Category Archives: The Art of Microbiology

“Taking the crap out of enteric 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

 

“Workflow trumps Fancy Tests”

I happened to be visiting a microbiology lab in a large teaching hospital last year. We were shown all the assays they used to rapidly identify a pathogen from positive blood cultures: PCR assays, FIuorescent In-Situ Hybridisation (FISH). They had the works!

The range of tests available was very impressive, and would be the envy of most diagnostic microbiology laboratories.

But there was a catch… At 8pm in the evening, the microbiology department shut up shop and everybody went home. The blood culture analyser stood there completely untouched until 8am the next morning, including any bottles that flagged positive during this time.

So a blood culture that went positive at 9pm would be sitting in the analyser for at least 11 hours before any attempt was made to identify the pathogen.

This got me thinking!

It actually doesn’t matter that much how many fancy assays you have, or how much money your laboratory has. If you can’t get your workflow right then it all becomes a bit academic.

I am a big proponent of 24/7 staffing of microbiology laboratories, or at the very least the processing of positive blood cultures being done 24/7. It is after all one of the most important samples in the microbiology department. We have plenty of lesser importance!

Turnaround times generally don’t just include the actual analysis of the sample. More often than not, it includes storage time, transport/courier time, registration time, verification time, etc.

And then the final result has to be both received and acted on by a clinician. This communication step is also vitally important. There are so many steps, pre-analytical, analytical and post-analytical that contribute to the total turnaround time.

It is useful to do intermittent vertical timeline audits of your critical samples, to see where the delays are occurring, and then sort these out first before you consider fancy assays. And often such delays can be sorted without having to spend a lot of money. It might just be a case of relocating a blood culture analyser, or adding an extra courier run…

I am not against fancy assays, they have their place, but only as part of the whole process…

Michael

“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…

Michael