Tag Archives: clinical microbiology



Clinical Microbiology, like many areas of medical practice these days is becoming increasingly dominated by guidelines. This is generally a good thing. They are usually evidence based where possible, and written by people who know (or should know) what they are doing.

However guidelines are not perfect for the following reasons:

  • They are generic:- Not every case can be covered in guidelines, so generally only the most common scenarios are covered. More uncommon diseases/presentations are often free of guideline interference!
  • They are conservative:- Guidelines are generally not radical in nature. If a guideline is followed and things subsequently go pear-shaped then the authors will not want anything too radical within the guideline in case there are legal implications. This is especially true for guidelines which rely on expert opinion. If you feel your patient needs a radical solution/treatment, then guidelines are not necessarily the best place to look.
  • They are cohort specific:- Guidelines usually originate from specific areas, and are often based on specific patient cohorts, so they may not apply to your particular patient cohort.
  • There may be conflicts of interest:- Guidelines may be written with other agendas at stake in addition to patient care. Cost, acceptability by the public and political agendas may all contribute to producing guidelines that are sub-optimal from a patient perspective.

As Healthcare professionals we are coming under increasing pressure to follow guidelines. However too much reliance on guidelines might stop us considering patients as individuals, with specific problems and specific solutions.

Is it ok not to follow guidelines sometimes?

In certain circumstances yes, absolutely, but I strongly believe that one must understand the rules fully in order to break them properly.

“Learn the rules like a pro, so you can break them like an artist”   (Pablo Picasso)


Please note my tech savvy son is setting up a Microbiology Matters YouTube channel for me so I can record some irreverent microbiology videos! Will keep you posted on this over the next couple of weeks…


“Why bother?”


White_square_with_question_markWhy bother doing a diagnostic test on a patient if there is no specific treatment?

That question is certainly very plausible now. For example multiplex respiratory PCRs are available which diagnose a whole range of respiratory viruses, in real time, for which no specific treatment is available. Ditto that for enteric viral PCRs.

There are a few possible retorts…..

When the diagnosis is established:

  • it may prevent further unnecessary investigation.
  • it may prevent further unnecessary treatment.
  • it may allow earlier discharge.
  • it may have infection control implications (isolation, cohorting etc)

It is a simple and fundamental question. However we often think of the answer in simplistic and fundamental terms.



“All samples are equal but some are more equal than others…”

Most samples that arrive into the microbiology laboratory are processed. However there are some where the clinical usefulness of the result must be almost negligible.

Let me give you a few examples…

Swabs of boils that have just been lanced. It is the lancing (draining of pus) which will almost certainly lead to the infection being cured. Much the same applies for peri-anal abscesses.

Swabs of chronic ulcers, including pressure sores. These will almost certainly be colonised by bacteria. Even if a “pathogenic” organism is isolated, it is impossible to say what it means in this setting.

Culturing drain fluids from drainage bags where the drain has been in for more than 5 days. Whatever bacteria are growing in the drainage bag will bear little relation what is growing in the collection that the fluid has come from.

Swabs from ears where the history is of a straightforward otitis externa. Outer ear canals grow all sorts of junk which rarely means much in this clinical setting.

Samples from long term urinary catheters where urine has become cloudy or smelly. This demonstrates that urine has become colonised with bacteria which will always happen eventually when a catheter is in situ. Usually an indication to change the catheter.

Follow up urines after a urinary tract infection has been treated. Rarely indicated, except in pregnancy, pre-urological surgery and in transplant patients. Treat the patient, not the laboratory result.

and the list goes on….

I suspect samples from the above list make up a good 20% of the daily workload of a microbiology laboratory.

But how do you police it?

Not easily. Probably needs a combination of the following:

  • Education of Laboratory Users: Grand Rounds, Clinical Updates etc etc
  • Feedback in the form of a comment added to the test report where the test looks to be unjustified.
  • An insistence on clinical details supporting a rationale for the test.

Regarding the last point, I think the establishment of electronic ordering, which is now starting to come into many labs, may facilitate this, effectively making it impossible to complete test ordering without a supporting clinical rationale for the test.

We process most microbiology samples that come into the lab because it has always been done this way. However with the health budget becoming ever tighter, it is time for the laboratory to move from being the passive recipient and start becoming the gatekeeper for what should be done and what should not.

Think how much time it would free up with at least 20% of the workload gone, and also with the knowledge that the vast majority of specimens that you were working on were genuinely important….


On another topic altogether, click here for an interesting article on looking for anti-microbial substances on the seabed, a good place to look in my opinion.