Monthly Archives: August 2017

“The Knee Aspirate….Telling stories”

Confessions of a Microbiologist, ,

We receive a lot of knee joint aspirates into our laboratory. But often we don’t know the story as to why the sample has been taken and sent to us…

  • …It might be a elderly patient with a knee replacement who has gradually decreasing mobility over the past 6 weeks.
  • …It might be a young sex worker who has an acutely swollen hot knee with associated fevers.
  • …It might be a middle aged male with a history of recurrent gout.
  • …It might be a patient who got a prosthetic joint inserted a couple of weeks ago and now presents with a discharging wound and fevers.
  • …It might be a patient with osteoarthritis who got a steroid injection into their knee joint a couple of weeks ago and it is now red and painful.
  • …It might be an aid worker who has just returned from working in Sub-Saharan Africa for two years.

or it might be something else altogether.

Who knows? Unfortunately not always the microbiology laboratory.

There are so many ways in which the “story” that comes with the sample can affect the microbiological processing:

  • Whether additional tests in addition to standard culture are indicated?
  • Whether a Gram stain and/or crystal microscopy is performed?
  • What incubation conditions are used (aerobic/CO2/anaerobic) for the culture plates?
  • Which culture media are set up on the sample?
  •  Whether the culture isolates are deemed to be significant or not.
  • Whether susceptibility testing should be performed, and what antimicrobials to test against?
  • Which culture isolates should be reported to the requestor?
  • Which antimicrobial susceptibilities are released to the requestor?
  • Whether an interpretative comment is added to the report, and what the comment should entail?

If we recieve a sample into the microbiology laboratory which has no clinical details on it, then we return the following comment to the requestor:

“No clinical details have been received with this specimen. The lack of clinical information provided to the laboratory represents a potential clinical risk. In the absence of clinical details, optimal test and media selection, susceptibility testing, and result reporting cannot be guaranteed by the laboratory.”

By the end of this year we hope to have introduced a policy of mandatory clinical details in order for laboratory testing to proceed. However, “critical” or “difficult to get” samples such as knee aspirates are always going to have to be exceptions to such a policy. We cannot reject a knee joint aspirate, just because we don’t know the story behind it…

This is a bit of a shame really because ironically it is these types of samples where the clinical details can potentially have the biggest impact on microbiological processing.

And there will always be a small minority of clinicians that will grumble at having to put clinical details on the request form.

Such grumbles are for me however, simply water off a duck’s back…

Michael

“Are you doing what you should be doing?”

Confessions of a Microbiologist, ,

If you are a microbiology scientist and spend a good chunk of your day setting up samples and aliquoting urines, you should be worried. I am sure you didn’t go and spend 4 years in university in order to do this.

If you are a clinical microbiologist and spend a good chunk of your day signing out/authorising routine urine and wound swab results, you should be worried. You didn’t achieve multiple degrees and other qualifications to do this day in day out…

If you are a microbiology technician, and spending a good chunk of your day unpacking boxes and carrying stuff around the lab, you should be worried. Someone off the street could easily come and do this…

And if you are a microbiology lab manager and find yourself spending a good chunk of your day on the bench, you should be worried. Old habits die hard, and who then is managing the lab?

Of course we all need to do things occasionally that we are over-qualified for, or that is not specifically in our job description. But when such tasks are taking up a large proportion of our jobs, we need to take a close look at ourselves, and what we are actually doing from day to day.

We need to make absolutely sure that we are performing tasks that justifies both our position and our qualifications. If we are not, then we need to do something about it.

If you spend most of your day doing something that is likely to be automated a few years down the track you should be concerned. But if you are doing lots of  things daily that could be getting carried out by someone else less qualified, you should be even more worried.

It is easy to get very comfortable when you fall into one of the categories above “This is easy money, I can do this with my eyes closed, there is no need to change anything.” It’s a dangerous mindset to get into however, because in my experience, such scenarios as described above are never left hanging indefinitely in the long term…

Diagnostic medical laboratories are businesses nowadays, and employers are always on the lookout for ways they can get the same job done for less money.

And they are very good at it…

Michael

 

“Time Wasters”

The Art of Microbiology, ,

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