I have noticed while authorising sputum culture reports, that some people have high thresholds for working up suspect colonies from plate cultures, only proceeding when the potential pathogen is dominant amongst the upper respiratory tract flora that is also inevitably present.

Other people have very low thresholds for working up suspect colonies, painstakingly trying to pick out potential pathogens even when there only a few of the same colony type present in the milieu.

Depending on what your threshold is, it clearly has the potential to produce a different result for the clinician.

But who is right and who is wrong? Is it that sometimes we just try a bit too hard?

My gut instinct is that a few colonies of a respiratory pathogen (e.g. Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis) nestling amongst a mass of mixed upper respiratory tract flora is unlikely to be significant, but I am not aware of any literature that supports such an assertion.

I tend not to get too excited by sputum cultures as a rule… Clinicians don’t hang around waiting for the patient to firstly produce a sputum sample, and then wait another 2 or 3 days whilst the microbiology laboratory processes it. They treat the patient empirically, according to guidelines that are hopefully formulated by laboratory data outlining the expected pathogens and antibiograms in the local area.

Only on rare occasions does a sputum culture result actually change patient management.

If “sputum culture” were a new immunoassay, and therefore subject to FDA approval before being released to the market, it wouldn’t have a prayer of being accepted. The sub-optimal sensitivity and specificity (even with prior filtering of samples using macroscopic appearance and Gram stain) would simply not cut it from a regulatory point of view.

So we will continue to grapple with the vagaries of sputum culture, but I suspect it will be around for many years yet.

But we should not lose any sleep over it, whatever your threshold is…


“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…


“Too soft, too generous, too nice, and too slow…”

Guidelines for antimicrobial stewardship often include only a cursory mention of the role of the clinical microbiology laboratory, which is a shame, because in my opinion it is one of the key areas where real change to anti-microbial stewardship can be effected. (The other key area is in the writing of sensible narrow spectrum empiric antibiotic policies.)

But we don’t help ourselves…. Speaking generally, I think clinical microbiology laboratories are notoriously bad at antimicrobial stewardship.


Several reasons actually.

Because we are too soft: We often release antimicrobial susceptibilities from the laboratory even when we have no idea what is going on with the patient. I.e. no clinical details have been provided. Therefore we think nothing of releasing a range of antibiotics to the clinician when we don’t actually know what is wrong with the patient, whether they have an infection, and how severe it is.

Antibiotic susceptibilities should not be released unless the laboratory has reasonable evidence that they are required.

Because we are too generous: We are happy to test a whole range of antibiotics (often up to 20 for the one isolate!), “just in case” one of them might need to be used. This range often includes both narrow spectrum and broad spectrum agents. Probably over 95% of all the susceptibilities that we test and report are never utilised.

We need to dramatically reduce the range of antibiotics that we test for and we need to focus our reporting to the narrowest spectrum antibiotics that we can get away with.

Because we are too nice: We have a low threshold for releasing antibiotic susceptibilities on putative pathogens“. By doing this, we have just given the green light for the clinician to classify a putative pathogen as an actual pathogen, and therefore start/continue antibiotics.

If we have isolated a putative pathogen, let’s keep it putative. Report the organism, and ask the clinician to make a clinical assessment, and then to get back to the laboratory if susceptibilities are required.

Because we are too slow: We are certainly quicker than we used to be, thanks to MALDI-TOF, smart incubators, and increasingly rapid PCR platforms, but we need to be quicker still… We need to get rid of self-congratulatory, retrospective infectious serology testing and channel our test budgets into real-time diagnosis with PCR or similar, and on patients who fulfil well defined clinical criteria for testing. We need to get rapid molecular platforms for STDs into Sexual Health clinics so they are not required to prescribe an antibiotic for everybody who walks through the door. We need to increase Influenza and RSV testing during the winter season to try and reduce unnecessary antibiotic prescribing for viral infections.

Not only do we need to be quicker, we also need to be smarter…

The clinical microbiology laboratory doesn’t score very well in the antimicrobial stewardship report card. We need to be bold and innovative to change things for the better.

But it is entirely up to us…