Tag Archives: PCR

“Echoes from a Distant Land”

A few years ago, I had never heard of parechovirus. Echovirus yes, but not “parecho”.

I would not have been alone…

However our ability to diagnose such viruses now (using PCR) means that myself and my colleagues now need to go and learn something about such viruses.

And here is a summary of (more or less) all I know about parechoviruses…

  • I know that the “ECHO” bit is an acronym (Enteric, Cytopathogenic, Human, Orphan). That probably tells me as much as I need to know about the background information on the virus. I have no idea what the “Par” stands for. Any help welcome…
  • You can theoretically perform viral culture for parechovirus, if you are happy to wait a couple of weeks for the result. We aren’t, so along with most other diagnostic laboratories in the world now, molecular methodologies have taken over.
  • Parechoviruses are the 2nd most common cause of viral sepsis like illness and meningitis in infants (after enteroviruses). Therefore if you are performing a CSF PCR panel in children, then it must include parechovirus. (Unlike enteroviruses, parechoviruses are a relatively rare cause of infection in older children and adults)
  • In complement to the above, parechovirus infection in the CSF does not give a positive enterovirus PCR test. They are sufficiently different viruses.
  • Unlike most other viruses, parechovirus meningitis does not cause a significant CSF leucocytosis. This has been our personal experience in the laboratory, and also that of other people in the medical literature. This is important because if, like us, you have testing criteria in place for CSF viral PCR based on leucocyte count, then you need to make neonates & young infants an exception to the rule.
  • Parechovirus (like enteroviruses) belongs to the picornaviridae family, and because of this may be susceptible to the viral capsid inhibitor pleconaril. However the jury is still very much out on pleconaril, and as such I would want to be speaking to someone who knows much more about viruses than me before even considering its use in a sick child.

So I now know a little bit about parechovirus, not a lot, but enough to allow me to do my job.

We don’t need to be “walking encyclopaedias”, just knowledgable enough to function in an information overloaded world…


“What we know is what we get”


We are all familiar with chlamydia, gonorrhoea, syphilis etc when thinking about STIs.

But when it comes to Mycoplasma genitalium, the knowledge base might be a little more patchy…

Mycoplasma genitalium has been associated with urethritis since the early 80s. However in those days, the only means of diagnosis was culture.

Have you ever tried to culture a Mycoplasma? It is not surprising that Mycoplasma genitalium was kept in the dark as a causative agent of Non-specific Urethritis (NSU) for a couple of decades. Quite simply, it was put in the ‘too difficult basket’ in terms of laboratory diagnosis.

It is only in the past few years that commercial PCR assays have become increasingly available for this pathogen. Consequently clinicians and microbiologists are becoming much more aware of it.

As a cause of urethritis it is more common than Neisseria gonorrhoeae, but less common than Chlamydia trachomatis.

Most labs still do not test for M. genitalium routinely, restricting testing to treatment failures or other special circumstances. However I think this will change in the future, and it may well be included in an NSU panel with C. trachomatis and N. gonorrhoeae.

If I was an examiner, and it is a relief to many that I am not, Mycoplasma genitalium would be one topic that I would ask about. I suspect it would be a good topic to separate the passes from the distinctions…


Click here for a short CDC review article on Mycoplasma genitalium (about a 5 minute read)

“Ignorance is bliss”

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…