Monthly Archives: January 2016

“A Site for Sore Eyes”

It is not just the clinical details that are important in how a microbiology sample is worked up. It is also where the sample was taken from, as you will be perfectly aware.

However sometimes the site labelling can be a bit too “generic”.

For example an “ear swab” could potentially mean a swab from the auditory canal (i.e. in someone with otitis externae), or it could mean a swab from the skin on the outer ear (i.e. in a patient with impetigo lesions).

The same can apply to “nose swab”. This could mean the skin covering the outer nose as opposed to the inner nose or nostril.

As a final example a “penile swab” could mean a swab from the urethra or it could mean the skin on the outside of the penis.

and there are others.

But why does this matter?

You have probably worked this out already. The microbiological work up from the two different options on each “site” is completely different. We are looking for different microbes, using different media or tests, and even the reporting procedure, susceptibility testing and comments are all different.

It is therefore critical that the requestors (and sample takers as these are not always one and the same) are educated to be as specific as possible when describing the sampling site e.g. outer ear, ear canal, nostril, outer nose, urethra, penile skin, so that the scientist is in no doubt as to where the sample has been taken from so that correct processing can take place. The education needs to also explain why it is so important from a lab perspective.

Another solution is to define the sites in detail as tick boxes on the request form, but tick box request forms have their own set of problems….

The more useful the information that comes into the lab, the more useful the result is to the patient.


“The Inbetweeners”


Clinical Microbiologists, also known as Medical Microbiologists, now form part of the set-up of most clinical microbiology laboratories in the developed world. They are generally very well qualified people, most possessing a medical degree as well as post-graduate clinical and pathology fellowships. Thus they are not stupid, eccentric maybe, but not completely daft.

Their job description is sometimes difficult to define (I should know…). They are generally not clinicians, although they have a lot of clinical knowledge, nor are they technicians although again they know a lot about what happens on the benches.

They are essentially inbetweeners”.

So what exactly is the role of a clinical/medical microbiologist?

This of course varies depending on the type of laboratory and/or hospital you work in but I think the following should apply to and define all clinical/medical microbiologists:

  • Interfacing: Being able to form and strengthen the critical link between the laboratory and the clinician. This is not just about being a “result messenger”, but more importantly being able to communicate the importance/non-importance of specific results to the clinicians and along the same lines, being able to highlight the importance of particular samples to the scientists, so that time and energy can be focused.
  • Optimise use of antibiotics and the control of microbes within institutions: Better known as anti-microbial stewardship and infection control, which most clinical/medical microbiologists get involved with to a greater or lesser extent.
  • Ensure clinical appropriateness of testing: Ensuring that the tests being offered by the microbiology laboratory are the best that can be offered within the given budget, are the most clinically appropriate, and are utilised sensibly and appropriately by requestors. Clinical/medical microbiologists should also be responsible for filling in gaps in the microbiology testing profile of a laboratory and for getting rid of tests that are no longer current or best practice.
  • Guide the future direction of laboratory: Being able to outline where the microbiology laboratory needs to be in the future in terms of equipment, testing strategy and profiles offered, expected turnaround times etc.


Unlike clinicians with a list of patients, or microbiology scientists with a batch of tests, clinical/medical microbiologists may not have a lot of pre-determined tasks sitting waiting for them when they arrive at work in the morning. Thus a high degree of self motivation is necessary to address some of the “less than concrete” objectives above on a daily basis. This can be difficult when you are tired or under the weather, and at such times it can be easier when your day is mapped out for you….

Clinical/medical microbiologists overlap considerably with Infectious Diseases physicians in terms of their knowledge, but at the same time it is important to acknowledge that each group also possess distinctive skill sets. Will the “inbetweener” speciality of clinical/medical microbiology survive the automation of the microbiology laboratory? For my sake, I hope so, but it is important that the profession is able to accurately define itself, so that it can continue to fill a niche, and to serve a useful purpose.


“The Shopping List”

shopping list

Take the following hypothetical list of laboratory tests:

  • FBC
  • U&Es
  • LFTs
  • Thyroid Function tests
  • Hepatitis A, B & C screen
  • HIV
  • Treponemal screen
  • ANA
  • Coagulation screen
  • Complement
  • Autoantibody screen
  • EBV serology
  • CMV serology
  • Urine culture
  • MRSA screen
  • Serum lipids

In laboratories across the world, this kind of “shopping list” request form coming into the laboratory is seen all too frequently, and often without any clinical justification or rationale included.

Add up the costs of these tests and you have a total of several hundred dollars, maybe even over a thousand. A CT scan would be roughly an equivalent cost, and you would be hard pushed to get one of those without justifying exactly why you wanted it….

There may of course be a very valid reason for ordering all the tests above, although it is difficult to think of a clinical syndrome which would justify everything in the list above.

Such a list may be done as a “wellness screen”, but whether you believe in wellness screening or not, there are tests in here (EBV, CMV, urine culture for starters) which should never be part of any wellness screen laboratory testing.

Such a list may be done as a “fishing expedition” when the patient presents to the clinician with vague or ill defined symptoms. The problem is that the prevalence rates for most of these tests in such patient populations are going to be very low with the consequent problems of low positive predictive value and false positive results.

Personally I don’t believe that shopping list requests such as the above that are sent into the lab by clinicians should be permitted unless there is a clear rationale on the request form detailing why so many tests have been requested in the first place…..

Courtesy, respect, and common sense.


Of course if your laboratory is on a fee for service funding arrangement you might welcome “shopping lists” or at least turn a blind eye to them…. Personally however I have never been a great fan of shopping!