Category Archives: Confessions of a Microbiologist

“COVID-19 at the bottom of the world”

We have all become amateur epidemiologists… “Epidemic curves, flattening the curve, attack rates, etc.” We know all the lingo now, and we all have an opinion..

I am lucky enough to live in the beautiful country of New Zealand. With regards to COVID-19, New Zealand has some inherent advantages. It is an island, 3 hours flight from anywhere else in the world, not that anyone is flying these days. Auckland aside, it is also relatively sparsely populated. In addition to these natural advantages, it also has a very good Public Health system and tight border controls.  People coming into New Zealand are now required to self-isolate for 14 days. All these factors added together are probably why New Zealand has been fortunate enough to avoid widespread community transmission to date. As of today (17th March), there have only been 11 cases of COVID-19 in New Zealand and all the cases have been directly related to overseas travel.

So Kiwis are watching with some anxiety the skyrocketing COVID-19 numbers from Europe and elsewhere in the world, along with the “lockdowns”, the school closures and other drastic measures to try and “flatten the curve”. And we in New Zealand are left wondering just what is in store for us…

In my opinion, the most likely scenario is that we (NZ) will eventually get community transmission, but probably not at the same transmission rates as we have seen in mainland Europe, giving us a flatter but possibly more prolonged epidemic curve, i.e. a “slow burner” of an outbreak.

Next most likely is an outbreak with a fast rise in numbers, a high peak and a rapid decline induced by herd immunity, giving the classic bell-shaped epidemic curve. This scenario would stretch our Healthcare resources to the limits and beyond.

It is probably wishful thinking that New Zealand could completely avoid a COVID-19 outbreak, whilst the rest of the world suffers, although this is not completely implausible. The chances of this happening are reduced further by the fact that our nearest neighbours, Australia, have just had approximately 70 cases in the past 24 hours, so they are “off and running”, so to speak…

If we do manage to stay COVID-19 free in the community, the downside will be that we have a population in New Zealand with no immunity and which will therefore continue to remain vulnerable to a COVID-19 outbreak into the future. This scenario could potentially lead to prolonged travel restrictions both in and out of the country and may not be the ideal outcome that it first looks like on paper.

The worst thing is actually not knowing what is in store for us. We really know very little about this virus, so we are essentially in uncharted territory with regards to disease modelling and management. Public Health decisions globally are being made more on expert opinion as opposed to any strong evidence base, and during a pandemic, everybody becomes an expert, including the politicians!

So all we can do in New Zealand is wash our hands and wave at each other, watch the politicians look increasingly rattled day by day,  check our bank accounts as our pension savings fall through the floor, and wait and see what happens in this unfolding drama.

Due to their geographic isolation, Kiwis are a resilient people. Recent events such as the Christchurch earthquake, the Mosque shootings and the White Island volcano eruption has only hardened the national psyche further. NZ will cope with whatever scenario is played out, and we will recover quicker than most!

Michael

(These views are my own, and do not necessarily represent those of my employers or children.)

“The Paradox of COVID 19 and ECCMID 2020”

ECCMID is probably the biggest microbiology and ID conference in the world, attracting over 12000 delegates, and is being held this year in Paris, in six weeks time.

ECCMID seems like the ideal forum to discuss COVID19, bringing together a lot of the world’s experts, and may even lead to breakthroughs or at the very least, research collaborations on how to answer questions regarding the infection.

The only problem is that you are going to have 12000 people from all over the world meeting in the one place! This is hardly conducive to minimising the risk of coronavirus transmission, with a potential risk to both the attending delegates and also to the areas they will return to.

As of today, there have been 285 confirmed cases of coronavirus in France, the numbers having climbed significantly in the past few days. The French government have banned all public gatherings of more than 5000 people in closed spaces. However it is not known whether ECCMID will be an exception to this ruling.

The ECCMID organisers have been conspicuously quiet with regards to whether the ECCMID conference will go ahead this year. This conference is now big business, with a huge exhibition hall and representation from hundreds of infection related industries from around the world. Furthermore, thousands of delegates have booked travel and accommodation for a week in one of the most beautiful cities in the world, many of whom will be enjoying their yearly junket!

There are an awful lot of people with a vested interest in seeing this conference go ahead…

Personally (and purely by chance) I am not planning to go to ECCMID this year,  but I look on with considerable interest at whether this mega-conference goes ahead, and if it does, how will the organisers justify this decision in the current environment?

Michael

Building the CDC in your community

I am not referring here to the Centre for Disease Control, which is a great resource which I use often to look up things I should know anyway, but don’t.

I am referring to the acronym “Clinical Details Culture”, an equally important CDC in my mind.

At the laboratory I work in, we have just implemented a mandatory clinical details policy for all microbiology samples. The only exceptions are those “difficult to obtain” samples taken from sterile site areas. For everything else, if there are no clinical details supporting the testing, then no testing is performed by the laboratory.

Now when I sign out a list of microbiology results I have clinical details on each and every request form. This is wonderful! In a good percentage of cases it changes both the testing and reporting of results. In other words the quality of results being produced has improved. And no longer will I get staff complaining to me that there are no clinical details on forms!

This has not been an easy policy to implement. Even after several months of preparation, there have been a few (almost inevitable) teething  problems which have had to be worked through. One key area is ensuring that all the staff members assess the clinical details provided in a consistent and standardised fashion. This has involved a lot of protocol development and these protocols are still in a process of evolution. For example “Erythema and increased pain leg ulcer” are acceptable details whilst “chronic leg wound” is not, and then there is the myriad of word variations in between. It is not straightforward!

Although most of the clinicians have been supportive of such a policy and indeed have embraced it by including excellent clinical details, there remains a small cohort who refuse to believe that the inclusion of clinical details on microbiology request forms is important. There are a few others that believe in the policy in principle but have concerns over the logistics.

The goal over the next year or so will be to continue to build a clinical details culture amongst clinicians so that clinical information on microbiology forms (and all laboratory request forms) is the expected norm. This represents a positive step for all the involved stakeholders; clinicians, laboratory staff and patients alike.

Along the same lines I hope that many other diagnostic microbiology laboratories both nationally and internationally adopt a similar stance. The presence of clinical details is a key element of effective diagnostic stewardship. Without them, you are already on a hiding to nothing…

Michael