Monthly Archives: July 2016

“How long is a piece of string?”


A question that often ‘scunners’ me is “What should the duration of the antibiotic course be for this patient?”

Let me get out my crystal ball…

It is a question I get at least once a day.

And my heart tends to sink a little on hearing it…

I have no problem (and quite enjoy) guiding the clinician to the right antibiotic, but I find this particular question on duration very hard to answer with any degree of personal conviction.

I usually give one of the ‘magical’ and hallowed numbers such as 3, 5, 7, 10 or (god forbid) 14,  usually along with a sizeable disclaimer saying that for the most part, antibiotic duration is very much an arbitrary and non-scientific decision.

Sure, for the more critical infections such as endocarditis, osteomyelitis and prosthetic joint infection there are guidelines on antibiotic duration which I try to adhere to, but even then there is not a lot of evidence to back these durations up, and such guidelines tend to compress all patients into the one category…

And for hospitalised patients with infections that don’t fall well into any particular guideline, my response is often along the lines of “Until they are better”, “As long as it takes” or even “How long is a piece of string?”

I suspect 95% of antibiotic courses are longer than they need to be, and this may well have undesirable effects, and not just on the patient themselves. I am a strong advocate of putting mandatory limits on the duration of antibiotic that can be prescribed in “one go” by the prescriber without clinical review. For me it is a key element of anti-microbial stewardship.


Check out this related article on antibiotic duration…


“The Trade-Off”



Do you culture all urine samples that arrive into your microbiology laboratory?

If so, why?

Is it for reimbursement purposes? I know this is necessary for some parts of the world.

..or is it because you are scared not to?

…or is it because you think it is in the patient’s best interests?

Now that automated urine microscopy analysers are commonplace, some microbiology laboratories selectively culture urine samples based on various microscopy parameters, of which the leucocyte count is a principal criterium.

In addition some urines are cultured based on clinical criteria and regardless of microscopy findings; e.g. pregnancy, immunocompromise, neonates, etc.

In my microbiology laboratory just over 50% of urine samples that arrive into the laboratory find their way onto culture plates. The rest do not get any culture whatsoever.

Do I feel nervous about not culturing half of all the urine samples?

Not in the slightest….

Many “positive” cultures with low numbers of white cells simply represent contamination and can thus lead to overdiagnosis, overinvestigation and overtreatment, not to mention the potential for resistance selection.

It is simply a question of sensitivity v specificity for true infection. By altering the microscopy parameters you can make the urine cultures more sensitive but less specific for true urinary tract infection, or vice versa.

There are no right or wrong thresholds for culture.

And on the ones we don’t culture, we always give the clinicians the option of getting back to us by telephone if they feel culture is strongly indicated despite the microscopy findings.

But they very rarely do…


“If it’s good enough for me…”


I do a fair bit of running, and I often think about what condition my joints will be in thirty years down the line.

Because I am a microbiologist I see first hand the devastation that can be caused by an early prosthetic joint infection (PJI) with Staphylococcus aureus.

It actually doesn’t matter whether it’s MSSA or MRSA. Either way, it’s not pretty…

For this reason, and in the knowledge that most Staphylococcus aureus PJIs are usually caused by the patient’s own colonising flora, I would be very keen to ensure that my nasal area is completely clear of Staphylococcus aureus before going under the knife.

And if it’s good enough for me, then I should definitely be considering it for my patients, and I am. The evidence is building, slowly but surely, that this is a very reasonable thing to do.

See here and here for a couple of sample papers.

There are essentially two ways to approach this:

  • Screen all patients pre-operatively for Staphyococus aureus and then give mupirocin (or another antibiotic) to those that are culture positive on screening culture.
  • Give all patients intra-nasal mupirocin prior to hip and knee joint arthroplasty surgery.

And often chlorhexidine body washes are thrown in as well to form a “bundle”.

I know there may be some institutions which are already performing Staphylococcus aureus decolonisation prior to joint replacement, but in my experience it certainly is not common practice (yet) in New Zealand. However that does not mean it is not the correct thing to do…

Obviously one would need to monitor mupirocin resistance rates, but on a population scale, giving mupirocin to a few hundred patients in a focused fashion like this does not actually represent a lot of selection pressure.

There are certainly plenty of my peers who would do exactly the same as I would when my joints wear out, even if it wasn’t “standard practice”. This is telling me something, and I hate to see “us and them” medicine practiced.

If it’s good enough for me…