Monthly Archives: February 2016

“What we know is what we get”

The Science of Microbiology, ,

Myco_culture

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…

Michael

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

“Getting Rid of Unwanted Guests”

Confessions of a Microbiologist, ,

OLYMPUS DIGITAL CAMERA

Week 4 of the Kiestra TLA at the lab I work in. Things are starting to settle, routines are being adopted, and life is becoming boring again!

One thing I have been thinking about though, is whether contamination rates will be lower for sterile site samples, and in particular for orthopaedic samples, which often get prolonged incubation periods in the laboratory. It is not something that is talked about much when one listens to the company reps about the pros and cons of smart incubators, but there are good theoretical reasons why this might be the case.

Think about the traditional way of plate inspection. The plates are handled by human hands day after day, the plate lids removed for anything up to a couple of minutes, breathed on and occasionally coughed or sneezed on… It is actually quite an achievement to incubate a plate for 10 days without getting a contaminant somewhere along the line!

Then think about how these plates are handled by Kiestra. The plates rarely, if ever come into human contact. The lids are only removed for a few seconds in a Hepa-filtered environment for imaging.

It would be difficult, but not impossible to perform a trial to prove this hypothesis. The main difficulty is in deciding what is regarded as a contaminant and what is not. Hopefully someone will do it however.

Obviously not much can be done (in the lab) about contamination of the sample at time of sampling (in theatre etc.) but I would like to think that the (laboratory) contamination rates will be less.

And when I think about how many orthopaedic patients worldwide that are likely to have been overtreated because of plate contaminants, that cannot be a bad thing…

Michael

“Testing according to Twitter”

Confessions of a Microbiologist,

aedes egyp

Zika virus is all over the newspapers and social media just now, in a manner of speaking. The general public are aware of it. All the general clinicians are aware of it. Even the clinical microbiologists and infectious diseases physicians are aware of it!

As a consequence we are getting a relatively large number of test requests for Zika virus into the laboratory. (NZ has no endemic Zika but gets a good number of returning travellers from the Pacific Islands) Some requests are appropriate, particularly those ones related to pregnancy. Others I have no doubt would never have been requested if there hadn’t been so much about Zika in the news…

Some of the testing is driven by patients demanding testing from their primary care physicians, other testing is initiated by the clinicians themselves. Meanwhile the laboratory plays catch up and tries to introduce some rational testing guidelines/algorithms to ensure that the testing is ‘reasonable’, and testing volumes remain under control. A reasonable proportion of my working day over the past couple of weeks has been ‘dedicated’ to Zika.

One also worries that amidst all the hype about Zika, with the brain focused on the one pathogen, one might forget about the other arboviruses causing similar clinical presentations in endemic areas.

In a few weeks/months time, Zika virus will likely have disappeared from the headlines, to be replaced by another pathogen of interest to the media. That is the way the media works. Zika testing will return to ‘normal’ levels. Zika will still be there, for consideration in the differential, but it will no longer be at the forefront of people’s minds.

We like to think that our testing habits and our daily workload are not influenced by the media, that testing is always based purely on the clinical presentation, and that guidelines and protocols are always written due to clinical need.

But in the real world, to a certain extent, we are subservient to what happens in the media, whether we like it or not.

Michael