Tag Archives: clinical details

“Painting Pictures”

A wound swab arrives into the microbiology laboratory..

…Because there are no clinical details we don’t know whether a Gram stain might be worthwhile.

Because there are no clinical details, we don’t know whether to add anaerobic culture or set up a yeast agar for this  swab.

Because there are no clinical details, we don’t know whether this Pseudomonas aeruginosa isolate on the plate is potentially significant…

Microbiology laboratories all over the world (including our own) receive hundreds of wound swabs every day. Often there are no clinical details or only a very cursory acknowledgement to this requirement, such as “?infection”, or “discharging wound”.

You know the story well…

So often we are left to process and report the wound swab with no idea of what is actually wrong with the patient, and what exactly we should be doing with the swab.

In my opinion clinical details involve two main elements, which overlap to a certain extent:

  • Contextualisation- What type of infection are we dealing with here? Taking the example of skin infections; Is it an impetiginous lesion, is it a boil, is it an area of cellulitis, is it a post-surgical wound, is it a burn, etc, etc? By providing clinical context we can start to work out what we are looking for and ascertain the importance of potential pathogens on the agar plates. Is there anything we should know about the patient? Are they immunocompromised? Do they have antibiotic allergies? Are they failing treatment? Is there anything unusual about the clinical presentation? Was it caused by a bite? Was there overseas travel?
  • Justification- Taking the example of skin infections again, most patients with impetigo & boils, along with many other types of uncomplicated skin infections, do not need a wound swab sent to the lab. For most skin infections, swabbing should be the exception, not the rule. So what was it about this particular patient that prompted the clinician to send a wound swab? Was it because the patient failed first line treatment? Was it because they had an associated fever? Was it because the infection was getting rapidly worse?

Here are a few examples of hypothetical clinical details that both contextualise and justify the swab.

  • “Impetiginous lesions on face getting worse despite topical anti-septic treatment. Past history of MRSA colonisation.”
  • “Area of spreading cellulitis L lower leg. Patient diabetic.”
  • “Carbuncle L buttock, patient has an anaphylactic allergy to penicillin.”
  • “Cat scratch to R hand. patient now has fever and increasing erythema. Commenced on amoxycillin-clavulanate.”

It’s not rocket science, nor does it have to be a story.

If the clinician is required to contextualise and justify the laboratory request, then the advantages are two-fold. Not only can the scientist paint a picture in their head of what is going on with the patient, and process accordingly, but also the clinician may start to think twice about why they are sending a particular sample to the laboratory in the first place…



“Staphylococcus aureus in sputum samples. A reporting conundrum.”

When I worked in a microbiology laboratory in Glasgow we hardly ever reported antibiotic susceptibilities on Staphylococcus aureus when cultured from sputum. Now I am working in New Zealand, and we almost always do…

So who is right and who is wrong?

The problem is that Staphylococcus aureus in the sputum can mean several different things:

  • It may simply represent oropharyngeal contamination of the sample.
  • On the flipside it may signify a severe necrotising pneumonia in an immunocompromised or post-influenza patient.
  • And thirdly, we know that Staphylococcus aureus can colonise or occasionally cause “low level” infection in the architectually damaged lung (e.g. cystic fibrosis, COPD, bronchiectasis)

So in summary, it can mean absolutely nothing, or it could signify a life threatening illness…

The clinical context and sample quality are clearly key here to working out what is going on. However, in actual practice, the sputum sample often arrives into the laboratory without any clinical details, so we are processing blind.

“Just do your stuff, and give us the result…”

So how should we manage this problem from a laboratory point of view?

Here are a few potential solutions:

  • Reject sputum samples for culture where the Gram stain shows lots of squamous epithelial cells representative of oropharyngeal contamination. (A lot of labs have now adopted this approach, including my own)
  • Report susceptibilities routinely on Staphylococcus aureus from hospitalised (& cystic fibrosis) patients only.
  • Add a comment saying that close clinical correlation is required in the interpretation of this result & susceptibilities will be available on request only.

or all of the above…

The clinical context is always important for the laboratory to issue a correct report. However, for sputum samples growing Staphylococcus aureus, it is absolutely critical.

Or one could be even stricter, and just say, “no clinical details, no test”…


“Time Out”


We have been implementing some quite big processing changes in the microbiology laboratory recently with significant effects on users. Examples include making clinical details pre-requisite for selected sample types, and restrictions on the use of faecal occult blood (FOB) testing for symptomatic patients. The changes closely follow best practice guidelines, but  have proved unpopular with some people. Sometimes politics plays a part, for others it is the inconvenience of having to justify laboratory requests. Occasionally it is just a general reluctance to embrace change…

This confirms to me what I already knew, that you just cannot please everyone all of the time…

And nobody likes to be told what to do. I should understand that. I hate it more than most!

Sometimes in the past few weeks it has felt like that the world is against me. At these points it is definitely worthwhile taking a step back, reminding yourself of why the changes were implemented in the first place, and trying to gain as much peer support as possible.

I have also improved somewhat at convincing others of my point of view. This is something I have always been notoriously weak at. I have learnt that “face to face” meetings are undoubtedly best for this, emails are the worst, with telephone calls somewhere in between…

In short, you need to show people that you are human.

In trying to get things done and make progress, I have also been learning that there is a very delicate balance between “unilateralism” and trying to get consensus from everyone by collaboration. You will never get agreement from everyone, but there does need to be a “critical mass” of believers in order to carry and enforce policies.

There is little doubt that a couple of years ago, I would have buckled under the pressure, reversed the changes and gone back to my lab cubicle with my tail between my legs.

My skin has become a little thicker…

I have definitely learnt to see past the initial pain, and to visualise the long-term quality gains that have been made within the department, and for the clinical microbiology service as a whole.

These things take their toll however over the weeks and months… When working on such issues without a break, both the stress and exhaustion levels build slowly over time. The two terrible twins form a synergistic relationship.

But there is light at the end of the tunnel!

Next weekend I am going on a 5 week road trip with the family across the USA, from LA to NY.

It couldn’t have come at a better time… I can forget all about the microbiology laboratory for a while, the incessant phone calls and emails, the complaints, the politics, and the bureaucracy. I can concentrate on my life outside of the microbiology lab and recharge the batteries.

And hopefully when I get back I will still want to be here!