Category Archives: Confessions of a Microbiologist

Building the CDC in your community

I am not referring here to the Centre for Disease Control, which is a great resource which I use often to look up things I should know anyway, but don’t.

I am referring to the acronym “Clinical Details Culture”, an equally important CDC in my mind.

At the laboratory I work in, we have just implemented a mandatory clinical details policy for all microbiology samples. The only exceptions are those “difficult to obtain” samples taken from sterile site areas. For everything else, if there are no clinical details supporting the testing, then no testing is performed by the laboratory.

Now when I sign out a list of microbiology results I have clinical details on each and every request form. This is wonderful! In a good percentage of cases it changes both the testing and reporting of results. In other words the quality of results being produced has improved. And no longer will I get staff complaining to me that there are no clinical details on forms!

This has not been an easy policy to implement. Even after several months of preparation, there have been a few (almost inevitable) teething  problems which have had to be worked through. One key area is ensuring that all the staff members assess the clinical details provided in a consistent and standardised fashion. This has involved a lot of protocol development and these protocols are still in a process of evolution. For example “Erythema and increased pain leg ulcer” are acceptable details whilst “chronic leg wound” is not, and then there is the myriad of word variations in between. It is not straightforward!

Although most of the clinicians have been supportive of such a policy and indeed have embraced it by including excellent clinical details, there remains a small cohort who refuse to believe that the inclusion of clinical details on microbiology request forms is important. There are a few others that believe in the policy in principle but have concerns over the logistics.

The goal over the next year or so will be to continue to build a clinical details culture amongst clinicians so that clinical information on microbiology forms (and all laboratory request forms) is the expected norm. This represents a positive step for all the involved stakeholders; clinicians, laboratory staff and patients alike.

Along the same lines I hope that many other diagnostic microbiology laboratories both nationally and internationally adopt a similar stance. The presence of clinical details is a key element of effective diagnostic stewardship. Without them, you are already on a hiding to nothing…

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