BCID FilmArray better by a country mile

In one of our latest offering, we show how a molecular method can speed up identification of bacteria in septicaemia by over two days. The FilmArray technique allows clinical lab staff to identify the bacteria  in an hour with pre-packaged reagents and a plug-and-play analyser.

This has to be a batter way of meeting the needs of patients in country communities, than shipping them or their specimens to the big city hospital labs.

FilmArray works by targeting a series of bacterial gene targets from species of interest and running an array of triplicate PCR assays for each target. It is an amplification method, unlike MALDI-TOF, which is used in larger clinical labs to speed up bacterial identification from blood cultures. For country labs to benefit from MALDI-TOF, the specimen or bacterial isolate has to be referred to the city lab, which adds a delay to the process. In our series, FilmArray successfully identified the bacteria from country labs containing, and even coped with mixed cultures. In other words, it performed better than MALDI-TOF for the range of bacterial that cause infections in our regional communities. The quicker time to identification should translate into real improvements in choice of antibiotics and subsequent clinical outcomes.

Other options for country settings & elsewhere:

  • FilmArray has been applied to rapid identification of bacteria in other sterile fluid samples.
  • For those who’ve been following our Ebola stories, a FilmArray has been used in the recent EVD epidemic and its performance assessed.
  • Further applications are appearing in the professional literature.

This interesting new technology is better than anything we’ve had for blood culture rapid ID by a country mile, but we need to be careful not to get too far ahead of ourselves. We have yet to demonstrate that the use of FilmArray for blood culture identification in country labs directly impacts clinical outcomes.

Expect more on better methods for country labs from the gnome factory in future.


The antibiotic tightrope

You’ve got to take your hat off to those brave souls with ice cool nerves who cross canyons, waterfalls and other natural obstacles on the narrowest of paths possible. There’s something about a tightrope walk that lifts the human spirit and inspires us beyond the sheer insolence of personal risk taking. Determination, concentration, skill or unique challenge all come to mind. But without a doubt, there is a fundamental need for a finely tuned sense of balance.

Tightrope walker

The tightrope walker is a useful picture of what is missing in the growing clamour over what we need to do about antimicrobial resistance (AMR). At one extreme, we have an urgent need to reduce every imaginable measure of antibiotic use in order to slow the emergence of resistance. That is not a matter for debate. We are up the creek with only half a paddle. Unfortunately, the complete removal of all or any currently used antibiotic from clinical use is not an option. They are just too useful to us. How can we justify restricting antibiotic use where they are clinically indicated, let alone potentially life-saving?

There is really no dilemma for the clinician faced with a serious infection: the immediate needs of the patient will win out every time. The long term consequences of escalating AMR are a problem postponed. The expectation that there will be an effective antibiotic for every infection; a pill for every ill, has a pervasive effect on every medical engagement with infection. The most minor infection might just morph into something much more serious. Even when the odds are heavily stacked against that eventuality, it is often easier to weigh in with an antibiotic just in case. After all, we’ve all heard of cases that have gone badly for lack of an early intervention.

This is why the O’Neill report cites better diagnostic tests as the circuit-breaker in the fight against AMR. The report spells out in detail the rationale for early resolution of the physician’s dilemma with better point of care tests. Those tests must address a series of three questions front line clinical staff must answer when handling any infection:

  1. How sick is this patient
  2. Why are they sick
  3. And what do we need to do about it?

Or to put it another way; better tests are needed to take the guesswork out of prescribing antibiotics. Escalating AMR will make that balancing act all the more difficult, lie a tightrope walk on a windy day.

If you would like to help us make AMR history, go to the website and join the campaign.

trw pic

Up the AMR creek without a paddle?

You must have been hiding under a stone for a long time if you missed the news on AMR. It’s that acronym that’s taking up space all over the media right now, since the World Health Organisation raised it up the flagpole in 2012. [AMR: antimicrobial resistance is the formal name for resistance to antibiotics] This year the World Health Assembly gave it another push and now it’s flavour of the month in government circles the world over. The reason for all this concern is the grim reality that we’re running out of options for some of the most challenging infections. The prospect of being up the creek without a paddle is drawing closer.

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The British government has weighed in with a detailed report from the O’Neil Commission. They calculate that in just 35 years, deaths due to antibiotic resistance will overtake cancer deaths. Worldwide, they estimate 10 million deaths due to AMR each year and a loss to the global economy of trillions of dollars.

Now the Micrognome likes an occasional paddle in the waters around Perth, and has been known to go a bit further afield for more challenging kayaking. Nothing like the Avon Descent, though. Imagine what that would be like without a paddle? So when the gnome got roped into the launch of a serious campaign to Make AMR history, the image that came to mind was straight out of the kayaking lexicon – up the creek with only half a paddle. You see, the current AMR state of affairs might be bad and getting worse. But it’s not as bad as it could be. We have half the antibiotic paddle, and have to use it twice as hard. Awkward though that might be.

We’ll get into the task ahead, how we’re going to implement and coordinate it in future posts. But for now, we’d like to reassure loyal readers of this Blog that we have not been drifting in the quiet upper reaches of the Swan River for the last six months. We’ve assembled a first class international group to help us make AMR history. For a few clues on how to turn the tide on AMR, have a look at the O’Neill Commission’s report on Rapid Diagnostics.

Our plan is  ready to roll.

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recent publications:






the Gnome returns

SE over TF gulls

Regular readers of this blog have been speculating about the Micrognome’s disappearance for some time now. Rumours about: had the Gnome become so micro that he became was invisible, or was he plucked from the woods by a large bird of prey? Those of you who know better realised that when the gnome needs a long walk in the woods, there’s usually a good reason. To put it another way:

“Not all that happens in life appears in Facebook”

So what has the Gnome been up to in the last six months?

[the extended micrognome family can find the downloadable version of scientific journal papers on ResearchGate

Ebolavirus response

Melioidosis, or why those cultures stink

Antimicrobial resistance countermeasures

Expeditions: Denmark, Norway, Sri Lanka

Language learning

Learning the lessons of history (the Battle of Waterloo bicentenary)


Don’t forget Ebola

Ebola 14Don’t give up on Ebola now

The current Ebolavirus epidemic in West Africa refuses to go away. No matter what we throw at the virus, it stays one step ahead and continues its destructive course through impoverished rural communities. There have been successes, but recent reports from the World Health Organization have been guarded. The optimism that set in after Liberia declared its hard won disease-free status in May, has given way to more sombre warnings. The reason for this new-found pessimism can be found in new cases occurring over an expended area.

Don’t ignore the latest figures

  • 27,305 cases (confirmed + probable + suspected
  • 11,169 deaths (probable + suspected)
  • 869 health care workers have contracted EVD

During the last week there were 24 confirmed cases, slightly lower than the 27 reported in the previous week. These occurred in Guinea and Sierra Leone.

Between 2nd and 14th June there were 76 confirmed cases, 69 (91%) of which were from just three prefectures in Guinea and two districts in Sierra Leone. Most of these were from identifiable sources or contacts, but 14 had no known source. Effective management of these unknown source cases is essential before a target of zero new cases can be achieved.

Enhanced surveillance has been introduced as follows:

  • Guinea. Health checkpoints, door-to-door case finding and surveillance, sanitization, tracing of high risk contacts
  • Sierra Leone. A large operation has been planned to end secret movement of cases, contacts and bodies

In March, one year after outbreak recognition, the WHO reported 77 operational field sites, more than 700 staff in three countries with continuing transmission. The epidemic officially ended in Liberia on 9th May. But after a 10 month low during the week ending 20th May, the Ebola epidemic started to increase in both intensity and affected geographic area. On 3rd June 25 new cases were reported, on 10th June 35 new cases (revised to 27 the following week), and on 17th June 17 new cases.

It is clear that the epidemic is far from over.

Don’t put West African Ebola in the too-hard basket

There has been a sustained push to improve Ebola countermeasures, summarised by the WHO:

  • Vaccines – 8 candidates under development. Not expected to be available for general release until the end of 2015. The low number of Ebola cases is an obstacle to the final (phase II) clinical stages of evaluation.
  • Convalescent blood or plasma – 3 main studies under way
  • Antiviral agents and immunotherapy – 10 candidates under investigation
  • Rapid Ebola diagnostic tests for field use – 4 methods brought into conditional use

Progress has been made in a short time frame. It is vital that this concentration of effort does not dissipate before the West African Ebola epidemic has been brought to an end.

Micrognome, 21st June, 2015.