T3-L4: Investigation of Specific Infections

Question 1

What is ‘M,C&S’?

Answer 1

M,C and S - Microscopy, Culture and Sensitivity
Microscopy is done in sterile site samples e.g. joint fluid or spinal fluid. We will use gram staining to see bacteria. Also we can get direct visualisation of organisms. It is also used to count white cells particularly in joint fluid and CSF to detect signs of infection.

Culture is done in nearly all samples that come to the test. It is difficult to culture media - selected based on the bacteria we would expect to find. We can then do further identification once grown.

Sensitivity testing can be done - using antibiotics around the organism and measuring the zone sites. Use EUCAST disc testing and strips.

Question 2

How can we use blood test for specific infections?

Answer 2

• Can look at immunity - IgG (previous infection), IgM (current infection or reactivation) and complement fixation tests
  
  • Detection of pathogen using blood culture, PCR and microscopy (direct detection such as in malaria) - done in patients who are septic for example

Question 3

What tests do we use in suspected meningitis?

Answer 3

A clinical history is very important - immunosuppressed, been aboard, been around people with meningitis?

• Assessed with radiology such as a CT and MRI head.
• Also assessed with a lumbar puncture.
• 2 sets of blood culture
• bacterial throats swab (N. meningitis is picked up through the airways and so can be picked up in a throat swab)
• Blood PCR for HIV, S. pneumonia and N. meningitis.

Question 4

What tests do we use in suspected brain abscess?

Answer 4

Brain abscess can result due to many causes - including infective heart valves, severe sinusitis and post-operatively. We don’t usually recommend lumber puncture as there is a risk of coning or adverse events. We usually aspirate or excise the abcess. Also consider if they are caused by more unusual things such as parasitic and fungal causes. There are blood tests to investigated this.

Question 5

Give examples of atypical causes of pneumonia.

Answer 5

Atypical pneumonia is tested using sputum and viral PCR looking for chlamydia mycoplasma and legionella antigen in urine - this may present with unusually chest X-ray and history.

Typical pneumonia has a small number of causes such as Strep. pneumonae and Haemophilius Influenza. Tested with radiological and clinical diagnosis.
We also use a blood culture if severe and sputum.

Question 6

Give example causes of viral pneumonitis.

Answer 6

• COVID-19
• Influenza A/B
• Parainfluenza
• RSV (important in children and neonates),
• Adenovirus
• Metapneumovirus
• Rhinovirus

Question 7

How do we test for TB?

Answer 7

• TB is a disease requiring exposure then reactivation
  
  • Tested using radiology/clinical/epidemiological
  • Active TB - present with fever, weight loss etc - we usually have 3 sputum samples, 8+ weeks culture, whole-genome sequencing, PCR and sensitivity testing

Question 8

How do we test for exposure of TB?

Answer 8

• Exposure testing - Mantoux, IGRA’s (interferon gamma release assays). These test look at if they have had exposure in the past even if they are not presented for the disease. We usually use this screening patients before immunosuppression. If see did immunosuppression, this could reactivate and cause severe infection.

Question 9

What respiratory tract infections are seen in the immunocompromised?

Answer 9

Fungal:

• Aspergillus fumigateurs
• Cryptococcosis
• Mucormycosis

bacterial:

• Nocardia sp.
• Gram negatives - resistant

Other infections:

• CMV
• HHv6
• Penumocystis jirovecii
• Non-tuberculous mycobacteria
• Measles

Question 10

How do we test skin infections?

Answer 10

Culture results are less useful here form intact skin. Broken skin may find better results.

We look for MRSA swabs/status and a history of water contact, travel and animal contact.

In necrotising fasciitis we need to excise the rotten flesh.

Cellulitis – usually treatable with empiric antibiotics, rare to get a diagnosis of a pathogen

Question 11

At what point should a diagnosis of a UTI be made?

Answer 11

Only when the patient has clinical symptoms.

Question 12

What is persistent UTIs of the same organism in an otherwise healthy male indicative of?

Answer 12

Prosthatitis - treated with ciprofloxacin. Treatment is 28 days, you can get prostatic abscesses as well.

* Clinical examination is key
* Urine for MCS useful to target therapy

Question 13

What are causes of epididymo-orchitis?

Answer 13

Inflammation of the epididymis and/or testicle
2 aetiologies – STI/enteric. Diagnosed on USS (to differentiate from testicular torsion and other differentials)

* Urine for MCS
* Urine/swab for chlamydia/Gonorrhoea NAAT (PCR)
* Presents with testicular pain and UTIs as well 
* May be acquired through gram negatives (the same that cause UTIs) or STIs

Question 14

How do we test for endocarditis?

Answer 14

3 blood cultures should be taken at different times during the first 24 hours at the same site. Usually they present without much else going on - non-specific features. Also a clinical history is very important.

Question 15

How do we test for a GI infection?

Answer 15

A lot of community acquired gastroenteritis is self-limiting. If severe or prolonged we can do testing.

1. Stool for M, C and S - bacterial testing
2. C. diff testing - GDH, toxin PCR
3. Stool for Viral PCR
4. Stool for ova, parasites and cysts

Question 16

What are common causes of community acquired gastroenteritis (bacterial, viral and parasitic)?

Answer 16

Bacterial:
- Salmonella sp. 
- Shigella sp.
- E Coli 
- Campylobacter sp. 
- C diff
Viral 
- Rotavirus 
- Norovirus 
Parasitic 
- Cryptosporidium 
- Giardia

Question 17

How do we test a liver abscess?

Answer 17

• Picked up on Imaging – USS/CT
• History is important as it can result on a number of aetiology (endocarditis, biliary tree, post-operatively). They can be:
  • Pyogenic (bacterial)
  • Hydatid
  • Amoebic
• Pus (if safe to aspirate) but not in a hydatid as this can cause adverse affects
• Blood cultures
• Stool for OCP (ova, cysts and parasites)
• Hydatid serology

Question 18

How do we test for a diverticulitis/biliary infection?

Answer 18

• Bloods – FBC, U&E, LFT, Clotting, Amylase
• Blood cultures
• Imaging is very important as complications such as perforation and abscess can be picked on
• Bile/pus from surgery/aspiration

Question 19

How is HIV tested for?

Answer 19

• HIV Ab/Ag combined test
• HIV PCR if the above is positive - used to test the viral load
• HIV resistance testing to look at the best retroviral testing

Question 20

How is Hep B tested for?

Answer 20

Antigen and antibody testing of the surface, core and e antigen. This tests to see if there is an active or past infection.

Question 21

How is Hep C tested for?

Answer 21

Antibody and PCR.

Question 22

What are common causes of meningitis?

Answer 22

Step. Pneumonia or Neisseria meningitis are common causes. Listeriae can be seen in the elderly and neonates. Group B strep or E.coli in neonates also. These are looks in the culture plates. We also get viral causes and so would use uPCR - (enterovirus, adeno, VZV, HSV and parechovirus).

If immunocompromised there is a lot more possible causes such as TB, toxoplasma and cryptococcal antigens. The additional tests are done if there is a risk.

Question 23

How do we test for Syphilis?

Answer 23

• Early, latent or late infection.
• Congenital infection
• Detection by PCR
• Serology
  • Screening with IgM
  • Treponemal specific antibody (TPPH/TPHA)
  • Non-treponemal antibody (VDRL, RPR)
  Expressed as dilution (1:16)