Tag Archives: enteric processing

“Perfect is the enemy of good (microbiology)”

The Art of Microbiology, ,

This quote attributed to Voltaire (“Le mieux est l’ennemi du bien”), rings true to me. I have never been a perfectionist, and the idealistic pursuit of perfectionism can hinder real-life achievement and progress. 

The quote came back into my conciousness during the early days of the COVID pandemic when I listened to a great speech by Dr Mike Ryan from the WHO when urging countries to act quickly in the face of the rapidly developing COVID situation.

Of course, such a concept can also apply to the microbiology laboratory.. Here are a few examples:

Protracted work-up of samples: When a sample arrives into the microbiology laboratory, the clock is ticking. In relentless pursuit of isolating that fastidious bacterium, time passes by and before you know it a week has passed… The clinical usefulness of a microbiological result is inversely proportional to the time spent to produce it. In the hospital setting, the average length of stay is 3-4 days… Excessive time spent on certain samples is not only a waste of resources, it also generally does nothing for the patient. Get a result out, even if it is not the perfect one that you are striving for.

Excessive work-up of samples: The classic example of this is identifying every bacterial isolate in a mixture of enteric flora. For the most part, such an exercise is futile, even when isolated from a sterile site. Enteric flora isolated from sterile sites usually represent a source control issue, and who knows what the pathogen might be in the mixture, if any. Such practice is generally a waste of resources, and reporting individual isolates along with individual susceptibilities is time-consuming and often leads to poor antimicrobial stewardship. Working up bacteria within a mixture of enteric flora might be “technically perfect” but does little to help the patient.

Excessive testing protocols: A good example of this is stool samples arriving into the microbiology laboratory. There are many microbiological tests that one can do with a stool sample, culture, PCR for bacterial & viral pathogens, microscopy for parasites, C. difficile testing, the list goes on. However, to perform all the available tests on every stool sample in the hope of maximising the odds of isolating a pathogen would be incredibly expensive, but in most cases would do little to change patient management. Enteric testing should very much be tailored depending on what is on the microbiology request form.

I am sure there are many other examples that one could think of. Perfection in the microbiology laboratory is very much a pipe dream, and can actually be detrimental to good patient care. We cannot possibly hope to identify all potential pathogens in every sample and do it in a timeframe that is beneficial to the patient. We need to move past our fear of missing something…

When developing testing methodologies or reviewing individual patient samples, we should always be asking ourselves “By doing what we are doing, are we providing overall value to the patient?” 

Michael

 

 

“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

 

“Messy and Clean”

Future of Microbiology,

(Apologies for the paucity of posts recently, has been difficult to find the time…)

Processing by the traditional way is a messy business – Not just literally, but metaphorically as well.

Think about it.

Numerous different tests, lots of different agars, enrichment broths and sub-culturing, different incubators, wet films(that is if you believe in them, I don’t), C. difficile testing algorithms (everyone does it different), parasite concentrates and stains, EIAs.

Lots of labour and bench space required, a large skill mix, and truckloads of QC.

The list goes on.

And all for tests, some of which are not actually that sensitive at diagnosing the pathogen…

It is thus no wonder that laboratories are so keen to adopt multiplexed molecular methods for enteric testing. One test, one person, one run, one set of results to interpret. In other words it is clean.

Molecular processing of enteric samples has been difficult for some labs to justify on the grounds of cost. However traditional methods have so many hidden costs associated with them. It is important to dig them all out for the business case.

In the home environment I am not a very tidy person, but I love a clean laboratory…

Michael