteritis?
- Salmonella sp.
- Shigella sp.
- E. coli
- Campylobacter sp.
- C. difficile
What are the 2 viral causes of gastroenteritis?
- Rotavirus
2. Norovirus
What are the 2 parasitic causes of gastroenteritis?
- Cryptosporidium
2. Giardia
What tests should be requested for infective gastroenteritis?
Stool for M, C & S –bacterial testing, some labs will do more
C. difficile testing – GDH, toxin PCR
Stool for viral PCR – range of tests differs between labs
Stool for ova, parasites and cysts (OCP)
BUT – often self-limiting, testing not always required
When should infective gastroenteritis be tested for?
ONLY if symptoms are severe or prolonged
What are the different types of liver abscesses?
Pyogenic (bacterial)
Hydatid
Amoebic
How can liver abscesses be diagnosed?
- Imaging: USS/CT
- History
- Pus (if safe to aspirate)
- Blood cultures for bacteria
- Stool for OCP
- HYDATID SEROLOGY
- Liver biopsy
What can cause liver abscesses?
Abdominal infection, such as appendicitis, diverticulitis, or a perforated bowel
Infection in the blood
Infection of the bile draining tubes
Recent endoscopy of the bile draining tubes
Trauma that damages the liver
What is cholangitis?
Cholangitis is an inflammation of the bile duct system
In most cases cholangitis is caused by a bacterial infection
What is cholecystitis?
inflammation of the gallbladder
What complications can diverticulitis lead to?
fistula, abscess, perforation
What are the blood borne viruses?
HIV
Hep B
Hep C
What tests should be done in blood borne viruses?
Serology: Antibody (IgG, IgM) and Antigen (component of virus)
PCR: DNA/RNA from living or dead organisms (usually active infection)
How is HIV tested for?
HIV Ab/Ag combined test. If positive then:
HIV PCR - how much virus is present?
HIV resistance testing - best antiretroviral therapy?
What testing is done for Hep B?
The “Hepatitis B Panel” of Blood Tests
HBsAg (Hepatitis B surface antigen) - A “positive” or “reactive” HBsAg test result means that the person is infected with hepatitis B
How is Hep C tested for?
Hep C antibody - to find out if someone has ever been infected with the hepatitis C virus
Hep C PCR - active infection?
Syphilis testing:
Can detect early, latent or late infection.
Congenital infection
Detection by PCR
Serology:
- Screening with IgM
Key learning points:
Only request tests when you have clinical suspicion of infection, unless screening an asymptomatic individual as part of national programme
Detailed history, including travel, will help guide investigations
Review carefully for source of infection before selecting appropriate tests
Most patients require both generic tests and focused tests
Sensitivity is a calculation of…?
The proportion of people with the disease who test positive
What is the ‘positive predictive value’ of a test?
The probability that people with a positive test who truly have the disease
What is the ‘negative predictive value’ of a test?
The probability that people with a negative test who truly don’t have the disease
Specificity is a calculation of…?
The proportion of people without the disease who test negative
Detection of measles IgG in the blood suggests…
Suggests PAST infection with measles
Detection of measles IgM in the blood suggests…
Suggests current infection with measles
A patient presents to A&E with headache, neck stiffness, fever and photophobia.
What are the most appropriate tests?
Suspect meningitis:
Blood cultures (meningococcus, pneumococcus)
Throat swab (meningococcus)
CSF
Blood for PCR
What is organism is meningococcus?
Neisseria meningitidis (bacteria)
What type of pneumonia can Legionella pneumophila cause?
Atypical pneumonia
What is the first choice antibiotic for typical pneumonia?
Amoxicillin
Which organisms cause atypical pneumonia?
Mycoplasma pneumonia caused by the bacteria Mycoplasma pneumoniae.
Pneumonia due to Chlamydophila pneumoniae bacteria
Pneumonia due to Legionella pneumophila bacteria - seen more often in middle-aged and older adults, smokers, and those with chronic illnesses or a weak immune system.
What are the most appropriate tests for a patient with suspected pulmonary TB?
Chest xray
3 sputum samples for AAFB MC&S
Typical presenting symptoms of pulmonary TB?
Weight loss, fever, productive cough
If a urine dip stick shows leucocytes and nitrites but the patient has no fever or urinary symptoms, what should you recommend?
Do nothing, reassure the patient
In Hep B testing, what does:
a) HBsAg mean?
b) anti-HBs or HBsAb mean?
c) anti-HBc or HBcAb mean?
a) Hepatitis B surface antigen - a positive result means the person is INFECTED with Hep B
b) Hepatitis B surface antibody - a positive result means the person is PROTECTED against Hep B (either vaccine or previous infection)
c) Hepatitis B core antibody - a positive result means a PAST or CURRENT Hep B infection (the core antibody provides NO protection unlike the surface antibody)
