Tag Archives: clinical microbiologist

“When the patient and the microbiology lab don’t agree”

I am signing out blood culture results. A patient has an E. coli resistant to amoxycillin clavulanate (augmentin) in both their blood culture and urine specimen. I ring up the patient’s doctor to see how the patient is doing. The patient is currently on augmentin but is nevertheless feeling much better, has been switched to oral augmentin and is ready to be discharged home. Hmm… What should I do? Should I change the antibiotic or am I just treating myself rather than the patient…?

Or the patient who develops a post-operative wound infection and they get treated empirically with flucloxacillin, to which they “respond” well, becoming afebrile and the wound discharge dries up. A swab of the wound then grows an MRSA. Should they complete their course of flucloxacillin or should they switch to an antibiotic to which the MRSA is susceptible to?

The joys of being a clinical microbiologist!

These scenarios have a few possible explanations:

  • Some patients will get better from infections, even bacteraemias and septicaemias, whatever you have used to treat them. Not all patients who contracted infections in the pre-antibiotic era succumbed to them.
  • Just because an antibiotic has tested resistant in the lab does not mean there will be no clinical response. Lots of other factors come into play here, e.g. dosage and pharmacokinetics, penetration into site of infection, host immunity, etc.
  • The isolated pathogen is not actually the cause of infection.

Clinical microbiologists are often left in a difficult situation here. Do they listen to the laboratory telling them that the isolate is resistant to an antibiotic, or do they listen to the clinician telling them that the patient is better. And what happens if they listen to the clinician and then the patient takes a turn for the worse…

It is almost a no-win situation. Is it any wonder that older, more experienced clinical microbiologists like myself end up becoming slightly insane!

These scenarios, or something similar happens to me every few weeks. It is not often discussed how to approach this situation, and it is probably glossed over somewhat in clinical microbiologist training. I was certainly never trained how to deal with it. In fact it could even be regarded as something of a taboo subject…

I think the answer lies in a case by case approach, taking into account the type of infection, the pathogenicity of the organism, the degree of resistance to the antibiotic, the reserves of the patient and how unwell they were on presentation, and a multitude of other factors that cannot possibly be learned from a textbook.

There is a lot of science in microbiology, but sometimes experience, intuition and common sense count even more than knowledge. Antimicrobial susceptibility results are important, but they are not the whole story by any stretch of the imagination.


Apologies for the paucity of posts recently, a combination of busyness and laziness!


“The Charlatan Microbiologist”

I still get a little nervous every time my work phone rings…

Will it be a question that I am unable to answer? (I get a few of these)

Will it be a complaint about a result or some aspect of laboratory policy. (I get quite a few of these as well..)

Or will it just be a standard “bread and butter” clinical enquiry where the answer is engrained in my cerebellum?

Fear of the unknown…

I am not very good at remembering the 3rd line treatment for recalcitrant giardiasis.

I am not very good at thinking on my feet, especially in a stressful situation.

and I am not very good at documenting all the clinical advice I give out.

Sometimes I feel like a bit of a fraud…

But then I remember the things I am good at.

I am good at building relationships with clinicians and gaining their trust.

I am good at turning the conversation from “result interpretation” into “patient interpretation”

I am good at diffusing complaints with a healthy dose of empathy and a bit of Irish charm.

I am good at knowing when and who to ask if I have a difficult microbiological problem.

On reflection, I am not completely useless.

Maybe we are all charlatans in some respect. We all have limits to our microbiological knowledge, our patience, our energy reserves.

And it is good to remind ourselves that it is often the non-microbiological aspects of our job that are the most important…


“A decade as a microbiologist in New Zealand”

"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….