The 2013 Micrognome Report

The 2013 Micrognome Report

And what a year it’s been for the Micrognome. We’ve been sent in a spin by moves this way and that. But as 2013 comes to a close, we can say that we have a new home at last. So, thank you to all those kind souls who helped us along the way.

Fligt out crop

View towards Boram airport from Wewak Hospital

This year some of us have had the pleasure and privilege of working with inspiring colleagues in remote places like northern PNG. We salute their gritty determination in the face of an overwhelming burden of disease, and hope to be able to provide practical support in future through the Lab Without Walls and its partner organisations such as the Living Child.


Teaching and training have figured a lot in the 2013 calendar. We were able to launch a major eBook on Clinical Microbiology and made good use of the Pathology eLearning centre at UWA to flip the classroom. Despite this, we successfully debated against the tide of Dr Google. How long we can keep this up remains to be seen.


small group at work during malaria?TB ePrac

Small group at work during malaria/TB ePrac

Finally, in 2013 we said our final farewells to two international figures who stood at opposite ends of the development spectrum: Nelson Mandela, who sought understanding, respect and reconciliation; and Mikhail Kalashnikov whose AK-47 automatic rifle became synonymous with another method of dispute resolution. There is little doubt whom we admire the more. By the end of the year we had engaged in health development projects overseas in Africa, the Indian Subcontinent, Southeast Asia and Oceania. We don’t know everything in store for 2014, but we can expect a steadily expanding programme.


The Great White Shark attack debate

The Great White Shark attack debate

The great shark debate has stirred once again, just as Western Australia gets into summer holiday mood and heads for the surf. Why, in a year when there has been only one fatal shark attack off the Western Australian coast, have we got into such deep water over shark control? This hotly debated issue is unlikely to be resolved in the near future.


GWS mini

Are shark attacks on the increase?

The experts who keep the Australian Shark Attack File (Taronga Zoo)records note that there has been a global increase in shark attacks, but the proportion of attacks that result in a fatality is close to the global average of 30%. The general consensus is that the number of attacks is a function of the increasing number of people getting into the water. You can read the WA figures from the last decade several ways, which might explain the wide differences of opinion. It looks like there might be a general trend upwards in fatal attacks. That is particularly true if you include likely or presumed fatal shark attacks. But the figures fluctuate wildly [detailed figures], and the annual numbers are too small to spot a local trend. As noted by several expert groups, drowning deaths are many more times commoner than fatalities from shark attacks.  But it seems that most people know someone who has been in the water during a shark attack.

SA graph 2013

Fatal shark attacks include those deaths presumed due to shark attack. Data sources: Australia Shark Attack File, Taronga Zoo and Global Shark Attack File.

Can they be controlled?

Perhaps the heart of the shark debate is what we should do about it. Shark patrols are controversial. Official warnings are all too often ignored by the more adventurous. Water sport enthusiasts and recreational fishermen will go far beyond the limits of nets, patrols or other surveillance. The shark net programme in South Africa has been relatively successful. But the value of shark culls is more hotly debated. Their appeal may be more a matter of revenge or retribution, rather than evidence-based risk reduction.

Read more about the background to the debate in the links below.

Shark attack prevention; some useful information sources


Back story

Back story or back to basics?

Our tale of a bad back, recently posted online by no less than the New England Journal, has a bit of background for students of microbial trivia. The Klebsiella that caused that specific infection had a collection of nasty attributes. This is the back story.

For some years now we have recognised a particular collection of destructive outcomes from Klebsiella pneumonia infection. These include liver abscess, meningitis, pleural empyaema or endophthalmitis, all of which are more common when the Klebsiella strain makes a sticky mess on the agar plate. Hence the name for the condition: hypermucoviscous (HV) Klebsiella syndrome. These strains can be detected in the clinical laboratory using the string test,  which uses a bacteriological loop to tease out a long string of mucoid Klebsiella capsule material.

string test

That’s all very well, but doesn’t completely explain why gas forms in tissues or in the case we reported, a vertebral body. And here’s where a knowledge of bacteriology comes in handy. Klebsiellas produce a compound called acetoin during fermentation reactions (demonstrated by a positive Vosges-Prokauer reaction). And the acetoin pathway produces twice as much CO2 during glucose fermentation than the alternative pathway used by E.coli and many other enteric bacteria. From there on it is easy to put the story together. Klebsiella will use glucose in anaerobic conditions to form acetone and gas.

Now, some people suggest that the hypermucoviscous Klebsiellas are very different from the strains with multiple antibiotic resistance. But recent data from the Indian subcontinent tells a different story. There, highly virulent Klebsiellas can also be very antibiotic resistant. Though we have yet to see a convergence of these on a large scale closer to home,  it is clear that HV Klebsiella is gaining prominence on a global scale.