Monthly Archives: December 2016

“The Fishing Expedition”

Confessions of a Microbiologist,

As a clinical microbiologist I occasionally get asked to recommend suitable microbiology tests for a patient, e.g. a returned traveller with a fever, a patient with encephalitis, an immunocompromised patient with CXR changes, etc., etc.

It is always tempting to show off, and display whatever knowledge you have of exotic and peculiar diseases, and give to the requestor an exhaustive (and exhausting) list of investigations to carry out…

There are however a few things to reflect on before constructing such a list:

  • Common things are common:- It is important to exclude all the common diagnoses, before considering the more unusual causes of the patient’s symptoms. Returned travellers get flu as well…
  • Familiarity leads to competence:- Laboratories are not as good at testing for conditions which they don’t see that often, with the consequent increased likelihood of a false negative or a false positive result. Trust me, you would not want me trying to diagnose your sleeping sickness..
  • The laboratory can’t be perfect all the time:- If you request sufficient tests on the one patient, then the odds are you will eventually generate a (false) positive result.
  • For each test, think about pre-test probability:- The more exotic your test requests become (“long shots”), the lower the pre-test probability and  positive predictive value.

Fishing expeditions need planning and experience. I also prefer a staged approach… “If tests A & B are negative, only then consider tests C & D.”

And whilst on a fishing expedition, don’t forget to treat the patient…  There will always be a proportion of patients where you will never get the diagnosis, no matter how hard you try. In the midst of an “investigative frenzy”, don’t forget to cover for the most common and most serious differentials.

No patient was ever cured by investigation alone…

Michael

Just to let you know that the Microbiology Matters website has now accumulated 200,000 “visits” since its inception in 2013. It may be some time however before it reaches a million!

 

“Keeping it simple or keeping it accurate…”

Antimicrobial Resistance, The Science of Microbiology, , ,

Let’s say you are a clinician and you are looking at two different microbiology results on two different patients (A&B). Both have an E. coli UTI. Both results state that the E. coli is susceptible to trimethoprim. However what you don’t know is that the E. coli isolate on Patient A had a trimethoprim disc diffusion zone of 18mm (right on the EUCAST breakpoint), whilst for patient B the corresponding zone was a much more comfortable 26 mm.

And who knows, if you repeated the same testing on patient A a dozen times, the chances are you would have a few “non-susceptible”results, due to the natural margin of error of the test.

If I was a clinician, and had this extra (zone diameter) information, I would be a lot happier prescribing trimethoprim to patient B, even though they both have in-vitro “susceptibility” reported on the result. (The same principle of course applies if we were talking about Minimum Inhibitory Concentration (MIC) values instead of zone diameters.)

But do clinicians really want this extra information?

They are usually very busy, …and not particularly interested in microbiology.

In my experience all clinicians generally want to know is if an isolate is susceptible or resistant. They are not particularly interested in the details, with the exception of blood culture and sterile site isolates, when there is at least a modicum of interest in the degree of susceptibility or resistance.

So which is better.. a susceptibility result full of information, but potentially difficult to understand and interpret, or a result reduced to its simplest form.

There is no right answer of course…

I am not even convinced antimicrobial susceptibility breakpoints have a long term future.

More and more, year by year, the anti-microbial susceptibility committees (EUCAST, CLSI) are trying to take into account antibiotic dose,  renal function, degree of infection, etc. when setting antimicrobial breakpoints.

But they are really only scratching the surface…

Time for some major disruption!

Michael

“A decade as a microbiologist in New Zealand”

Confessions of a Microbiologist,
"There are worse places to work than the Bay of Plenty, NZ"
“There are worse places to work than the Bay of Plenty, NZ”

It is now 10 years since I started working as a Clinical Microbiologist in New Zealand. When I first arrived here from the UK, young, fresh faced and a little naive, I never dreamed I would still be in the same job 10 years later. For someone as restless as myself, 10 years is a Herculean effort, even if it was intersected by a 6 month sabbatical in Paris…

A lot has changed in my workplace over that decade. Paperless processing, laboratory mergers, Maldi-Tof technology, new laboratory buildings and the introduction of Kiestra TLA have made it an interesting and challenging period.

Outwith work, but within microbiology, I have enjoyed creating this website, and writing the book “The Art of Clinical Microbiology”. I just wish I had a bit more time to better develop and market these personal projects…

Likewise outside of microbiology, life has been equally eventful. Over the last decade, my family has grown from 3 to 7, one of whom needed emergency open heart surgery to successfully  correct a congenital heart condition. Running, travelling and learning French have been my other passions in my spare time. New Zealand is a beautiful country, which I have enjoyed getting to know.

I have a lot to be thankful for…

The 10 years in New Zealand have passed quickly. When you think about it, a decade is a big chunk of your life. I find it difficult to get used to the fact that I am no longer a “young” clinical microbiologist. Most days I reflect on where I am and where I am going.

I have aged somewhat in the last 10 years… I have become more streetwise, my skin has got thicker, and I am definitely more prepared to take risks. However I still love to daydream and create. I still have that rebellious streak in me and I like to do things a little bit differently from everyone else. I am still very much of a loner. Maybe I am becoming a middle-aged existentialist!

The world of Clinical Microbiology in New Zealand is a small one. New opportunities are not abundant. The politics can be difficult, with laboratory services here tendered out to private providers on a contractual basis. Worldwide, the whole practice of microbiology is changing quickly. The ability to direct that change to some extent locally is absolutely key to keeping my notoriously low boredom threshold under check.

I love change. 

Where will I be in 10 years time? Who knows? Hopefully still alive, maybe even still a clinical microbiologist. 20 years in the same job would really be pushing the boundaries of my sanity, but I might hang on for a year or two yet….

Michael