Category Archives: The Art of Microbiology

“Time Wasters”

If you work in a diagnostic microbiology laboratory, have a look at the list below to see if there is anything that sounds familiar in your workplace:

  • Performing susceptibilities on beta-haemolytic streptococci: Beta-haemolytic streptococci are invariably susceptible to penicillins, everywhere. If the patient has anaphylaxis to penicillin documented on the request form then fair enough. Otherwise, it is all a bit academic.
  • Culturing for anaerobes in areas of the body where anaerobes live (peri-anal area, vagina, oral, gastrointestinal): This is not very wise because if you manage to grow anaerobes from such sites then it may well represent normal colonising flora.
  • Susceptibility testing where topical antibiotics are the mainstay of treatment: Ear swabs and conjunctival swabs are the classic examples of these. It is well documented that in-vitro susceptibility testing correlates poorly with clinical response to topical antimicrobials, so why bother doing them in the first place?
  • Working up individual organisms where the culture plates clearly show”enteric flora”: For superficial swabs, this is a no-brainer. But even in sterile sites, the work up of each individual organism when they clearly represent enteric flora is of little clinical value. The classic example is culture of peritoneal fluid post perforation of the appendix.
  • Culturing sputum samples where there are lots of epithelial cells on microscopy: Because if you do so, you will simply be culturing a sample originating from the mouth or oropharynx, which will bear little relation to what is happening down in the lungs.
  • Culturing for bacteria in vaginal swabs: Vaginal flora contains lots of different colonising bacteria, most of which very rarely causes problems. It is probably only worthwhile looking for staphylococci and streptococci when there has been instrumentation or trauma (e.g. post-natal). The vast majority of vaginal swabs do not need cultured for bacteria.
  • Looking for bacterial vaginosis and yeasts in vaginal swabs where the patient has no symptoms: Vaginal swabs are sent to the laboratory for lots of different reasons. Often we do not get this reason, and when we do it is often not because the patient actually has physical symptoms. Looking for bacterial vaginosis and yeasts in the absence of clinical symptoms is rarely of any value.
  • Testing for Hepatitis A IgM where the liver enzymes are normal or only marginally elevated: Acute hepatitis A infection cause transaminases (ALT & AST) to increase into the hundreds and thousands. Testing for acute hepatitis A because the ALT is noted to be mildly elevated is not a useful exercise, and may cause more harm than good
  • Testing for Epstein Barr virus (EBV) infection when the patient already has positive VCA or EBNA IgG present: A lot of EBV requests come into the lab in patients who have already tested positive for EBV in the past. Symptomatic EBV reactivation in an immunocompetent patient is rare, if such a condition exists at all…
  • Performing a CSF viral PCR  in a patient after they have been discharged: The classic example is a patient who comes into hospital on a Friday with meningitic symptoms, and a CSF examination shows a lymphocytosis. As is often the case with so many molecular departments, the viral PCR will not be performed until Monday… At which point the patient could easily have recovered and be sitting at home or in the pub completely asymptomatic.

Not only are many of the examples above a waste of time, they are also a waste of both money and staff resources.

Furthermore, in many of the cases above, processing such samples may simply give misleading results and lead to inappropriate treatment.

This is only a list of 10. It would not take too much further thought to think of an additional list of 10. In fact the list could go on and on and on…

There are some ridiculously good new microbiology assays coming on to the market nowadays. Highly sensitive and specific PCR tests which can give highly accurate results back to the clinician in less than an hour. These are quite literally game-changers in terms of altering clinical management.

How can we afford to introduce these new modern assays? Only by looking at everything we do in the microbiology department, again and again and again, and assessing whether each test/process that we perform has clinical value.

Let’s not waste time, getting rid of the timewasters…

Michael

“Testing ad infinitum”

Take for example the patient who presents with “recent weight loss”, even though their recorded weight is exactly the same as it was 6 months ago.

…or the patient who “bounds” into the surgery, looking far healthier than the doctor will ever be, and then complains of “tiredness”.

…or the patient who has diagnosed themselves with “Chronic Lyme Disease” on the internet, even though they have never travelled to an area endemic for Lyme disease.

The temptation for the clinician in such cases above is to order a whole battery of tests in order to prove to, or reassure the patient that they have no organic pathology.

The patient then leaves the clinic with a whole list of (often expensive) laboratory investigations, and thinks to themselves;

“Wow, look at how many tests I am getting. The doctor must be worried for me. I really must be sick!”

And thus the cycle goes on. The tests come back negative, but the sick role is now reinforced. The patient then often comes back for more, or goes off elsewhere to seek a second opinion…

Worse still, if enough tests are performed, then one will eventually come back falsely equivocal or positive, confusing the issue even further for the clinician. And the positive reinforcement of the sick role in the patient has just gone through the roof!

Everyone is scared of missing something, of not diagnosing that long shot… But sometimes it is best just to trust good clinical acumen, and appreciate that laboratory testing can occasionally cause more harm than good…

Michael

“The Requesting Pyramid”

In many laboratories, clinical details on request forms can be structured into a pyramid shape as below.

Let’s take the example of otitis externa.

A good proportion of request forms will be at the bottom of the pyramid, where there are no clinical details present to suggest that otitis externa is the clinical suspicion (as opposed to otitis media, cellulitis of the pinna, or some other condition). Also included in this category are cases where clinical details have been included but are unrelated to sample type, e.g. an ear swab sent with clinical details of “sore throat”. This scenario happens in all sample types with disturbing frequency… (e.g. mid-stream urine sent for a patient with clinical details of chest pain!)

The next level up in the pyramid is where clinical details are present but are insufficient to justify the sample being sent to the laboratory. For example the clinical details might state “Otitis externa“. However most patients with straightforward otitis externa do not need an ear swab sent to the laboratory. Laboratory culture of an ear swab in clinically suspected otitis externa should be the exception as opposed to the rule…

The top level of the pyramid is where clinical details are not only present, but they also give a sound rationale as to why the laboratory is receiving a sample. e.g. “Recalcitrant otitis externa not responding to topical treatment.” or “Diabetic with painful inner ear and fever, clinical suspicion of malignant otitis externa“.

This requesting pyramid applies to most different sample types and clinical scenarios.

At my laboratory, we are doing our utmost to turn this pyramid on it’s head. We have made significant progress to date. In fact our pyramid is starting to look more like a rectangle.

By the end of the year we hope to have removed the base of the pyramid altogether by adopting a policy of having accompanying clinical details pre-requisite for all microbiology tests. I.e. No clinical details, no test.

And that is the way it should be…

Michael