Category Archives: Confessions of a Microbiologist

“Vanquishing VRE”

Confessions of a Microbiologist, ,

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…

Michael

 

“The dying art of traditional microbiology”

Confessions of a Microbiologist,

 

I had the opportunity to visit a food microbiology laboratory a few weeks ago. It was clearly a good laboratory with excellent quality assurance measures, but it was interesting to visit a microbiology lab that did not have a MALDI-TOF platform in place. The lab still relied very much on traditional identification techniques for identification such as colonial morphology, Gram stain, oxidase, catalase, and of course the API biochemical strips!

This made me reminisce about my training days in microbiology in Glasgow back at the turn of the century, when we still used Kohn’s tubes for Salmonella & Shigella identification, X and V discs were used for Haemophilus influenzae, and the CAMP and Reverse CAMP test were used for Streptococcus agalactiae and Clostridium perfringens respectively.

Nowadays, in most clinical diagnostic microbiology labs, everything just gets “thrown” on to the MALDI-TOF platform and an ID is usually forthcoming. In the rare occasions that a “Maldi” ID is not obtainable, one can always send the isolate for 16s/18s RNA sequencing.

It is a changed world, and all the mystery has disappeared..

There are of course very good reasons for clinical microbiology labs to move to MALDI-TOF identification. It is fast, mostly accurate and cost-efficient when utilised in a mid to large sized laboratory. It is also probably safer in terms of risk of laboratory-acquired infections.

But it is a little bit dull, tedious even. I do miss the old-fashioned methods, their variety and their idiosyncrasies. It also gave staff a good grounding in the basic principles of microbiology and bacterial identification. Most new staff that start in medical microbiology laboratories these days will be unfamiliar with anything else apart from MALDI-TOF.

Traditional diagnostic microbiology is a dying art, and the labs that still practice it are becoming fewer by the year. 

I am by no means a luddite, and I am all for progress, but I don’t think the recent technological advances have necessarily made us better microbiologists, or made the job more enjoyable…

Michael

 

“Linchpins and why you should avoid being one”

Confessions of a Microbiologist, ,

For seven (long) years I was the only clinical microbiologist in the laboratory I work in. Most of the important decisions in the laboratory rested on me. This made me feel important, even a little indispensable. I got to call the shots, and pay negotiations were straightforward! For a while I was even reluctant to ask management for assistance because I did not want to share my high level of responsibility.

But such a set-up is never good for the laboratory itself. I was on-call 24/7. When I was on leave, the clinical microbiology service suffered. Although I thought I was making the best management decisions for the patients I could never be sure as I had no peers to obtain feedback on my actions, nobody to bounce ideas off, and most importantly no-one to learn from.

Now I have two consultant colleagues and a registrar in place. I can be away from the lab for days/weeks and normal service will continue quite happily without me. If I am unsure about a microbiological problem (most days), then I can “phone a friend”. I am now part of a team, as opposed to being a linchpin.

New Zealand is a small country with a population of around 5 million people. As such, there are only a small number of clinical microbiologists (around 20). Laboratory services are fragmented with a mixture of public and private providers and there are still some lone clinical microbiologists who are working in relative isolation. We need to create better networks and regional services so we are all working as a team together.

The same principles apply within the microbiology lab itself. It might be a nice feeling to be the only one who can read dermatophyte slopes, the only person who can troubleshoot a molecular testing platform, or the only individual who can perform a particular microscopy stain. But if you are the only one, then it is a terrible position for the lab to be in, and they need to take remedial action to rectify this.

There is no place for linchpins in microbiology, even if our egos might tell us otherwise…

Michael