“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

 

“The Sputum Factory”

It is the peak of the (Southern Hemisphere) influenza season here in New Zealand. Influenza has come early this year, and the season has been relatively busy to date, with a fairly even mix of Influenza A&B.

And it is not just influenza, there is plenty of circulating RSV, rhinoviruses and all those other less well known respiratory viruses that we know best by their appearance on extended respiratory viral panel menus.

However it is not just GPs and Emergency departments that feel the effects of the wave of respiratory viruses during the winter season. Microbiology departments get a surge in sputum samples arriving at the laboratory. Recently it has felt like my laboratory is simply a sputum processing factory!

And this is because any microorganism which infects the respiratory epithelial cells (bacteria or viruses) will inflame the respiratory epithelial cells and increase the production of “purulent” sputum. It doesn’t matter whether it is a bacterium or virus. Can the sputum colour discriminate between the two?? Only in the textbooks…

Sputum for bacterial culture is one of my least favourite microbiology samples! This is not just because of its appearance, but more because it suffers from appalling sensitivity and specificity when diagnosing bacterial pathogens, even when a pre-screening Gram stain is performed, as many labs do nowadays.

If sputum culture was subject to to FDA approval as a “diagnostic assay”, it wouldn’t have a prayer…

During the winter season when respiratory viruses abound, the prevalence of bacterial infection in the tested population will be relatively lower, with a consequent further deterioration in positive predictive value.

There are many guidelines that show the extremely limited value of sputum culture, particularly from the community setting, for the management of non-specific cough symptoms, acute bronchitis, and COPD. The most common clinical details we receive on sputum samples are things like “Cough”, “cough with purulent sputum”, “COPD”, or simply nothing at all. Yet we still accept these samples without question.

As a profession, sometimes I think we are too soft…

My lab is planning to introduce restrictions on what sputum samples are acceptable from the community setting, according to the published guidelines, so hopefully by next winter, we will be a haven of tranquility as opposed to a sputum processing factory.

Michael

Apologies for the picture, but it had to be done!

 

“Manipulating your microbiology job…”

“New Yorker Cartoons”

I haven’t always been passionate about microbiology. As a student there were a lot of more interesting things on my mind. So it was somewhat of a surprise when I found out I was going to be a microbiologist…

None of my six children want to be microbiologists. Even my 1 year old daughter shows little interest in microorganisms! I am sure they will find their own passions in life, and I will support them, whatever they choose to do (I may draw the line at real estate however…)

So microbiology is my work passion. Or to put it another way (and more realistically), there are some areas of clinical microbiology that I am passionate about. I love the concept of diagnostic stewardship, mainly because I hate unnecessary wastage. I enjoy antimicrobial stewardship, because I don’t mind taking responsibility for my actions, and mistakes. I  find microbiology automation and molecular diagnostics fascinating, because I have always been someone who looks forward to the future as opposed to looking back at the past. I have a keen interest in the diagnosis and psychology of sexually transmitted infections, mainly because I live a sheltered life!

I quite enjoy doing data analysis, probably because I loved mathematics at school. I much prefer writing protocols as opposed to following them, likely the result of a rebellious personality. I love challenging traditional microbiological methods and processes, simply because there is so much dogma and inefficiency to challenge. And I don’t mind teaching, because I quite enjoy showing off whatever knowledge I have!

But there are plenty of things I am not passionate about with regards to microbiology. I have no interest in the 10 different carbapenemase genes most commonly found in New Zealand, because I have never been a details person. I am not much good at leading research, because I simply don’t have the patience or persistence. And I am not a big fan of meetings because I am not a great talker. I also believe in the mantra that the productivity of any committee is inversely proportional to the number of members it contains. 

There are usually many facets to a job in microbiology, whether you are a technician, scientist, or clinical microbiologist. You can be sure that you won’t love them all. I don’t believe anyone loves absolutely everything they do on a daily basis. Lucky for them if they do. 

I think the key is to slowly but surely manoeuvre, or fashion your job, into one where the majority of stuff you are doing each day are things you are passionate about. This may involve volunteering to take extra pieces of work on, but also actively seeking to drop things you have no interest in. It is a long process, but one we should approach conciously.

There would be no point in me spending the majority of my days doing research or sitting in tedious committee meetings. That would drive me insane.

If you can spend two thirds of your working day doing things you love doing, you are not too far off the mark.  Have you managed to manipulate your job into one you love? The alternative of course is to get another job, but often exactly the same principles apply. Every job has lots of different facets. We cannot possibly love them all…

Michael