Tag Archives: molecular testing

“The Dying Art of Infectious Serology”


Most diagnostic laboratories have now left viral culture behind, but a lot still have sizeable Infectious Serology departments.

However there are a lot of infections where molecular methodology now gives a more sensitive and specific diagnosis. Take for example measles, mumps, pertussis, and herpes simplex virus for starters.

In addition, for those infections that require the interpretation of both acute and convalescent serology, molecular methods are also a lot faster.

Looking at the more serious end of the spectrum of infectious diseases, for example the haemorrhagic fevers, leptospirosis, and some of the arboviruses such as Dengue, Zika and Chikungunya, a lot of clinicians are still used to diagnosing these conditions by serological means, because for a long time this was the only means available. However for a lot these conditions, PCRs are now available and it is a responsibility of the microbiology lab to educate requestors as to what is available locally in order to offer the most rapid and sensitive diagnosis for the (often sick) patient.

The molecular methodology may still be more expensive (the price is coming down all the time) but the cost benefit analysis for a lot of these conditions is starting to weigh more in favour of molecular.

There are two areas where Infectious serology is still well established and may well be for some time yet:

“Infectious mononucleosis” screens. In this area there is still a lot of serology performed for EBV, CMV and Toxoplasmosis. The serological tests for these pathogens are relatively cheap, and outwith the immunocompromised/pregnant cohort, of relatively low clinical importance.

Hepatitis & HIV Screening: The cost of Hepatitis A, B and C PCR tests is still quite significant, so I think serology will stick around in this area for a while yet. In addition for Hepatitis B serology there is quite a lot of information one can gleam from the serological pattern of results regarding the epidemiology, chronicity and time course of infection.

Despite the above I can only see Infectious serology departments gradually shrinking over the years, at the expense of expanding molecular departments.

Infectious serology has always been and always will be a bit of a dark art. I do foresee the time (and possibly during my career) when serological testing will be restricted only to confirming past infection/immunity and all acute infections will be diagnosed by molecular methods such as PCR.

I believe one of the roles of clinical microbiologists and senior scientists is to weigh up the cost-benefit analysis for each of the pathogens where infectious serology could be potentially replaced by molecular methods. Such changes may not always be popular, as funders may baulk at the costs and serology staff may see their jobs on the line, but that is part and parcel of creating a lab that is future-proofed….



“Something for the weekend”

Molecular testing in the clinical microbiology department has traditionally been performed Monday to Friday 9-5pm. There are various reasons for this. Twenty years ago, this  area was highly specialised hands on work. Turnaround times were long and the results often did not effect an immediate change in patient management.

Times are changing…

Nowadays molecular tests for bacteria and viruses can be performed in real time, with results that can dramatically change the patient’s management. The tests are becoming automated and simplified to the extent that they can often be performed by scientists who are not molecular experts. The newer molecular platforms, being completely enclosed, are “coming out” into the main laboratory, and the whole discipline is becoming more mainstream.

In light of this we need to start thinking of providing “molecular services” not just from Monday to Friday, but during the weekends as well, and overnight when necessary.

The laboratories that succeed in making this sort of progressive change, will be seen as giving the best service to their patients, and will be the laboratories that are still around in twenty years time….


It is not the most intellectual of the species that survives; it is not the strongest that survives; but the species that survives is the one that is able to adapt to and to adjust best to the changing environment in which it finds itself”


“Lumbar Puncture: Creating headaches not only for the patient…”


25 years ago, examination of cerebro-spinal fluid (CSF) was a fairly straightforward process. You got a cell count, Gram stain, protein and glucose levels. For the really complex patient you might have added a couple more tests like an Indian Ink or a TB culture.

Not any more….

There are now dozens of tests that can potentially be performed on CSF, most of them molecular, and a particular increase in viral PCR, e.g HSV, EBV, CMV, VZV, HHV6, etc. etc. The acronymical list goes on…

If you work in a clinical microbiology lab, then the chances are you will have come across one of the following scenarios:

  • A CSF sample arrives into the lab with a long list of molecular tests requested. The cell counts, protein and glucose are then completely normal on initial testing.
  • A CSF sample arrives into the lab with a long list of molecular tests requested by a doctor who is in the process of studying for post-graduate exams and wants to show off his/her expertise.
  • A CSF sample arrives into the lab with a long list of molecular tests requested. By the time some of these tests are performed, the patient has long recovered and is sitting at home watching ER with a glass of wine in hand.

CSF testing can now be fairly problematic. Cost issues, poor positive predictive value of individual tests, available CSF volume, distributing bits of CSF to different reference labs, lack of clinical details can all contribute to this headache. Not to mention that the results of these tests often have little or no direct effect on the management of the patient. 

I am convinced that there are huge numbers of molecular tests performed on CSF samples which turn out to be completely unnecessary.

Good communication between the laboratory and clinicians is obviously key, but I also believe that more and more the laboratory needs to become the gatekeeper for complex CSF testing, as opposed to being the submissive, and passive recipient of such requests.


I have added a short powerpoint on toxoplasmosis to the website