Microbiology Discussions

A lot of your time as an FY1 will be spent on the phone to various other specialities. You’ll come across patients with infections in all your rotations, and – if they don’t present with one – it may develop during admission. So, it’s a good idea to make talking to Microbiology as productive (and painless!) as possible.

Calling micro for advice
Calling other specialities to ask advice was always a palm-sweating, tongue-tying experience for me. Thankfully many principles are the same as referrals to other specialities and good structure can really help.

It’s also helpful to know a bit about who you’re calling and their agenda. You’re speaking to one of the clinical micro team (usually made up of consultants, clinical scientists – who’ve come from a lab background – and registrars). In some hospitals, there is an infection ward round and MDTs for selected patients, however elsewhere your phone call may be all the information micro receive about the patient whose samples they are processing. Also, in larger hospitals, virology may be a separate department with its own advice system.

My proposal for a successful call:
Before you call, ensure you have checked with your seniors for advice first. Many common investigation or antibiotic plans can be made by your seniors rather than micro. Also, check your local antimicrobial guide (or Microguide app if your hospital uses this). If the question can be answered using this, reconfirm whether you still need to contact microbiology. This way you’ve saved yourself a job!

Ensure you know the patient(s) you are phoning about, including:

  • Presenting complaint, PMH including surgical history and prostheses (lines, hip replacements etc – really important as bugs can stick to them), any immunodeficiency, travel history
  • Drug chart and allergies (if the allergy is ‘unknown’ try to establish the exact nature of the allergy as if mild this can mean 1st line antibiotics are still given, which may be more effective or have few side effects)
  • Examination findings
  • Progress notes – what has happened to them this admission, including any surgeries? What is the plan now?
  • Observations – have the chart in front of you. Current obs and trends are important, particularly the presence or absence of fever and how long they have been apyrexial.
  • Investigation results
    • Bloods (WCC and CRP are key for monitoring infection, renal and liver function are useful for the pharmacology of antibiotics)
    • Radiology, especially in surgical patients (remember there may be several CTs over the admission)
    • Previous microbiology (particularly results from another hospital/country which micro will not have access to)
Get an SBAR together, but don’t include all the info from above. Remember you’re trying to ask specific question(s). Ensure you ask your seniors a clear question or reason for calling them otherwise the call will be difficult. It is important you do this to get the correct advice. Here is an example:

Situation: Hello, I’m Emma Chisholm Urology FY1. Mr Brown my consultant has asked me to call for your advice about appropriate antibiotics for Beatrice Smith [insert unique patient no].

Background: Mrs Smith is 55 years old and was admitted yesterday with 3 days of fever, vomiting and left flank pain. Before this, she had a week of dysuria and had oral trimethoprim from her GP. She has a history of renal stones and had an obstructing stone removed by ureteroscopy and a left sided ureteric stent placed this January, which is still in situ.

Assessment: Currently, she is alert with a NEWS of 5: T38.5 RR 24 SpO2 99% on air HR 120 BP 140/80. She has left flank tenderness but no peritonism. CTAP shows inflammatory stranding around the left kidney but no hydronephrosis or ureteric stones.

Recommendation: Mrs Smith is planned for stent removal this afternoon. We have sent urine and blood cultures and started IV amoxicillin and gentamicin. However, she has previously had several positive urine cultures with a multi drug resistant enterococcus, resistant to Amoxicillin and Vancomycin. Can you advise on an IV alternative for the enterococcus? Is there anything else we should add to the antimicrobial regime?

See how the key information is conveyed i.e. new episode of pyelonephritis in a patient with a ureteric prosthesis. The clinical team’s plan is clear: removal of the stent for source control and IV antibiotics. Their question is clear: given previous resistant organism, what antibiotics should they add? And they have likely checked the local guidelines already and cannot give 1st or 2nd line treatments.

  • If you don’t know everything they want to know, don’t panic. You can always ask what more is needed, collect it then get back in touch.
  • Sometimes, it may be more appropriate for a senior to speak to micro e.g. complex surgical patient. Don’t feel bad about this and remember point (1) – asking micro usually means the question is more specialised than the experience of your seniors, so they know best what they want to ask.

Calling outside of working hours: 
Out of hours calls should be essential and urgent. The on-call microbiologist is usually at work the day before and after, so being disturbed can be quite exhausting. Additionally, they often do not have access to the lab systems for sensitivity and other information out of hours. Do not handover plans to call microbiology, instead ask for the plan in hours e.g. “if the patient becomes pyrexial, add in a stat dose of gentamicin as per microbiology”.

Being called by micro
If micro are calling you it is about something important, like a positive blood culture or CSF.
So, what should you do?

Think: are you the best person to answer questions about this patient? If your colleague knows them better, it’s probably best to pass this one on.

Don’t panic: If you are the only available person and don’t know the patient, document the information in the notes and let your senior know. If it is easy to collect the required information, do this and rediscuss with micro. If not, ask for your senior’s help.

Learn: If you do know the patient, this is a great learning opportunity as well as making the call quicker and providing good continuity of care. Again, document the call clearly, discuss with your senior and implement further investigations/treatment as appropriate.

Example: positive blood cultures

This is a classic. Micro will usually phone you about positive blood cultures, partly because of the high mortality associated with bacteria in the bloodstream. It’s important to find the source and treat as soon as possible. e.g. In the UK with non-MRSA Staph Aureus bacteraemia ~1 in 5 people will die of any cause within the next 30 days!

You’ll probably receive several calls about the same blood culture. This is because initially they are grouped into gram-positive or negative and by shape based on microscopy. Then once it grows, its identity is checked. Finally, the resistance profiles and sensitivities are reviewed (usually by machines). At each stage, antibiotics and plans may change. Growing organisms takes days and sometimes is not possible. So, it’s important to be familiar with some common organisms and their likely sources, though the micro team will guide you, particularly if the source is unclear.

e.g. positive blood culture ‘Gram-positive cocci in clusters – likely staphylococci’. 

The most likely organisms of this appearance are staphylococci, including staph aureus. Micro will then want to know of the likely source so that this can be controlled to stop the source of bacteraemia. For staphylococci, common sources are skin/soft tissue infections or evidence of infected prosthetic devices, septic arthritis /osteomyelitis /discitis, or endocarditis. [A slight caveat with this type of result is that these organisms are a common part of normal skin flora, so if the culture taking procedure isn’t sterile this could be a contaminant, rather than a true bacteraemia. These are often coagulase-negative on reports]

Further easy-to-read info about different types of bacteraemia is available through the Microguide app under Cardiff and the Vale Trusts. This has a great introductory section under heading ‘Interpretation and clinical guidance of Gram results in blood cultures’ on ‘look for possible sources’ within each option. Of course, be mindful that the treatment and other sections are trust specific!

Suggested reading:
Your local antimicrobial guidelines – at the least know how to access them and be familiar with what’s recommended.

Microbiology nuts and bolts. Key concepts of microbiology and infection. 2nd edition. Dr David Garner.
Pocket-sized book giving a great overview to infections by system and infection control principles. I wish I had read this during foundation or medical school. Around £20 on Amazon


Written by Emma Chrisholm ST1 Radiology

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