End of year review, 2016

2016 in review

A lot has happened this year. Sometimes it’s been like doing traffic duty during rush hour in the centre of Rome: lots of decisions, vehicles coming at you from all angles and no obvious coffee break on the horizon. It has left little time to review the bigger currents in the overall tide of events until now, when clinical demands continue to compete for time in the few days remaining. This review will be brief.

Antimicrobial resistant infections continue to dominate our work. The rise and rise of antimicrobial resistance grabbed the news headlines in August when the UN General Assembly debated the scale of the problem and the need for a global action plan; only the fourth time the UN has given a health issue this level of priority. As a result of securing support from the Bill and Melinda Gates Foundation for work on a new method for detecting antibiotic resistance, we had a presence at the Gates Foundation annual scientific meeting in London. It was a great opportunity to hook up with other impatient innovators and pool our efforts in the search for technology solutions to some of the world’s biggest health challenges. The conference was an important boost to our R&D programme in the last quarter, when most people are preparing for the long summer holiday. We end the year on a positive note, expecting some important news early in 2017. We’re going to have to keep readers in suspense until then.

Review 2016 in Sri Lanka

Rambutan seller, on the road between Colombo and Peradeniya

Our itinerary took us to Sri Lanka for training twice in 2016. The first time was a Rotary Global Grant activity that trained a group of clinical laboratory scientists and doctors in molecular biology methods. The top trainees were selected for a vocational training team, which visited Western Australia for additional immersion training with PathWest and University of Western Australia staff. But before that visit could take place, molecular biology equipment was delivered to Sri Lanka, and installed in clinical laboratories in Central and Northern Provinces. Lab Without Walls members travelled to Sri Lanka twice this year to support the project, and are helping Sri Lankan colleagues complete the next stage of a surveillance project on the potentially fatal tropical infection known as melioidosis.

Review 2016

Real time thermocycler’s first run in Northern Province, Sri Lanka.

Laboratory support for patients with sepsis was the focus of our initial work on regional diagnosis of septicaemia, and continued in field trials of the FilmArray technology in regional pathology laboratories. That work has expanded into a health economic study and evaluation of a similar FilmArray method for meningitis. This work in regional Western Australia was presented at national meeting in Perth and Melbourne, and European meetings in Wurzburg, Munich and Prague.

Those who want to hook up with our lab team can have a closer look at current projects via ResearchGate.

In many ways 2016 has been a year of the internationally bad, the sad and the mad. One of the sadder losses we ought to note is the passing of Jack Woodall, founder of the ProMED alerts for emerging infectious diseases. The world needs much more of his brand of enthusiastic internationalism. Considering his passing puts the work we’ve done this year into perspective. As we gaze into the start of 2017, how can we seize the day, strive to be our best and close in on those elusive millennium development goals? Let’s aim to achieve more than a bit of order in the rush hour traffic.




Missing Micrognome found lurking in northern Europe

Rumours of the Micrognome’s demise have been gathering for some time. So a search party was sent out to locate the missing gnome or confirm his fate. Fortunately our efforts have not been wasted. True, there were a few false trails, but we can now reveal that we have been able to verify recent sightings in northern Europe.


Frightened of resistance?

According to our gnomefinder-general, the Micrognome took to the woods at the news of resurgent antimicrobial resistance. At present Europe is at the forefront of the battle against resistance, bringing global attention to the subject. So no quiet retirement for the Micrognome, his colleague the MicroB, located on a mossy birch stump, or their friend the Lab Rat seen here boxed in at the Nobel Museum.


Taking AMR seriously

For those who have been waiting patiently for reassembly of our intrepid team, the wait is almost over. But there are a few skeptics out there who still don’t think antimicrobial resistance is anything worth bothering about. Well, our three bug-busters respectfully suggest they take a look at what the adults are saying about untreatable infection:

Tragedy of the commons

The Micrognome’s considered opinion is that there may be a consensus on AMR strategy, but there is still a long way to go on the application at ground level. We are missing a plan. Good ideas from the great and the good rarely percolate down from the lofty mountain heights to the the murky depths of pine forests and birchwoods where micrognomes are at home. The specific tasks to control, turn back and eventually eliminate AMR are going to take more than just the micrognome and friends to set in motion. It needs to be a giant effort to conserve the dwindling stock of effective antibiotics, reserve them for evidence based use so that their benefits are preserved for those in most need. Conserve. Reserve. Preserve. These will be the watchwords for the coming fight to overturn the AMR tragedy of the commons.

So don’t leave it to infection to test how much you’re missing on AMR. You really don’t want to end up like this interesting specimen.


Breakfast by the wooden bridge

In the second of our occasional series on breakfast refuelling points for early morning canoeists, we take a look at Lo Quay; a café on the northern side of Riverton Bridge. This crossing point is the wooden piled structure built in the 1950s to replace an earlier bridge that supported the main route East from Fremantle. When Leach highway’s heavy traffic demanded a larger crossing, and Shelley Bridge was built, Riverton Bridge settled on its timbers and now manages the slower paced traffic of a pleasant riverside suburb.

Rivo bridge

Close to the southern end of Riverton Bridge is a canoe-friendly launching ramp, and access to the stretch of the Canning River between Riverton Bridge and Kent Street weir. An early morning paddle on a lazy summer’s day is a good time to see herons, pelicans, grebe, cormorant and the occasional sea eagle sorting out their breakfast menu. The smaller birds look like they’re hovering centimetres above the water surface in the shimmering heat. Jellies get this far up river, and shoals of fish break the surface to taunt the predatory birdlife perched in branches of drowned trees at the water’s edge. A short paddle upstream through the Canning River Park  takes you past river islands, banks of reeds and one or two shore-bound fishermen. But your human company is almost entirely the handful of kayakers who pass with a brief greeting and get on with their personal journey. Less than 10 in 2.5km today. This is delightful solitude; decompression after the rigours of  a fast -paced week at work. Afterwards come the breakfast.

Floating birds

Lo Quay is a bustling Saturday morning breakfast/brunch hub with a loyal following of local clients. We were introduced to the place when it was still a burger and sandwich bar several years before the dawn of good coffee. After a rebuild it took on a new purpose in life: bringing a bistro menu to this perfect location under the trees on the northern bank. Its appeal spans family groups, couples, weekend cyclists, social canoeists and suburban residents who have to make do with breakfast here if they run out of sourdough bread, eggs and smoked salmon. Service can be a bit slow during the breakfast rush hour.


Too late for breakfast? The lunch menu is not bad.


Zika infection – five facts


5 facts

  1. Zika virus is a flavivirus, the same group as dengue virus

  2. Infection is spread by Aedes mosquitoes

  3. Congenital anomalies including microcephaly have been linked with Zika virus infection during pregnancy

  4. Women who might fall pregnant are being asked to postpone travel to active transmission locations

  5. Zika virus is not endemic in Australia

  • Zikavirus é um flavivirus , o mesmo grupo que o vírus da dengue
  • A infecção é transmitida por mosquitos Aedes
  • As anomalias congênitas , incluindo microcefalia têm sido associadas com a infecção Zikavirus durante a gravidez
  • As mulheres que possam engravidar estão sendo convidados a adiar a viagem para locais de transmissão de activos
  • Zikavirus não é endémica na Austrália

For guidance on how to assess the strength of evidence for a causal relationship between an emerging infection and its effects, see Principia Aetiologica.

For updates on Zikavirus infection see:

Breakfast rocket science

The weekend breakfast

OK, so there are a few secret breakfast haunts hidden away in the southern suburbs: essential support stops for urgent calorie replacement after a brief burst of uncharacteristic activity. Perth has grown a good crop of decent breakfast venues in neat beach or riverside locations these last few years. Some of them have come and gone. Others have sprouted wings and flown off elsewhere. This post is not about the high turnover crowd pleasers. The Micrognome, while considering the challenges of a new semester, has discovered a collection of hidden gems. And here’s one for starters: Coco Belle in Mount Pleasant.

CB breakfast

Rocket food: Back a few streets from the Canning River. Unencumbered by  river views, or a super highway for the lycra-clad, Coco Belle has quickly found a place on this social paddler’s Saturday morning breakfast map. The menu options offer an indy twist on the standard menu. No common-or-garden eggs benny here. Three of us went for wildly different options, and were all rewarded with palate pleasing dishes. The field mushrooms with goat’s cheese, rocket and poached egg was masterly. The goats cheese was delicate and ever so slightly sweet. The rocket got a kick from the few chives they stirred through, complemented nicely by a hint of sweet balsamic. No risks from dodgy lettuce there. The poached eggs were at that critical tipping point shortly after arrival at our table.The gnome was outclassed by his partner’s generous bowl of granola with rhubarb and berry compote, and had to face off against a stack of pancakes with a side serve of bacon.

CB plate

Ambience: relaxed Saturday morning haunt with varied seating options from sit up to sit back

Price point: $$

Location: corner Queens Rd and Reynolds

CB map