Tag Archives: PCR

2026: The NZ Year of the “RAT”

The Art of Microbiology, The Science of Microbiology, , , , ,

In 2026 we have seen the widespread adoption of Rapid Antigen Tests (RATs) for the diagnosis of Influenza A&B, RSV and SARS-CoV-2 in Emergency Departments, Acute Receiving Units and Paediatric Wards, in many hospitals throughout New Zealand.

The main drivers have likely been both PCR costs and quicker time to result using RATs,  with the acceptance that one must sacrifice a degree of result sensitivity when doing a RAT instead of a PCR. There is some evidence that the RAT result can act as a surrogate for the degree of transmissibility of the pathogen at the time of testing. i.e. Negative RAT=relatively low viral load=low risk of onward transmission.

And in New Zealand, it has been a baptism of fire for these “QuadRATs”… After very little winter respiratory virus activity in NZ up until the start of August, we have had a massive spike of Influenza cases, probably the biggest in many years. (See PHF Science Resp Illness Dashboard).

How have the RATs fared with this avalanche of Flu Cases? Fairly well, by and large. We are certainly seeing plenty of positive results, allowing rapid clinical management. We have had a little bit of push back from clinicians where patients have tested negative by RAT and then positive by PCR, but this result scenario is not at all surprising. When you use a test with sub-optimal sensitivity on a population with very high underlying prevalence of disease (as it is for Influenza at the moment), then your negative predictive value is always going to be low (see this article). So a negative result will certainly not always mean absence of infection.

One potential issue has been “capturing” the QuadRAT results to provide local surveillance data. Because these tests are performed outside the laboratory, collating the results to provide local surveillance data on respiratory virus activity has been problematic. Hopefully a solution will be up and running soon.

Another thing to consider with RATs (not just respiratory QuadRATs), is how to put a Quality Assurance Framework around the testing, something we are well used to doing in the lab environment. There are several different commercial QuadRATs available in NZ, each with slightly varying performance. When the test “leaves” the laboratory it becomes more difficult to control the performance of the test. Hence the importance of Point of Care Testing (POCT) coordinators to oversee this area.

About 15 years ago, when PCR started becoming more routine in mainstream diagnostic laboratories, I spent quite a bit of time persuading clinicians to switch from Influenza and RSV RATs over to PCR testing. Now I am doing the exact opposite! Swings and roundabouts.

Many jurisdictions in NZ have jumped on the (quad)RAT bandwagon for respiratory virus testing. The story of the Pied Piper of Hamelin is a reminder that blindly following a tune without asking where it leads does not always have a happy ending. However, we now have multiple different testing modalities at our disposal for winter respiratory viruses; multi-plexed RATs, fast turnaround PCRs, multiplex PCRs, etc. The key is to find a diagnostic algorithm that plays to the strengths of the different assays, keeps both the clinician and the lab happy, and most importantly, works well for the patient…

Michael

 

 

“The Molecular Revolution”

Confessions of a Microbiologist, Future of Microbiology, , ,

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?

Michael

“Ageing methodology”

The Science of Microbiology, , , ,

The laboratory detection of verotoxin/shigatoxin producing E. coli (sometimes called enterohaemorrhagic E. coli) has caused much grief for diagnostic microbiology laboratories over the decades. It is a relatively nasty infection, and it can cause bloody diarrhoea in a good proportion of patients. In a small minority it can cause severe complications such as Haemolytic Uraemic Syndrome (HUS) or Thrombotic Thrombocytopenic Purpura (TTP).

Diagnosis was initially centred on the culture of E. coli 0157 which can produce verotoxin/shiga toxin.

SMAC (Sorbitol MacConkey) agar plates were all the rage in the 1990s, taking advantage of the fact that E. coli 0157 does not ferment sorbitol. 

How lucky is that?

These were soon replaced by the more selective CTSMAC (Cefixime Tellurite Sorbitol MacConkey), with the cefixime and tellurite inhibiting other annoying non-sorbitol fermenters such as Proteus Spp.

The only problem is that E. coli 0157 is not the only E. coli serotype that can produce verotoxins. Lots of other E. coli serotypes are capable of doing this as well, e.g. 0111, 026, 045, 0145, etc.. As time passed, and our understanding of the infection improved, it became very apparent that a very significant proportion of VTEC induced diarrhoea was actually not due to E. coli 0157.

How inconvenient…

Nevertheless, CTSMAC plates were now entrenched in laboratories. And it was better than nothing.

As the years passed,  alternative methods came onto the scene.

ELISAs used for “direct” VTEC toxin detection in stool were employed in some labs in the early 2000s. At least they detected non-0157 associated disease, but sensitivity remained an issue when used directly on samples. They were not widely adopted by diagnostic laboratories.

Chromagar plates have also been developed to pick up the main VTEC serotypes. A little pricey however, and still need follow-up work for confirmation.

Then came PCR, and more recently multi-plex PCR, not only detecting (the toxins of) VTEC, but all the other common gastrointestinal pathogens as well.

In the molecular age, CTSMAC plates are starting to look a bit dated. What was seen as  modern methodology a generation ago no longer cuts the mustard.

As we move through this transition period for VTEC detection there is a real mish-mash of different VTEC methodologies used in laboratories worldwide. I don’t think this messy situation will last. In a decade or so I suspect 90% or more of microbiology laboratories will be using molecular methods for VTEC detection (and everything else stool related).

However at the moment, there are still plenty of CTSMAC plates being manufactured worldiwde. We still (guiltily) use them at our lab, as we continue to work out how to afford molecular testing for enteric pathogens…

But now they are used in the knowledge that they will clearly not pick up all VTEC strains in the patient samples, or anywhere close.

CTSMAC plates are getting old, and I for one can’t wait to see the back of them…

Michael

Note that the Infectious Diseases Society of America has just brought out updated guidelines on Infectious Diarrhoea, including quite a bit of detail on VTEC/STEC. Apart from the incorrect spelling of diarrhoea, they are very good!

I will add them to the guidelines section of this website also.