Category Archives: The Art of Microbiology

“We’ll see what we can do…”

You might be familiar with the following phone calls to the microbiology laboratory:

  • “I know you only have 0.1ml of CSF left at the lab. Can you still do a viral CSF panel for me?”
  • “Although (I swear) the blood culture was from Mr X, the bottles were accidentally labelled as Mrs Y. Can you still process it?”
  • “The patient is currently on erythromycin for a chest infection. Please can you test the E. coli in the patient’s urine against this antibiotic?”
  • “Regarding that stool sample that we sent to the laboratory five days ago. Can we now check it for C. difficile toxin?”
  • “My patient has a mixed growth in her urine. Can you check to see if everything that you have grown is susceptible to augmentin?”
  • “Sorry I sent the B. pertussis PCR swab in the wrong transport media. Would you process it nevertheless?”

We’ll see what we can do….

We often get requests to do something in the laboratory which is either simply inappropriate or has a good chance of producing a sub-optimal result. This might be because of inadequate sample volume, transport delays, labelling errors, wrong sample type, etc. etc.  Because we want to be nice, because we want to keep everybody happy, we often pander to such requests. However by doing so we compromise the quality standards in the laboratory, with potential harm to that all important end user, the patient.

And we also set a precedent for further such requests…

The staff working in the microbiology laboratory are the key gatekeepers of a high quality service. If a sample or test is unacceptable for whatever reason, they should have the authority to reject/refuse it, and this authority should be backed up to the hilt by lab managers and pathologists.

It is only by doing this consistently that high quality standards become the norm within the department. And what’s more, laboratory users soon learn that future requests of a similar nature will be futile. With time, laboratory users will increasingly understand why you take this approach.

So instead of saying “We’ll see what we can do,” we should be replying “Sorry we are unable to do this.” to such requests.

Occasionally this might provoke a grumble or even a complaint. I have had my fair share!, but trust me, such complaints are completely ungrounded and never go very far. If you don’t receive the odd “complaint” from time to time, you probably aren’t doing your job properly.

When it comes to test quality, ensure your microbiology laboratory is both strict and consistent in its messages, and the respect will come…



“Choosing wisely bacteriology II: Swabs from the peri-anal area”

There is so much scope for “choosing wisely” in general bacteriology, it is difficult to know where to start…

Peri-anal swabs are rarely of value in changing patient management. That is primarily because you are swabbing an incredibly “dirty” area in the first place. You can be sure that your peri-anal area will almost inevitably grow mixed enteric flora on culture. That is completely normal. It is no reflection on your personal hygiene!

So as a result the following swabs have very dubious microbiology value:

  • Swabs from peri-anal abscesses:- The very fact that you can swab a peri-anal abscess means that it is either self-discharging or has been intentionally incised. Either way the patient should be well on the way to recovery. And you will probably grow mixed enteric flora. On occasion, antibiotics may be indicated if there are systemic symptoms such as a fever, or there is extensive erythema surrounding the abscess. If an antibiotic is used, then it should be necessarily relatively broad spectrum, covering staphylococci, streptococci, anaerobes, and enterobacteraciae. The swab result rarely impacts on the choice of antibiotic.
  • Swabs from sacral ulcers:- This condition has the double whammy of not only being chronic, but is also in the peri-anal region. Rarely, if ever, does a superficial swab from a sacral ulcer change management. A well taken punch biopsy might…

We still accept such swabs at my laboratory, although sometimes I wonder if we are just encouraging poor practice.

Maybe we are just too nice…

We do however put a comment on all such swabs stating the following: “Superficial swabs from the peri-anal area are generally contraindicated. These swabs often grow a mixture of enteric flora, and are unhelpful in making clinical management decisions.”

I like report comments. Unlike one off educational material,  report comments offer continuous feedback to the lab user and can hopefully induce a change in culture over the long term.


“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…