Tag Archives: clinical details

“Taking the crap out of enteric microbiology”

The Art of Microbiology, ,

Just because a stool sample turns up at your microbiology laboratory, it doesn’t mean you have to test it… This is old style microbiology reasoning, testing for everything in the hope that you will find something!

There are many different microbiology tests that one can do on a stool sample. Here is a sample list of what is offered at the lab I work at:

  • PCR for common bacterial pathogens, e.g. salmonella, campylobacter, shigella, VTEC, yersinia.
  • Culture for more opportunistic bacterial pathogens such as Aeromonas
  • EIA for cryptosporidium and giardia
  • GDH/PCR for C. difficile toxin
  • Faecal concentration and trichrome stain for ova, cysts and parasites
  • Immunochromatographic assay for rotavirus
  • Multiplex PCR for other enteric viruses (e.g. noro, astro, sapo)
  • Faecal antigen test for H. pylori.

With appropriate clinical details present, we can then choose objectively from the list above which tests are appropriate to perform for a specific sample.

However, without clinical details, it would be utterly unreasonable for the lab to do all of these tests, and without clinical details there is no way of deciding which tests we should be doing.

Yet so many microbiology labs still take this approach. Receive a stool sample and test it for something! This is blindfold microbiology.

Extending this philosophy further, clinical details of “diarrhoea” doesn’t really cut the mustard either. That is to some extent stating the obvious!

Fit healthy adults who present with a short history of diarrhoea in general do not require laboratory testing. Personally I get 2 or 3 episodes of loose stools every year. I am sure the rest of the world has a similar experience! I do not need laboratory testing. So clinical details simply of “diarrhoea” or “loose stools” is insufficient to justify testing. There needs to be more than that…

The lab I work at will only test stool samples if one of the following applies, even when clinical details of “diarrhoea” or something similar is on the form:

  • Something to indicate an illness on the more severe end of the spectrum, such as prolonged diarrhoea, bloody diarrhoea, hospitalised, systemic symptoms, etc.
  • Or something that suggests there might be a public health issue, e.g. food handler, group meal, overseas travel, farm worker, etc.

“Carte blanche” approaches to enteric microbiology are hideously costly, and also give rise to quality issues such as overdiagnosis and overtreatment.

If you test every stool sample you receive for putative pathogens such as Blastocystis hominis or Dientamoeba fragilis, you are going to end up overdiagnosing and overtreating a whole heap of people. Don’t go there!

By taking a considered and objective approach to microbiology testing of stool samples you can dramatically reduce the amount of testing that you perform, and increase the quality of results at the same time.

Michael

 

“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

“The Requesting Pyramid”

Future of Microbiology, The Art of Microbiology,

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