Monthly Archives: December 2015

“Out with the old and in with the new”

The Art of Microbiology, ,

EMpylori

An apt post to finish the year off with!

Many laboratory networks (including my own) are currently in the process of changing our testing protocols for Helicobacter pylori over from the traditional serological testing to the more specific faecal antigen test.

The faecal antigen test for H. pylori has the obvious advantage of picking up only current infection, whereas serological testing can also pick up past infection, even if it has been treated. The only caveat to this is that for faecal antigen testing the patient should be off their proton pump inhibitor medication for at least two weeks before testing. If this is not possible, then this would be one of the few indications for serology testing instead.

International guidelines on this topic are moving slowly but surely from serology to faecal antigen testing for the diagnosis of H. pylori infection.

However such a change is not necessarily always easy to effect. Clinicians, for whom H.pylori is only a small part of their day to day work, are very used to ordering Helicobacter pylori serology. They may not be that familiar with the faecal antigen test, or still see it as a research/reference laboratory type of test.

It is our job as microbiologists to help facilitate this transition across to best practice.

How can this be achieved? I would suggest the following:

  • One-off educational updates: Both flyers and talks can educate laboratory users of the latest testing algorhythms.
  • Result comments: Add a comment to every Helicobacter pylori serology result stating that faecal antigen testing is now the preferred test. This modality can be very effective as (depending on the number of H. pylori tests the clinician orders) it can provide continuous feedback, unlike the one-off updates above. This approach often produces a slow but sure switch over to the desired testing algorhythm.
  • Gatekeeping: Only allow serological testing for Helicobacter pylori if it is clear from the clinical details that the patient is unable to stop their proton pump inhibitor therapy.  This is a little harder line, but in my eyes perfectly acceptable. A few laboratories have discontinued Helicobacter pylori serology altogether…

Although this “modernisation” aspect of laboratory practice is often not assessed by accreditation agencies, I believe it is an important quality marker of a laboratory to show that they can both keep up to date with current best practice testing, and encourage their users to do the same….

Michael

“Saving Grace”

Confessions of a Microbiologist,

FreezerWhen working on sterile site isolates or blood cultures, our gut instinct is to save and store the isolates that are well recognised pathogens. However in my experience it is the putative pathogens for which we are just as likely to need to go back to and do further work.

Take the following hypothetical situations:

Multiple specimens are sent on a joint revision to exclude low grade infection. A couple of colonies of Staphylococcus epidermidis is grown from one of the samples, (rightly) thought to be of uncertain significance. It is decided not to treat, but the surgeon comes back to the laboratory a couple of months later saying that the patient’s symptoms have not improved, and is wondering whether that coagulase negative staphylococcus may have been significant after all. “Has the isolate been stored?”

or for another example..

A Propionibacterium acnes is grown from a blood culture after 4 days incubation. No clinical details were provided on the request form and the isolate is reported as a likely contaminant. However a couple of weeks later it transpires that the patient has a pacemaker in situ which is showing signs of chronic low grade infection and the cardiologist would like to do further work-up on the P. acnes. “Has the isolate been stored?”

Putative pathogens are exactly the ones that the clinicians start looking towards when things are not going quite right from a clinical point of view, or something has been missed in the initial clinical assessment (like the presence of prosthetic material). The laboratory needs to be ready for such scenarios, because not everything happens the way we expect them to.

I am not saying that we should be doing extensive antibiograms on such isolates, “just in case” one of them turns out to be significant, but I do believe in storing them, at least until the patient is clinically improving. Once the cultures have gone in the bin, there is no going back….

Michael

“The Dying Art of Infectious Serology”

Confessions of a Microbiologist, Future of Microbiology,

2000px-ELISA-sandwich_svg

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….

Michael