Monthly Archives: July 2015

“Ignorance is bliss”

Confessions of a Microbiologist, , ,
B. hominis
B. hominis

PCR for enteric pathogens is starting to take hold, both locally and internationally.

One area where there is a significant difference between traditional methods and PCR is in the area of enteric parasites.

PCR is much more sensitive than microscopy at picking up faecal parasites. This has shown great benefit when trying to diagnose conditions like Entamoeba histolytica, (not only in faeces, but also in liver abscesses as well)

So far, so good,

but there are downsides as well….

PCR for Blastocystis hominis and Dientamoeba fragilis are generally much more sensitive methods than their microscopical counterparts. This leads to high numbers of “positives” being reported, particularly in children. However these two parasites are putative pathogens at best, potentially causing symptoms in a small and select number of patients only. Most of the time they are probably just there for the ride.

Using such a sensitive assay for parasites of uncertain significance like this can thus lead to misdiagnosis, over treatment and undue anxiety. More is not always better.

Sometimes ignorance is bliss…

Michael

“Hidden Agendas”

The Art of Microbiology, ,

Urine_sample

In my pursuit of clinical details for all request forms, I have been asked a few times specifically about urine samples. Why bother adding clinical details for a urine sample that is sent to the lab. Is the request not obvious?

However when you think about it and examine a little more closely there are actually many “less obvious” reasons that a urine sample is sent to the lab. Take the following examples below:

Test of Cure: Once symptoms have settled, this is generally not indicated.

As part of an admission screen: Positive predictive value, even in an elderly patient, must be awful.

Prior to orthopaedic (or other) surgery: With the exception of urological surgery, the evidence is now strongly against this.

Wellness check: Just in case…even if you did culture bacteria, treatment would not be indicated in an asymptomatic patient.

Insurance/Immigration requests: as above.

Looking for proteinuria or glucose: In diabetics. Requestor not interested in culture result.

Looking for haematuria: If lab not aware, likely to increase risk of false negative due to sub-optimal testing.

Cloudy/smelly urine in catheter bag: Sending such a sample to the lab is hardly ever indicated.

 

So as you can see there are actually many reasons that urine samples sent to the lab. There are probably many more which I have not thought of from the top of my head. Many are inappropriate, others are nothing whatsoever to do with infection.

With regards to patients with “symptoms”, there can be a whole range of clinical scenarios, from acute dysuria and frequency to non-specific fatigue. Each set of symptoms will have a different pre-test probability and will therefore potentially affect how the test is reported and interpreted, particularly for borderline results.

And then there all the supporting clinical details which may affect how the test is processed and reported, e.g. pregnancy, immunocompromise, antibiotic allergies, presence of catheter, presence of urinary stents etc etc..

So if someone says to you there is no point in submitting clinical details for urine specimens, I would strongly object to this for all of the reasons above.

In short there is no excuse for not submitting clinical details, not for urine samples or any other samples. Don’t let anyone tell you otherwise….

Michael

 

“Ward based PCR”

Future of Microbiology, , ,

There are a couple of new systems just on the market which I suspect will revolutionise PCR testing, particularly where an urgent result is desirable. This is often the case when trying to diagnose Influenza and RSV in the acute care setting.

Cepheid and Roche have both released benchtop PCR systems for Influenza and RSV testing which can be placed in the ward/ED environment, requires minimal training and can give you a highly sensitive result for influenza/RSV in well under an hour.

“Highly sensitive” are the key words here. This is in contrast to rapid antigen tests for Influenza and RSV which although can be useful in certain circumstances, are limited in their clinical usefulness by sub-standard sensitivity. RSV and Influenza rapid antigen tests are now living on borrowed time….

The other highlight is “under an hour”. This allows real-time management of the patient in the ED./acute assessment ward (including treatment, isolation, cohorting, discharge etc.) based on the result of the PCR test.

The big downsides of course are the cost and the “one at a time access”. More expensive (the cost will come down)than traditional batched PCRs it might be a while before such testing systems become commonplace. (A lot depends on the funding model of your healthcare system.)

But they will, you can be sure of that.

Michael