Category Archives: The Art of Microbiology

2026: The NZ Year of the “RAT”

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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

 

 

“Too much information”

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Can the microbiology lab give too much information to the clinicians?

Take the following hypothetical example regarding reporting of enteric type organisms:

Patient X presents with acute appendicitis with perforation. They are taken to theatre for appendicectomy and peritoneal washout, and started on IV cefuroxime and metronidazole. The sample of peritoneal fluid is returned from the microbiology lab as being “mixed enteric flora”. the patient recovers well, and they are discharged after 3 days on oral co-amoxiclav to complete a 1 week course of antibiotics.

Patient Y presents with acute appendicitis with perforation. They are taken to theatre for appendicectomy and peritoneal washout, and started on IV cefuroxime and metronidazole. However, in this patient, the microbiology lab decides to work up the individual organisms in the peritoneal fluid sample. The report states that the patient has grown an ESBL E.coli, an Enterococcus faecium, a Pseudomonas aeruginosa and a Candida albicans. Even though the patient is recovering well, the clinician feels obliged to cover the organisms that the micro lab has grown and reported, and changes the antibiotic therapy to meropenem, vancomycin and fluconazole. The patient unfortunately develops a bout of Clostridium difficile diarrhoea (!), extending their hospital stay by a week.

Microbiology labs can get very nervous about reporting “mixed enteric flora” from sterile site samples. They really shouldn’t be.

Here are a few pointers as to when it may be reasonable for the microbiology laboratory to report “mixed enteric flora”

  • Non-sterile site samples:- almost always
  • When several organism types are present- the number of different microorganism types present in a sample is inversely proportional to the value the lab can provide to the clinician
  • When no specific organism is dominant over the others
  • When source control has been achieved-this is important as in the hypothetical example above.
  • Drain samples- generally of low value unless the drain has just been inserted
  • When the clinical microbiologist has liaised with clinical team and clear that patient is doing well on current therapy- Treat the patient, not the result.

Such an approach saves the lab time and money, and may also be beneficial to the patient, as demonstrated above. Sometimes in our efforts to do the right thing, we end up trying just a bit too hard…

Michael

 

 

 

“Less is more in the microbiology laboratory?”

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I am by nature quite a lazy person. Don’t get me wrong, I am not afraid of working hard at times, but I am always on the lookout for ways in which I can optimise the productivity and the quality of the laboratory, whilst creating time and resource for other opportunities.

Time and effort are terrible performance metrics…

Aside from efficiencies, can doing less work in the microbiology laboratory actually lead to better patient outcomes? We know that our ultimate aim is to improve patient management. Are there circumstances where in our enthusiasm to optimise patient care, we might actually do the opposite?

Here are some examples where doing less work in the microbiology lab might actually be beneficial to patient care:

Minimising work up on probable contaminants – If coagulase negative staphylococci isolated from blood cultures are routinely reported with susceptibility profiles without any supporting clinical information that they might actually be significant, this will lead to unnecessary antibiotic use with the potential for adverse effects, along with the potential for delayed patient discharge.

Avoiding tests with low clinical utility – Sputum cultures in the community setting are rarely useful, and the results may lead to undertreatment, overtreatment or simply the wrong treatment.

Reducing unnecessary microbiology tests– Rejecting urine cultures from patients where there is no evidence of UTI symptoms on the request form prevents unnecessary treatment of these patients with antibiotics.

Not processing duplicate specimens – Rejecting repeat samples (e.g. urine, sputum, stool) submitted on the same day from the one patient means that conflicting results are avoided.

Avoiding overuse of broad-range multiplex PCR panels – Running a full respiratory viral panel for a simple upper respiratory tract infection may end up delaying patient discharge from hospital. More targeted testing is often better.

Following proper sample collection and rejection criteria – Rejecting poorly collected specimens (e.g., saliva instead of sputum for pneumonia testing) avoids misleading results and unnecessary treatments.

Optimised result reporting – For example, reporting Group C/G beta-haemolytic streptococci from throat swabs in patients with acute pharyngitis may lead to unnecessary antibiotic prescribing. Along the same lines, testing and reporting unnecessarily broad antibiotics when performing susceptibility testing can lead to unnecessarily broad antibiotic coverage with concomitant side-effects on the patient and selection of antibiotic resistant bacteria.

As demonstrated above, there are lots of ways in which doing less work in the microbiology lab is not only cost-efficient, but it can also improve the overall management of the patient.

As the range of different assays we are able to offer in the microbiology lab continues to increase, we need to constantly review our current test repertoire and whether it is providing significant value to the clinicians, and ultimately the patient.

Less is often more when it comes to the microbiology laboratory.

Michael