Tag Archives: cost

“Should peri-anal swabs be accepted by the microbiology laboratory?”

Superficial swabs in general have limited value, but few are as useless as the peri-anal swab.

Given the area that one is attempting to swab from, it is not surprising that a good proportion of these grow mixed enteric flora.

And if there is something to swab (either because the abscess has been incised or is discharging naturally), then most of the time the patient is well on the way to recovery.

I would love to survey 100 patients who had a peri-anal swab performed, to see what proportion it changed the management in. It will be low, very low..

In today’s microbiology lab, where we are trying our best to focus our efforts where we can make a difference, there is no place for peri-anal swabs.


My apologies for this website being out of action for the past few weeks. The new baby (Albie) arrived, just a couple of days late, but he then had to spend a few days in the Special Care Unit with an infection. All is well now, but it has taken a few weeks to get back to normal life..

Simultaneously to the above, the website went down with technical problems and it has taken until now to get round to fixing it.  With 5 young children, I have to grab an hour here and there to do this, usually in the middle of the night when everyone else is sleeping!

“PCR: A Multiplicity of Multiplexes….”

PCR multiplexes seem to be all the rage just now….

Here is just a selection of what is currently available in New Zealand:

  • CSF Multiplex: HSV, VZV, Enterovirus, Parechovirus, N. meningitidis, S. pneumoniae
  • Respiratory Virus Multiplex: Influenza A&B, CMV, Adenovirus, RSV, hMPV, Rhinovirus, Coronavirus, Parainfluenza 1-3, Bocavirus.
  • Atypical Pneumonia Multiplex: Legionella, Mycoplasma pneumoniae, Chlamydia, Pneumocystis, Bordetella pertussis & parapertussis.
  • Enteric Virus Multiplex: Norovirus, Rotavirus, Adenovirus, Astrovirus.

However there are some downsides to multiplex PCRs, both clinical and technical. These are as follows:

  •  Cost: The clinician may not want to test for all the assays within a multiplex PCR, therefore the cost may be more than with other individual assays that are required. For example, it is usually easy to differentiate between a viral and a bacterial meningitis based on initial CSF findings. However if the “CSF multiplex” includes both bacteria and viruses, then it may lead to unnecessary cost as well as problems with positive predictive value as described below.
  • Expertise: Carrying out a multiplex PCR still requires a reasonable amount of expertise, particularly if the reagents are being prepared “in-house” The expertise level increases further when troubleshooting is required.
  • Controls: Controlling each assay within the multiplex.
  • Test Volumes: Because of the amount of controls required per batch, significant numbers of tests are often required to make it cost-effective. Therefore may restrict some multiplexes to the larger centres.
  • Optimisation: Optimising each assay and avoiding competitive inhibition between the different reagents.
  • Positive predictive Value: If you have 5 tests in a multiplex PCR, then it is likely that at least one of these tests has a very low pre-test probability making interpretation of positive results difficult. For example, during the Influenza season, it may be prudent to test for Influenza first and then worry about other diagnoses if this test is negative.
  • More than one positive result: For example if you are doing a multiplex PCR with 7 or 8 respiratory viruses, it is not uncommon for 2 or even 3 assays to be positive. You then need to decide which one is causing the problem….
  • Only diagnoses what is tested for in the multiplex: I.e. It is not a catch-all method.

 Multiplex PCR can clearly be very useful in some situations. However it is important to be aware of the limitations as described above and have other testing options available. Otherwise the skill of utilising laboratory tests in a cost effective and clinically appropriate manner will be lost….


For a really simple walk through the basics of the PCR reaction, check out this website. I will go into a bit more detail next week on detection of PCR product, Real-Time PCR etc.


“Comparing Apples with Oranges.”

Apple_and_Orange_-_they_do_not_compareIn NZ (as with several other parts of the world) there is currently a significant outbreak of pertussis in the population.

In the acute phase of pertussis/whooping cough, some NZ labs offer culture for Bordetella pertussis (with an overall sensitivity of 60-70%) and some offer PCR (with a sensitivity of approx. 90%).

So which is the better test? Purely in terms of efficacy, there is no comparison. (I know which test I would want…)

However the cost of a Bordetella pertussis culture is a few dollars, that of PCR 50-100 dollars. So which one is best now? I guess it depends to some extent on your agenda.

The point I am trying to make here is that the overall value of a test to the health service should not only be considered in terms of performance but also in its cost-effectiveness. There is only a fixed amount of money in the pot with a lot of different hands dipping in.

I am always intrigued by the amount of times I have sat in a conference listening to a speaker discuss a new assay or a new technology. Yet, most of the time, very little is said about the cost, skills required, and the other practicalities of implementing the test in a routine diagnostic lab. To omit such details is essentially only giving half the story and for me indicates somewhat of a detachment from the real world.

I think cost should always be considered when discussing any test. I like to think that microbiology scientists and clinical microbiologists know as much about money as managers do about microbiology.


p.s. For those that are interested I have added a short tutorial to the website on Hepatitis B serological markers, something that always confused me somewhat as a student!