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

 

 

“Are we too protective of new antibiotics?”

Antimicrobial Resistance, Antimicrobial Stewardship, Confessions of a Microbiologist, ,

By reserving new antibiotics for the sickest of the sick and for the most resistant of resistant organisms, are we essentially making them commercially non-viable?

To be honest I am not really surprised that pharmaceutical industries do not want to invest in development of new antibiotics. Such drugs will only be necessary for a small proportion of the population and unlike many other drugs (e.g. cardiac, arthritis drugs) will only be given for a short duration (i.e. 1-2 weeks).

And then, as antimicrobial stewards, we make matters even worse by insisting that these antibiotics need to be fiercely protected in order to prevent or at least delay the development of antimicrobial resistance.

The consequence of this is that any new antibiotic needs to be priced at ridiculous levels to even have a chance at being commercially viable. Hospitals and governments baulk at such prices and subsequently the new antibiotic becomes almost impossible to get hold of. Industry then has to charge even more to make a return, and thus, a vicious cycle is started.

Have a look at the list of new antibiotics from 2000-202 below:
  • 2000: Linezolid (Zyvox) — The first oxazolidinone, a new class effective against vancomycin-resistant enterococci (VRE) and MRSA.
  • 2003: Daptomycin (Cubicin) — The first lipopeptide approved for skin and skin structure infections.
  • 2005: Tigecycline (Tygacil) — First glycylcycline, a derivative of minocycline designed to overcome resistance.
  • 2010: Ceftaroline fosamil (Teflaro) — First cephalosporin with activity against MRSA.
  • 2011: Fidaxomicin (Dificid) — A macrocyclic antibiotic for Clostridioides difficile.
  • 2012: Bedaquiline (Sirturo) — First diarylquinoline for multi-drug resistant tuberculosis (MDR-TB).
  • 2014: Dalbavancin (Dalvance) & Oritavancin (Orbactiv) — Lipoglycopeptides for acute bacterial skin and skin structure infections (ABSSSI).
  • 2014: Tedizolid (Sivextro) — A second-generation oxazolidinone.
  • 2014: Ceftolozane/tazobactam (Zerbaxa) — Cephalosporin/β-lactamase inhibitor combination.
  • 2015: Ceftazidime/avibactam (Avycaz) — Novel β-lactamase inhibitor combination for serious Gram-negative infections.
  • 2017: Meropenem/vaborbactam (Vabomere) — Combination targeting carbapenem-resistant Enterobacteriaceae (CRE).
  • 2017: Delafloxacin (Baxdela) — An anionic fluoroquinolone with activity against MRSA.
  • 2017: Ozenoxacin (Ozanex) — Topical quinolone.
  • 2018: Plazomicin (Zemdri) — Next-generation aminoglycoside.
  • 2018: Eravacycline (Xerava) — Novel synthetic fluorocycline.
  • 2018: Omadacycline (Nuzyra) — Aminomethylcycline for pneumonia and skin infections.
  • 2018: Sarecycline (Seysara) — Tetracycline for acne.
  • 2019: Cefiderocol (Fetroja) — Siderophore cephalosporin for MDR Gram-negative infections.
  • 2019: Lefamulin (Xenleta) — First systemic pleuromutilin for community-acquired pneumonia (CABP).
  • 2019: Pretomanid — Nitroimidazole for extensively drug-resistant TB (XDR-TB)

Then work out how many antibiotics on this list are available for use at your local hospital? In my local hospital in New Zealand, I could comfortably count on one hand the number of antibiotics from the above list that are available for me as a clinical microbiologist to recommend without multiple barriers to prescribing. The majority are just not available in New Zealand at all…

I would argue that increasing the range of antibiotic classes that are available for use is much more important than restricting the use of new antibiotics.

I am not claiming that we shouldn’t have good antimicrobial stewardship, of course we should. Neither am I claiming that antimicrobial resistance to new antibiotics will not develop if we use them, of course it will. However, if we have more classes of antibiotics available, then one would expect classes that are used infrequently over a certain time period to recover a degree of susceptibility.

I think we need to be encouraging the use of new antibiotics so that they are sufficiently used to get an idea of their efficacy, and so that any developing resistance can be effectively monitored.

If we reserve new antibiotics only for when there are no other options available, then in a country like New Zealand, we might only be using them a few times each year.

We need to be somewhat less zealous in our antimicrobial stewardship efforts when it comes to new antibiotics. We need to work alongside industry, not against them in maximising the range of antibiotics that are available to us. However, the goal should be sustainable use, not reckless use…

I know solutions have been proposed to the above problem, essentially allowing industry to get a return on their investment regardless of how often the new antibiotic is actually used (i.e. de-linking). I remain unconvinced by such proposals as a long-term solution, as it relies on successive governments to both prioritise and fund such initiatives.

I also know that some (possibly most!) of my colleagues will not agree with me on this particular topic. But when we sit on antimicrobial stewardship committees, we need to consider the whole picture, and not try and protect the sanctity of the new antibiotic at all costs…

Michael

“ASA Antimicrobials 2026 Adelaide”

Confessions of a Microbiologist, , ,

I was privileged to go to the ASA Antimicrobials conference in Adelaide last week. Although I have not been to this particular conference for a few years, it is one of my favourites. It is not too big, it has a good mixture of clinical microbiologists, ID physicians and microbiology scientists attending, and the quality of the talks is generally very high. there were very few talks that I did not take anything away from.

Here are a few of the highlights below:

Angela Huttner gave an excellent talk on UTI, and reminded us that the definitions of uncomplicated v complicated UTI have changed, moving more towards extent of infection within the urinary system, and away from host factors. This makes a lot of sense to me, and simplifies things a lot for the lab in terms of testing and reporting.

Angela also reminded the audience that enterococci and Group B streptococci are uncommon causes of uncomplicated cystitis in young women. Voided midstream urine culture and acute cystitis in premenopausal women – PubMed. I will need to go back to my lab and sort out suitable comments to go on enterococcal and Group B strep urinary isolates on this cohort. We almost certainly overplay their significance…

Hemalatha Varadhan informed us that they were no longer culturing central line tips at their institution in NSW, on the grounds of poor sensitivity, specificity, and the fact that it is not required for the definition of a CLABSI. Good for her I thought. If they can do it, why can’t we at our own lab. I will do some reading and have a chat to our stakeholders…

Chris Blyth presented on “newish vaccines” with a focus on RSV, meningococcal and emerging Gp B strep vaccines. He also reminded us that it is one thing to develop new vaccines, it is quite another to persuade people to get them…

Steven Tong presented an update on the legendary SNAP trial for Staphylococcus aureus bacteraemia. A good refresher, and a reminder that further evidence-based answers on SAB management issues are not far away. 

Tony Korman gave us an irreverent but highly entertaining review of 2025: The Year in Clinical Microbiology” and highlighted the debates on Twitter/X such as “Oral is the new IV”, “Shorter is better” and the CRP/ESR “Zombie tests”. Angela Huttner commented on the lack of nuance that sometimes occurs in such debates when the argument is presented in a black and white fashion. 

John Turnidge and his team gave an excellent EUCAST/AUSCAST session. It was a good reminder of the amount of work that goes into antimicrobial breakpoint setting. Tony Korman made the excellent point that implementation of EUCAST guidelines on a practical level is becoming increasingly problematic for diagnostic laboratories and that this should be taken into consideration by the EUCAST team when issuing their annual updates.

I was fortunate enough to be able to present myself at the conference, kindly invited by BD to present on diagnostic stewardship at the BD sponsored lunchtime symposium. Being an inveterate introvert, I was quite nervous to begin with, but soon settled down and got my diagnostic stewardship messages across to an audience which seemed engaged in my presentation (I think!). 

It was my first visit to Adelaide. It is a very nice place, nice climate, friendly people and quite a lot to do. Unfortunately, I did not get a chance to visit the Barossa Valley vineyards, next time hopefully!

Michael