Category Archives: Confessions of a Microbiologist

“A Question of Significance”

We may not always realise it, but reading and reporting bacterial cultures often involves several decisions, which are often performed sub-consciously. What do we work up on the agar plates? What do we report? How do we report it?  Do we perform and report susceptibilities? Should we add a comment to the report? All these decisions influence how the result is perceived and acted upon by clinicians. Don’t underestimate the influence that the microbiology report can have on how the patient is subsequently managed.

For example, let’s say we receive 5 theatre samples from a patient undergoing a routine prosthetic joint revision, and 1 of the 5 samples has a light growth of Staphylococcus epidermidis. If we report this out with antibiotic susceptibilities, and without a qualifying comment, there is a decent chance that the orthopaedic surgeon will act on this result and the patient may well end up on several weeks of antibiotics. On the other hand, if we suppress the susceptibilities, and add a comment stating. “This result is of doubtful significance. Clinical correlation is required. Antibiotic susceptibilities are available on request.”, then it is very likely that the surgeon will simply note the result and observe the patient.

On the other hand, if we isolated a Cutibacterium acnes from a shoulder aspirate in a patient with a history of rotator cuff repair, then it is likely that this isolate is significant and we should convey the result as such, along with antimicrobial susceptibilities.

Best of all in these cases of course is to liaise directly with the requestor/clinician/surgeon, so that further clinical details can be obtained, the likely significance can be better ascertained, and a subsequent management plan developed. However, this is not always possible, nor practical for every single patient.

Whilst I always encourage pragmatic reporting, one needs to be aware of the potential consequences of reporting something as a likely contaminant. I.e. What if this organism is genuinely causing infection? What are the likely consequences for the patient if it has not been reported as such? Can we obtain further samples for culture to confirm or negate the initial result? With sterile site samples & blood cultures, obviously the stakes are higher than with a simple wound swab, but the same principles apply for both scenarios.

Over-reporting of organisms on agar plates is often driven by inexperience or fear. I have seen it many times in my career. Scientists and clinical microbiologists alike are responsible for ensuring that over-reporting of results is minimised. This is very much a team game. In particular, colonies thought to represent plate contamination should hardly ever make it on to the laboratory report. Along the same lines, when an obvious pathogen, e.g. Staphylococcus aureus is found on a mixed plate, to what extent should the other organisms be worked up and reported. If a plate is clearly growing a mixture of enteric organisms, you need a very good reason not to report it as mixed enteric flora, and leave it at that.

The “easy way out” for the microbiology scientist and the clinical microbiologist is to report everything that is found on the plate along with antimicrobial susceptibilities, and then let the clinician make head or tail of it. However, this is dumbed down microbiology and often leads to sub-optimal management of the patient.


“Ten things I have learnt from conferences”

I have recently returned from back-to-back overseas conferences in Scotland and Ireland, along with the more important business of visiting family in between. Here are a few of my thoughts and observations from attending (microbiology) conferences:

  • I am immensely privileged. To be able to travel overseas and attend educational conferences is a real privilege. It combines my love of microbiology and my passion for travel. It is certainly something I never take for granted. I feel privileged, but definitely not entitled.
  • I am not the only introvert. Looking around the conference hall, it is easy to see I am not the only introvert in the room. I am not the only person that finds it difficult to speak to complete strangers whilst sober. For introverts who don’t know many people at the conference, talking to industry reps at the booths is an option, as at least you then have an excuse to strike up a conversation.
  • Industry presentations should be taken with a grain of salt. Whilst it is fine to chat to industry reps, care must be taken when attending industry sponsored presentations. One must always remember that the company is paying for the privilege of holding this presentation, and at the end of the day they are trying to sell you something. So, the chances of listening to a completely unbiased presentation is really quite slim. Don’t get me wrong, you can certainly learn stuff at industry presentations, but one should always keep in the back of your mind “What is the underlying agenda here?”
  • Doctors are generally quite posh. The clipped and well-polished accents. The confident voices & mannerisms…  My recent conferences reminded me that by and large, doctors come from well-to-do backgrounds and may not have that much in common with the patients they are treating. This has been an issue ad infinitum, and is still a work in progress.
  • People generally know a lot more than myself. The older I get, the more I realise I don’t know, and this is highlighted by conference presentations where I find myself saying to myself, I should have known that, but I didn’t. I realise that the presenter may have specialist knowledge in the area of their presentations, but there is nothing like a good conference to make me feel like a charlatan.
  • Post-graduate research presentations are fiendish. Post-grad research presentations, usually on PhD work, are often complex, esoteric and well beyond my intellect.  Very occasionally, one comes along where the concepts are explained really well. Most, however, are a hard listen.
  • It’s all about location, location, location. There is no shame in saying that I choose conference locations in order to combine a visit to family, or to visit somewhere I really like, or to see somewhere I have never been to before. Obviously, the conference has to be relevant to your specialist field, but if you are somewhere that you really want to be, you are more likely to learn more.
  • You don’t need to attend every talk. Big international conferences are often multi-day, 7am-7pm marathon affairs, with over 20 presentations a day. Few people, and certainly not me, can focus for this length of time, day after day. Pick talks you really want to attend and go to them. Along the same lines, look for time blocks where the topic content is not so relevant to you, and take some time out.
  • Nobody cares what questions you ask. Even introverts like myself should pluck up the courage to ask a few questions during a conference. It adds to your knowledge, and helps you remember the presentation. Even if you feel the question is not important enough for the occasion, trust me, no-one really cares what questions you ask. People have better things to worry about.
  • Onsite conferences will be around for a long time to come. To those people who thought the COVID pandemic would spell the end of onsite conferences, sorry, you are very much mistaken. People like to connect, to travel, to do something different. That is why onsite conferences will be around for a long time yet.


“Vanquishing VRE”

I am the master of false assumptions…

When a hospital close by was affected by a VanB VRE outbreak, I suspected that my local hospital would be relatively immune, due to its smaller size, different patient cohort and relatively strict antimicrobial stewardship policies.

Of course, my assumptions were wrong! It didn’t take long for the VRE to gain a foothold locally as well. (I am simply carrying my poor form on from the COVID pandemic, where I also made several false assumptions…)

MDRO rates in NZ are relatively low compared to many parts of the world. Even though I work in a reasonably big laboratory covering a population of approximately 500,000, up until recently we could go a whole year between VRE isolates! It has therefore been a bit of a shock to see them appear on an almost daily basis over the past few months, fortunately all from rectal screening samples.

Enterococci are hardy bugs and survive well in the environment, necessitating meticulous cleaning with high-level disinfectant to minimise the risk of onward transmission. Despite our best efforts to date, we have struggled to get on top of the outbreak.

However, the news is not all gloomy. All our isolates so far have been from screening samples, and we have yet to see any clinical infections. Can you really call it an outbreak if you don’t have any clinical infections? Personally, I find it difficult to get excited about something like this unless the patients are clearly unwell.

The laboratory I work in serves secondary level care hospitals and we don’t have many of those highly immunocompromised patients with lots of lines in-situ who tend to run into problems with VRE. Our annual number of Enterococcus faecium bacteraemias is low and it may be that we will not end up with many VRE clinical infections even if it does become endemic.

VanB VREs are still amenable to several different treatment options such as linezolid, teicoplanin, daptomycin, etc. In terms of the MDRO spectrum, VanB VREs are on the milder end, at least on a population level. I would be a lot more worried about a CPE outbreak in the hospital.

It is also a good reminder to us that we cannot afford to relax in the field of antimicrobial stewardship. VREs are in particular selected out by the “3Cs”, namely (3rd generation) Cephalosporins, Ciprofloxacin and Carbapenems. We do well in controlling usage of the first two, maybe not so hot on the carbapenem front.

At the moment we are still trying to “stamp out” VRE from our local hospital. The financial cost and staff time involved in managing a VRE outbreak are not insignificant by any means. At some point, one needs to weigh up the cost-benefit analysis of an eradication approach…