“The Molecular Revolution”

Time to get back to some writing “post” COVID!

When I started at the laboratory I currently work at in New Zealand in 2007, we only did one molecular assay, a chlamydia PCR, and we did this with separate extraction and amplification platforms on an open bench, with all sorts of potential for contamination. And we were/are not a small lab, a sizeable regional centre, processing well over 1000 microbiology samples a day.

2007, it’s actually not that long ago…

Fast forward 15 years and everything has changed. We now have a very sizeable menu of molecular assays performed on a range of different platforms. CSF, respiratory virus and GI panels, gonorrhoea, trichomonas, HSV/VZV,  HIV, HBV &HCV viral loads, Legionella spp., Mycoplasma pneumoniae, C. pneumoniae, C. difficile to name just a few. We even have a Mpox PCR!

A lot of these assays are now on commercial platforms that perform both the extraction and amplification steps in an automated fashion in a closed environment, essentially allowing placement of the platform anywhere, and can be run by most of our staff. The results are often available within a few hours of the sample being received in the laboratory.

In summary, the clinical service we can now offer is vastly improved from 15 years ago. I suspect it is much the same in many diagnostic labs throughout the world.

The big question is what will happen in the next 15 years? Will high volume sample types such as throat swabs, vaginal swabs, sputum samples, all still culture based at my lab, succumb to the revolution and go molecular? It is entirely possible that this will be the case. It will probably come down to cost first and foremost. Personally I see throat swabs switching to molecular very soon.

And what place will there be for whole genome sequencing in the diagnostic lab? That is a whole other question in itself but there are quite a few labs now in NZ who have acquired Nanopore Minions and are now “playing” with them in the areas of Infection Control and metagenomics.

My prediction is by 2030, for most diagnostic microbiology labs, their molecular department will be bigger than their traditional culture-based bacteriology department…

What do you think?


8 thoughts on ““The Molecular Revolution”

  1. We had been running MRSA through molecular until covid. Throughput limitations meant we went back to culture for those samples.

    Capacity trade offs may be a potentially interesting dilemma in the future.

    1. Very true. COVID put exceptional demands on molecular departments which led to some rationalisation/rationing in our department also..

  2. Haha, nothing wrong with the good old days, that was our first adventure into PCR testing. Won’t be long and lab staff won’t know what a bacteria looks like on a plate, it’s odour, preference or idiosyncrasies for growth etc, and will only have the internet etc for reference. I don’t know about Nanopore Minions but am sure by 2030 there will be plenty of Minions supervising in the microbiology department. Merry Christmas Michael.

  3. Hallo Michael! Reading from you again was a very pleasant surprise!
    Well, although I recognise that the future is inevitably molecular, I am a little bit sceptical about it.. In the lab I work at (rural area, Greece), costs are appreciable for now, in some cases prohibitive (for example, 200 euros/test for GI).. Furthermore, I wonder : is it really cost effective surching for trichomonas molecularly, rather than microscopically? can we be sure that the Salmonella we detected by PCR in stool specimen is the real pathogen here and it is not just a case of an old post-infection carrier? I really do not know..

    1. Hi Vassilios. Some of the high high volume molecular assays on high throughput platforms are now really cost effective, e.g. Chlamydia/Gono/Trich triplex. I.e. much the same cost as traditional methodology if not cheaper. I agree with you however on the hyper-sensitivity issues. I often see this for STEC positives on patients with chronic diarrhoea. I will write about this next week!

  4. I wish we can keep in mind for the “Gartner Hyper Cycle” (without leading by nanopore or illumina companies) and Dr.Maximum Bloomfield’s article is worth of a read, ‘
    Molecular testing for viral and bacterial enteric pathogens: gold standard for viruses, but don’t let culture go just yet?’. :O)

    1. I had to look up the “Gartner Hype Cycle”, had never heard of it!
      I think throat swabs are next for the chopping block as far as culture goes…

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