“Do we perform too much antimicrobial susceptibility testing?”

As lab workers, we like to be helpful. In general, we want to provide as good a service as possible. But sometimes I think we try a little too hard…

One of our key areas of work is antimicrobial susceptibility testing. This is our bread and butter of course. This is one thing that we can do but no one else can, and we like to show off our skills! But there are many circumstances where performing antimicrobial susceptibility testing adds little value for the patient and thus unnecessarily uses up valuable laboratory resources.

Polymicrobial cultures The clinical value of antimicrobial susceptibility testing is inversely proportional to the number of different organism types present in the sample. This includes sterile site samples. Many times in my career I have been asked to do susceptibilities on samples which have grown several different organisms. I almost always push back on this. It should very much be the exception as opposed to the norm.

Eye and Ear Swabs Conjunctivitis and otitis externa are primarily managed by topical preparations, which can even be antiseptics as opposed to antibiotics. In-vitro susceptibility testing correlates poorly with response to topical antibiotics. Antimicrobial susceptibility testing on ear and eye swabs should only happen in a small minority of cases.

Enterobacteriaceae, enterococci & pseudomonas in superficial wound swabs These organisms cause infection in only a very small proportion of samples that they are actually found in. Susceptibilities should only be performed when there is compelling evidence from the clinical details that they are causing problems. 

Enterococci in urines In contrast to wounds, enterococci commonly cause urinary tract infections (they can also represent contamination). However, because amoxycillin achieves concentrations in urine which exceed the MICs of most Enterococcus faecalis and Enterococcus faecium isolates (check out this reference), susceptibility testing is essentially futile, unless the clinical details suggest the patient has a penicillin allergy. A simple comment to this effect will suffice.

Beta-haemolytic streptococci Because beta-haemolytic streptococci are inherently susceptible to beta-lactams, susceptibility testing for these antibiotics is somewhat academic in the majority of simple wound/soft tissue infections.  I would do if the clinical details suggested penicillin allergy.

Anaerobes Anaerobes rarely require formal susceptibility testing. Bacteroides fragilis has predictable response to beta-lactam/beta-lactamase inhibitor combinations. and is often part of a polymicrobial infection anyway (see polymicrobial cultures). In our lab anaerobic susceptibility testing is most often performed for C. acnes causing joint infections, where we test penicillin (almost always susceptible, maybe we don’t need to test…) and clindamycin (very occasionally resistant).

Coagulase negative staphylococci from blood cultures Again these should only be performed when it is clear that the coagulase negative staph is the suspected pathogen (prosthetic material, premature neonates, etc.) which will only be the small majority of the total number of isolates.

Pseudomonas in sputa Once a patient with COPD becomes colonised with Pseudomonas aeruginosa in their sputum, it is generally there to stay. Pseudomonas susceptibility testing should only be done when it is clear from the clinical details that it is causing a problem, i.e. the patient is failing standard management. We also need to review susceptibility testing protocols on pseudomonas isolates from patients with bronchiectasis and cystic fibrosis. There is now increasing evidence that annual susceptibility testing on Pseudomonas isolates from Cystic Fibrosis patients is more than sufficient.

Candida from vaginal swabs It’s not just bacteria! Recurrent vaginal candidiasis is a common problem, and we are often asked to perform antifungal susceptibilities on such isolates. In my opinion it is hardly ever justified. Nystatin based topical therapy often works in these patients. Candida albicans isolates are usually susceptible to generous dosing of azoles. It is only Nakaseomyces glabrata (formerly known as Candida glabrata), where I occasionally acquiesce and perform susceptibility testing…

Of course, we can perform antimicrobial susceptibility testing but not report the results, having them stored just in case. But my view is that we should minimise this approach as it is generally wasteful. We should perform antimicrobial susceptibility testing when we are confident that we are going to report the results of at least some of the antibiotics from a testing panel.

At my lab we have progressed a lot in this area over the past decade and now perform minimal amounts of antimicrobial susceptibility testing in all of the areas above. What about your own lab? Is there room for improvement, and can you think of other areas where too much antimicrobial susceptibility testing is performed, that I have not thought of?


“A simple approach to uncomplicated UTI”

We have a “no clinical details-no test” policy at my lab, so in general, we get accompanying clinical details with the vast majority of samples received for microbiology testing. After all, at the end of the day, clinicians just want their requests processed…

This is great, but it always irritates me slightly when we get a urine sample into the laboratory from a young adult female with symptoms of a straightforward cystitis with no supporting clinical information to suggest that a “complicated UTI” is being queried.

My first reaction when seeing this is “Why are you sending this urine sample to the lab? Do you think this is going to help your patient?”

In New Zealand, and I suspect most of the rest of the world, uncomplicated UTIs are treated empirically according to local antibiograms, usually with a short course of nitrofurantoin or trimethoprim. In most cases, this settles things down, and no further medical input is required.

We receive approximately 400 urine samples for microbiology processing into our lab each day. My rough estimate is that 5-10% of these urines have clinical details that suggest an uncomplicated UTI. It doesn’t sound much, but it certainly adds up over the course of a year, and the total cost of processing all these would likely cover a scientist’s salary.

...And if we received urine cultures into the lab on every uncomplicated UTI diagnosis, then we would be completely overwhelmed!

During the early stages of the COVID pandemic, when we were getting hammered by SARS-CoV-2 PCR requests, we urged clinicians to send us critical samples only. This certainly reduced the number of requests where the clinical details suggested uncomplicated UTI. But old habits die hard, and now we are more or less back to baseline.

I have often wondered whether we should only accept urines where the clinical details are suggestive of a complicated UTI, but we have not gone there yet. Some might wonder if such an approach is too “hardline”, but it remains an option and I think a very reasonable one at that.

People sometimes think diagnostic stewardship is all about optimising the use of very expensive laboratory tests, e.g multiplex PCR assays, but in actual fact, looking after less costly but higher volume tests such as urine culture is every bit as important…


“The impact of COVID on the molecular department of microbiology laboratories”

COVID has had a profound, and ongoing impact on microbiology laboratories and everyone who works in them. But today I want to write about molecular departments in particular. This department and the staff that work in them have had some momentous experiences and unexpected changes over the last couple of years.

Prior to COVID, we just had a few staff working in the molecular department at the microbiology laboratory where I work. We had a limited after-hours and weekend service. Pre-COVID, we were working hard to expand our molecular menu and staffing but as with all such changes, it was a slow process.

COVID changed all that…

When COVID first arrived in NZ in early 2020, it took a few weeks for the first diagnostic tests to be set up in the reference centres, and another couple of months for such assays to arrive at our (regional) lab. When we were finally able to offer diagnostic testing in-house, we could not initially keep up with demand so testing had to be prioritised to hospital inpatients.

Pooling of samples and the arrival of new testing platforms allowed our test capacity to quickly increase, but that brought other issues. New staff had to be recruited & after-hours and weekend molecular rosters had to be dramatically extended. As these SARS-CoV-2 assays were all new, they had to undergo test validations, which then needed to be written up for accreditation purposes. This validation work put extra pressure on staff that were already processing far more samples than they would normally. In addition, worldwide demand for test consumables, along with border restrictions created supply issues, which meant maintaining an effective service could be extremely difficult at times.

Several of our non-molecular microbiology staff were periodically drafted into the molecular department to help with sample pooling and to process all the COVID PCRs. This allowed us to offer 24/7 COVID PCR testing. It was all hands on deck!

Other molecular (& culture based) tests were “rationed” in order to allow for the avalanche of COVID testing. Clinical microbiologists like myself tightened up the clinical acceptance criteria for molecular assays such as enteric PCRs & STI multiplex PCRs in order to free up both testing platforms and staff for COVID testing. We also clamped down on relatively low value culture-based testing such as sputum culture and skin and nail mycology from the community setting.  The other main role for clinical microbiologists was to approve out of hours “rapid SARS-Co-V testing” on rapid testing platforms such as GeneXpert. This led to several disrupted nights’ sleep, but we know we got off lightly from the pandemic compared with the staff who were actually doing the tests!

During the peak of the SARS-CoV-2 PCR testing surge, we were processing in excess of 3000 SARS-CoV-2 PCR tests per day. Normally we would do 1000-1500 microbiology and molecular tests in total per day, so the increase in tests was completely unprecedented.

Then COVID Rapid Antigen Tests (RATs) arrived in the community, and things changed dramatically… For various reasons, the introduction of RATs into NZ for COVID diagnosis arrived relatively late and it also occurred very suddenly.  Our COVID-19 test volumes went from 3000 per day to 200 per day, literally overnight.

Once this happened, the staff could take a breather, catch up on other tasks & projects that had been put on the backburner, take some well-deserved downtime, take some leave, and recharge the batteries.

Despite the trials and tribulations, I have no doubt whatsoever that our molecular department has been left in a better place as a result of the COVID pandemic. The increased resourcing has allowed us to offer more molecular tests after hours and at weekends, thus improving our clinical service. It has also given us the staff resource to validate and implement new molecular assays, further extending our diagnostic menu. The increase in testing platforms within the department have also given us more testing options. The molecular staff, battle-hardened by COVID, are now a resilient bunch and well prepared for future challenges!

We continue to work hard to position ourselves as one of the leading molecular departments in the country. COVID has undoubtedly helped that process along.

How has COVID impacted on your molecular department?