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.

POCP2

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.

 

Lab Without Walls reviewed

At long last we can go public on what the Lab Without Walls team have been up to in the last 12 months. Thanks to the American Society for Tropical Medicine and Hygiene, the story of the field portable molecular lab is now in print. The story so far, that is.

The Lab Without Walls is a collaborative, not-for-profit organisation (Lab Without Walls website). We welcome active participation from health professionals and lay people who want to help strengthen scientific support for health care in remote, rural and regional communities.

spot the lab in the suitcase

Gibb River Road, Aug 2012

For those with access to the American Journal of Tropical Medicine and Hygiene, the guts of the story can be found in two table and a map. The map provides a snapshot of where we’ve taken the Lab Without Walls. The summary of what we’ve done once we got there is in table form. So are the lessons learned.

Scientists, epidemiologists and pathologists who work in large clinical labs rarely enjoy these challenges. Deploying a field lab is no mean feat. A lot of planning goes into each expedition. You may find the additional details on the website useful. So, if you’re planning a public health or diagnostic laboratory response to emerging infectious diseases, we’d be grateful for your critical feedback.

 

Bread Winners in search of germs overseas

On the Asian bread trail

The crazy bug hunters have been at it again. This time they took to the air courtesy a mixed bag of budget Asian airlines. They converged on the northern Malaysian city of Ipoh for a field applications worship. There we were welcomed by the staff of University of KL’s Royal College of Medicine Perak. In Ipoh they take their hospitality very seriously. We were sampling fresh local bread less than 24 hours after arriving. Here is a view from the top floor of their rather smart building, looking over a nearby mosque.

And this is the first of our encounters with freshly made bread. It was served as an accompaniment to Moroccan lamb, tabouleh and other Arabic delicacies. By the time we’d made it back home, the team had sampled naan, dosai, pakoras and the wonderfully calorific murtabak. Plain white bread is, well, just plain by comparison.

Another bread for the team

The bug hunters did get down to some serious field work before knuckling under with their set of automatic pipettes. Here they are among the tea bushes in the Cameron Highlands (home of the giant strawberry, for Australian collectors of bizarre giant replicas). The last time we were in tea growing country was June this year when we deployed our field lab to Central Province, Sri Lanka. Our photographer captured the moment the yellow tops came into evidence among the bushes.

tea bags?

Once in the lab it was time to sweat the small stuff. That’s how we earn our crust, working systematically through a series of samples with our Lab Without Walls field portable equipment set. Here you can see a Micrognome demonstrating the use of a Mk I head as a substitute for an anglepoise lamp, while one of the workshop participants dispenses PCR reagents.

two legged lamp stand

And the results of our bread run?

  • blood culture confirmatory PCR panel run on positive cultures same day
  • 5 of 6 suspected Burkholderia isolates confirmed as B. pseudomallei AND shown to be SE Asian clade by PCR assay
  • 3 of 5 hospital admissions shown to have dengue virus genotypes 1 or 2 on same day
  • hands on familiarisation with field applications of molecular microbiology in national workshop
  • lectures on severe sepsis, melioidosis and other activities of the Lab Without Walls

out of the box and into action

Ipoh has a great reputation for Asian food and is now a direct budget flight from Singapore.

 

Melioidosis – the movie. The Lab Without Walls goes to air

ABC Catalyst feature in full (YouTube).

The Micrognome can now reveal what the team got up to during National Science Week  – caught on camera by the ABC’s Catalyst programme digging for bacteria.

Melioidosis shoot

The story is about a significant shift in thinking about the origins of a tropical infection well known in the gnome home. So we’ve gone up in the world, from our own YouTube videos to stunning professional documentary. Maybe not movie-length yet, but we’re working on it.

 

 

This is not the place to spill the beans on Catalyst’s storyline. You’ll have to wait for the programme to air on Thursday 1st November. But you can get a sneak peek here.

Other microbes on the map

The Catalyst feature tells the story of one of the major themes we pursued during the Lab Without Walls roadshow earlier this year. The other theme was a group of mosquito-borne infections present in the region: Ross River and Murray Valley Encephalitis viruses. Molecular biology on the move – arboviruses or tropical bacteria; take your pick. We took the augur. And the GPS. There’s a geographical theme emerging here and a lot of gaps to fill in. So it’s not surprising that the team had to cover a lot of ground (a) to get to sampling sites, and (b) to join the existing dots on the map. GIS meets Taq polymerase.

Road show

Catalyst interviewed melioidosis researchers from WA and the Territory, explaining the connection between the ecology of the causal bacteria and the infection it causes. The transcript is available in full on the Catalyst website, and is followed by an extended Q & A session with viewers.

End of the road for LWW roadshow

So that’s it: the end of our travels. The field survey team made it from one end of the Gibb River Road to the other without a single puncture. Quite an achievement when you consider the number of shredded tyres spotted by the side of the road.

National Science Week videos

Other than a hundred kilometers at the western end, and patches of road reinforcement on hilly sections, the Gibb is unmetalled dirt track. Graded once a year to make good the damage caused by wet season rains, this route heads off through the backblocks of the West Kimberley in an easterly direction. Its eastern end is near El Questro station, just west of Kununurra.

vibration damage to search engine

We covered more than 1,000 km including offshoots towards Mornington Wilderness Camp and Drysdale Station for overnight stops. This was the meat in the road show’s sandwich. National Science Week had the Lab Without Walls team in Broome and Derby for public demonstrations of mosquito trapping, soil collection and analysis techniques used in surveillance of tropical infectious diseases. These were meet-the-people public science events.

spot the lab in the suitcase

But once we hit the red dirt and flinty rocks of the Gibb River Road, all eyes were on the road ahead and its challenges. National Science Week activities through this stage of the roadshow comprised more informal encounters, such as conversations with road house owners during refuelling stops, or impromptu camp fire talks at outback stations. Not quite pathology in the pub, but a great setting in which to talk about your work and why it matters.

Gibb River crossing

The Gibb River Road stage of the road show was much more than soft science, since the team needed to get some serious work done along the way. It was a great opportunity to look for dry season environmental reservoirs of two distinct groups of tropical diseases; arbovirus (mosquito borne viruses) infection and Burkholderia pseudomallei, cause of melioidosis. That entailed soil sampling during the day and mosquito trapping at night. Drilling  out 10cm cores of heavy soil by augur down to 1.5m was hot work under the Kimberley sun. Mosquito trapping at night was a lot cooler, especially while the supply of dried ice held out.

Sampling a soil core

We processed our soil and mosquito samples at station after station, running the PCR assays every night along the way. Despite the bumpy ride, our portable thermocycler didn’t miss a beat, even continuing its analysis when a working station’s generator cut out briefly. Knowing the gear can survive these conditions is a big step towards equipping remote pathology centres with this kind of equipment.

Trapper at sunset

National Science Week brought us into contact with lots of delightful people we’d never have met any other way. Our overall score was over three hundred encounters between Broome and Kununurra. Local, State and national media (radio interview) ensured that news of our activities circulated much more widely. This blog will link you to additional media coverage of our road show as it comes up.

Lab Without Walls roadies

The team might have reached the end of the road, but we have plenty more work to do. An expedition like this always generates a heap of follow-on work. We will run confirmatory tests, write reports, answer some of the questions raised along the road, and possibly even draft a scientific paper. We kicked up a lot of dust between Broome and Kununurra. It will be a while before it settles. But we already know there are folks doing some great science in the Kimberley. A short list to watch out for includes:

  • PathWest clinical labs in Broome, Derby & Kununurra
  • the groups working on Roebuck Bay environmental sustainment
  • the Australian Wildlife Conservancy research group at Mornington Wilderness Park

Lab Without Walls thanks you all for your interest in our work. We look forward to helping you with yours.