Category Archives: Confessions of a Microbiologist

“Hand holding and Chinese whispers..”

As part of my job as a clinical microbiologist, I am usually on the telephone 20-30 times per day.

That is a lot of telephone time for a man…

With regards to outgoing calls, a lot of these are simply information gathering. For example, is this patient with Gram negative bacteraemia on appropriate Gram negative cover? Has this patient with Clostridium difficile infection been isolated and treated? Has this patient with Staphylococcus aureus bacteraemia been investigated properly?

Gathering this information by telephone is of course always a little fraught with difficulty. Trying to get hold of the right person to speak to can take up a lot of valuable coffee drinking time. There is also no guarantee that the information you are given is accurate, and has not evolved along a chain of “Chinese whispers”. Sometimes you finish the phone call no more enlightened than when you started…

Many of these calls would not be necessary if the hospital/health network had a live, real time “Electronic Health Record”, along with an electronic/digital drug chart for each patient. These innovations simply cannot come soon enough to my neck of the woods. Objective, readily accessible clinical information is what microbiologists crave.

Incoming calls are generally from clinicians looking for advice on antibiotics, infection control, optimal samples, etc. Much of the information that I give out could easily be accessed from published clinical guidelines. There is often an element of “hand holding” here, of sharing the responsibility for the decision made, and sharing the blame if something goes wrong..

Personally I was never very good at hand-holding…

And then, once or twice a day, an interesting phone call comes along, one which stimulates the mind, and prompts further thought and reading, and reminds me that I do after all work in a microbiology laboratory, and not a call centre…


“Gatecrashing: Neisseria meningitidis as a genital pathogen.”

Neisseria meningitidis is more classically known as the cause of meningococcal sepsis and meningococcal meningitis. However its role as a cause of urethritis/cervicitis has been the subject of ongoing speculation over the years, and several studies have backed such a link up. For example, check this study out, and this one.

A recent study has added more weight to this hypothesis, backing the assertion up with DNA studies of the N. meningitidis isolates showing adaptation to a genital environment. (loss of outer capsules, and acquisition of enzymes facilitating survival in a low oxygen environment)

So what does this all mean for clinical microbiology laboratories?

I guess it shows the inherent weakness of molecular diagnosis. There could be a widespread outbreak of urethritis due Neisseria meningitidis urethritis in your local area, but the laboratory would be completely naïve to it, if it only performs molecular testing for C. trachomatis and N. gonorrhoeae. Particularly in the Sexual Health Clinic setting, adjunctive culture of STI samples is important, and not just to obtain the N. gonorrhoeae susceptibilities.

It is also possible that the selective molecular diagnosis and treatment of N. gonorrhoeae will therefore create a “niche” for organisms like Neisseria meningitidis to adapt physiologically and “gatecrash” the party. (I will talk more about “selective pressure by diagnosis” in the next post.)

And finally on this topic, there is also intriguing data coming out that suggests that some meningococcal vaccines may have a protective effect for N. gonorrhoeae infection. Suspected for some time, this suggestion has been backed up by some observational data in this study. More research is obviously needed. We are still a bit away I suspect from a gonococcal vaccine.

The physiological and evolutionary relationship between Neisseria meningitidis and Neisseria gonorrhoeae is a fascinating one.  We shouldn’t think too much about one without considering the other…



“Notes from ECCMID 2017”

I was lucky enough to attend the ECCMID conference in Vienna last week, a mass gathering (11,000+) of people interested in infection and microbiology.

I have summarised a few of my takeaways from the conference below:

Bi-lingual presenters: It always amazes me how well presenters can present in what is often their second language. It makes me somewhat envious. One day I will manage to give a presentation in French!

Conference bags: Conference bags are becoming a little dated in the sense that all their contents could now easily be summarised on a USB stick or a Smartphone app. Still, they are often regarded as a souvenir. Maybe they also make you feel like part of a tribe…

“Kiestra” dinner: BD hosted a dinner for prospective and current Kiestra users at the conference. This was a rather lavish affair held in the opulent surroundings of the Palais Coburg, and I felt a bit like royalty for the evening. BD make a particular point of looking after their clients, and this conference was no exception.

Parallel Worlds: At any one time there were 12 parallel sessions taking place at the conference. There were a couple of my colleagues from NZ who also attended the conference whom I never met during the whole four days. Parallel worlds… Or maybe they were just avoiding me!

Networking for introverts: Being an introvert, I always find networking difficult at conferences, preferring to go and hide behind a poster! Nevertheless I did manage to catch up with a few old colleagues, and meet a few new people, and speak to the odd complete stranger!

A multiplex of PCR platforms: The exhibition hall was saturated with a whole array of multi-plex PCR platforms. Not all of them will survive the competitive market, but they are certainly driving each other down in terms of price and turnaround time, which is obviously good for the customer.

Whole Genome Sequencing: I got the impression that there was not a huge amount of progress over the past year with regards to Whole Genome Sequencing in diagnostic clinical microbiology. Even for a large regional laboratory network like my own, I still think we are several years away from making a successful business case for such technology.

CDSS on the rise: The big mover this year for me was Clinical Decision Support Systems. Everywhere you looked there were apps and software related to clinical decision support, including some very sophisticated ones such as Treat Systems.  I look forward to seeing how this field progresses over the next few years.

Vienna: Vienna as a city was very nice, modern and clean. It also felt very safe. The conference facilities were good, and the public transport was excellent. A good place for a conference.

WECCMID? I do worry however that ECCMID is fast becoming WECCMID in disguise. The vast majority of ECCMID conferences have been held in Western Europe, and delegates from eastern Europe seemed rather few and far between. Time to expand the horizons and pull that iron curtain down?

It was a generally good conference and I left it somewhat inspired, full of new ideas for research, presentations and even blog posts!

However now that I have left the slightly artificial world of conferences,  I am now back to reality, back to the daily grind of the clinical microbiology laboratory, and back to my cubicle.

Ho hum…