“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….





I get the occasional anxious phone call from clinicians concerned about the “rising rates ” of trimethoprim resistance to E. coli…

Not being entirely convinced, I did a (20 year) search for E. coli resistance to trimethoprim at my lab, analysing over 2 million isolates, and came up with the following graph.



I couldn’t work out how to insert a trendline into the graph (I am so useless…), but I think you will agree that it is going to be fairly flat.

The antibiotic apocalypse is not arriving in New Zealand anytime soon. In fact the whole concept of “antibiotic resistance” as perceived by the public is horribly generic and oversimplified…

This example above of course is just one microbe/antimicrobial combination out of many hundreds that could have been analysed, but the observation did highlight a couple of things to me:

  • If antibiotic usage is relatively constant in a population over a prolonged period of time, then antimicrobial resistance does not necessarily rise inexorably. (q.e.d.)
  • Always back your claims up with objective data wherever possible. It is the trends which are critical in the surveillance of antibiotic resistance. We are lucky that at my lab we can now search back through 20 years of electronic data. Before 1996 the data was paper based (and likely lost in a basement or incinerated by now!)

If you did a similar exercise for all the possible microbe/anti-microbial combinations (I just might if the Christmas holidays are quiet!), you will find some trends that are upwards, some that are static, and some where the resistance rate is trending downwards.

A bit like Twitter really….

So when someone says to you. “Antibiotic resistance is increasing all the time. In 10 years time, all infections will essentially be untreatable” (I really detest this type of generic, off the cuff, unsubstantiated statement…)

…you should respond with something along the lines of “Exactly which microbe and antimicrobial combination are you talking about?” and “Show me your data…”.

Some infections will be, and already are, untreatable (mostly due to extreme and focused selection pressure), but the chances of a whole bacterial species becoming pan-resistant are remote. There are two main reasons for this. i) Bacteria survive in open systems, and ii) Bacteria need to expend energy to become resistant.

But these are other stories altogether…


“Creating a rod for your own back”

la34808Treatment of sexually transmitted diseases in most places in the world is empiric in nature, based on the presenting clinical syndrome of the patient. A generation ago, the laboratory diagnosis of STDs was fairly rudimentary. No NAAT testing, viral culture and serology only for HSV, etc. Add this to the fact that getting some of the patients back for a second visit isn’t always easy and it is easy to understand why the Sexual Health community have traditionally gone for this model of care.

However things are changing, and changing fast… 

Our ability to accurately diagnose STDs has increased markedly over the past decade. C. trachomatis, N. gonorrhoeae, HSV are now all routinely diagnosed by NAAT testing in most laboratories. “Emerging” organisms such as Mycoplasma genitalium are now coming onto the radar of STD clinicians, primarily because we can now diagnose it…

Whilst empiric treatment works (most of the time anyway), it does have its downsides. Empiric therapy on a population basis usually leads to overtreatment. Resistance to N. gonorrhoeae has reached worrying levels for both fluoroquinolones and ceftriaxone. Resistance of M. genitalium to macrolides has been increasing, most probably in areas where azithromycin is used empirically for urethritis.

We need to be careful we don’t create a rod for our own back…

It may be that Sexual Health needs to start exploiting the progress in laboratory diagnostics that has been made over the past few years and start moving away from empiric based management of STIs. Some NAAT tests are now available (e.g. Cepheid CT/NG) that can give a result in around 90 minutes. Thus it could theoretically be possible to see the patient, take the samples, send the patient away for a coffee, test the samples in the clinic with an automated benchtop PCR analyser, and see the patients back in an hour or two with the results and directed management.

This might well be the future of STD clinics…




Clinical Microbiology, like many areas of medical practice these days is becoming increasingly dominated by guidelines. This is generally a good thing. They are usually evidence based where possible, and written by people who know (or should know) what they are doing.

However guidelines are not perfect for the following reasons:

  • They are generic:- Not every case can be covered in guidelines, so generally only the most common scenarios are covered. More uncommon diseases/presentations are often free of guideline interference!
  • They are conservative:- Guidelines are generally not radical in nature. If a guideline is followed and things subsequently go pear-shaped then the authors will not want anything too radical within the guideline in case there are legal implications. This is especially true for guidelines which rely on expert opinion. If you feel your patient needs a radical solution/treatment, then guidelines are not necessarily the best place to look.
  • They are cohort specific:- Guidelines usually originate from specific areas, and are often based on specific patient cohorts, so they may not apply to your particular patient cohort.
  • There may be conflicts of interest:- Guidelines may be written with other agendas at stake in addition to patient care. Cost, acceptability by the public and political agendas may all contribute to producing guidelines that are sub-optimal from a patient perspective.

As Healthcare professionals we are coming under increasing pressure to follow guidelines. However too much reliance on guidelines might stop us considering patients as individuals, with specific problems and specific solutions.

Is it ok not to follow guidelines sometimes?

In certain circumstances yes, absolutely, but I strongly believe that one must understand the rules fully in order to break them properly.

“Learn the rules like a pro, so you can break them like an artist”   (Pablo Picasso)


Please note my tech savvy son is setting up a Microbiology Matters YouTube channel for me so I can record some irreverent microbiology videos! Will keep you posted on this over the next couple of weeks…


“Too much knowledge…”


A little bit of knowledge can be a bad thing. So can too much…

The acronym  ESCHAPPM ( or something similar) will be familiar to most microbiologists. (a similar acronym SPICE, is sometimes used instead)

  • Enterobacter spp.
  • Serratia spp.
  • Citrobacter freundii
  • Hafnia spp.
  • Aeromonas spp.
  • Proteus spp.
  • Providencia spp.
  • Morganella morganii

Because we are clever microbiologists, we know this group of organisms may have inducible beta-lactamase activity, and we advise the clinicians of this, often provoking a reflex switch in anti-microbial therapy to carbapenems. Not only clinicians, but there are plenty of ID physicians who make this automatic transfer to carbapenems the moment the word ESCHAPPM is mentioned, my hospital included.

The thing is however, do all patients with infections by an ESCHAPPM organism require a carbapenem?

Almost certainly not…

If we use a carbapenem for every infection due to one of these organisms, then this amounts to a significant amount of carbapenems. This is therefore an important an important antimicrobial stewardship issue. We are supposed to be trying to decrease the use of broad spectrum antibiotics, not increase them.

But we have read the textbooks, and we are clever…

And yet, if we look at the literature, there is very little evidence to support the theoretical dangers of using a beta-lactam in such patients. In fact, there are several small studies out there that support the non-inferiority of beta-lactams in such patients, particularly in non-life threatening illnesses.

Not to mention there are other options out there, fluoroquinolones, sulphonamides, etc.

We are simply scared.

Here is what I generally do (rightly or wrongly):

  • In a patient with bacteraemia due to an ESCHAPPM organism, as long as they are clinically improving I am happy to continue therapy based on the phenotypic susceptibility results.
  • In patients with UTIs due to ESCHAPPM organisms, even if in hospital, I feel no need  whatsoever to move to carbapenems.
  • I reserve carbapenem use in “ESCHAPPM” patients to bacteraemic patients who are getting worse, and also for patients with chronic infections, e.g. prosthetic joint infection, on the rationale that the longer the treatment, the more chance you have of getting clinically relevant inducible beta-lactamase activity.

We need to take a more pragmatic approach to ESCHAPPM organisms and their treatment. We also need larger scale trials so we can be more confident in our decisions and adopt such approaches into guidelines.

and we need to be brave…