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.




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.


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


Cheese and disease

Cheese and disease

IJM cheeses
According to an eyewitness account, the pre-Christmas queue for the Stockbridge branch of cheesemonger IJ Mellis stretched out of the shop and down the street. Cheese, with crackers and dried fruit, has become a popular alternative to Christmas pudding in family dinners. The gnome wonders if there’s a belief that cheese is a solution to our annual season of over-indulgence. True: the enormous variety of specialty cheeses provides a decent choice of tasty nibbles to round off the Christmas feast. But it is not all plain sailing with water biscuits. Cheese has its association with a range of diseases.

Cheese and infection

Granada cheeses
Reliance on bacterial culture for the form, taste and texture of cheese introduces a potential risk of infection from cheese-borne species like Listeria monocytogenes, Salmonella enterica and Shigella-like toxin producing Escherichia coli. These infections are uncommon in the overall scheme of things. But changes in industrial cheese production in the 1970s and 1980s were associated with an increase in Listeria infections, generally attributed to low acidity, high moisture content (soft) cheese [1]. Since then there have been improvements in food standards, reducing the risk to cheese consumers. A recent American study showed that there were differences in the pattern of cheese-associated infection outbreaks between unpasteurised and pasteurised cheeses [2]. Mexican style soft white cheese (queso fresco) was the commonest unpasteurised source, while cheese made with pasteurised milk was a commoner source of infection when poor food hygiene practice resulted in contamination after cheese production. Some countries, such as Canada have introduced a short heating step to reduce pathogenic bacteria and spoilage organisms without losing the species that contribute taste and texture [3]. While some disease-causing bacteria can theoretically survive cheese manufacture, it appears that others including Campylobacter, Clostridium and Yersinia species do not last the entire production process which may explain their absence from cheese associated infectious outbreaks.

Cheese and non-infectious diseases
Cheese has been blamed for various ailments in some circles. But the news is not all bad. Cheese is one of the full fat dairy foods associated with better cardiac health in the long-running Luxembourg study [4]. For those interested in a possible explanation the French, who currently hold the world record for consumption of blue-veined cheese, may be reducing their risk of arteriosclerosis by consumption of an inhibitor of Chlamydia pneumoniae propagation [5]. More good news: the risk of pancreatic cancer does not appear to be influenced by consumption of any full fat dairy product including cheese [6]. But before the cheese lovers reach for another cracker, there are rumours that cheese consumption may be linked with a small increase in Parkinson’s Disease risk [7]. Clearly, this is a possibility that needs lengthy discussion during the final stages of dinner. Try talking with a mouthful of oatcake crumbs.

Cheese spoilage
Starter cultures for cheese production are usually pure lactic acid bacteria. Some strains are poor acid producers and are known as non-starter lactic acid bacteria. These may be important to the taste and texture of a finished cheese, but can contribute to increased acid, excess gas production or unpleasant flavour, and thus spoil the cheese. Foodborne infection attributed to cheese and cheese spoilage are not the same thing. But the two phenomena overlap, at least in the sense that spoilage can indicate poor hygiene during the production process. Cheese spoilage is important in its own right as a contributor to loss of taste, texture and consequent wastage. Greater reliance on refrigeration of milk before use in cheese production contributes to the presence of cold-tolerant bacteria that can cause discolouring of the cheese surface, unpleasant smells, a bitter or rancid taste. Pseudomonas species in particular can discolour cheese as in the blue mozzarella event of 2010 [8], interfere with ripening and increase the moisture content so that it becomes runny. Coliform bacteria (Escherichia, Klebsiella and other species) can cause an unpleasant or even putrid smell, or excessive gas. Could you pass the cheese, please?

TEL cheese

1 Lopez-Valladares G et al. 2014. Human isolates of Listeria monocytogenes in Sweden during half a century (1958-2010). Epidemiol Infect 142: 2251-60.
2 Gould LH et al. 2014. Outbreaks attributed to cheese: differences between outbreaks caused by unpasteurized and pasteurized dairy products, United States, 1998-2011. Foodborne Pathog Dis 11:545-51.
3 D’Amico DJ. 2014. Adventitious microbes can affect the safety and quality of cheese. Microbe 9: 99-104.
4 Crichton GE, Alkerwi A. 2014. Dairy food intake is positively associated with cardiovascular health: findings from observation of cardiovascular risk frequency in Luxembourg study. 34: 1036-44.
5 Petyaev IM et al. 2013. Roquefort cheese proteins inhibit Chlamydia pneumoniae propagation and LPS-inducted leukocyte migration. ScienceWorld J 140591.
6 Genkinger et al. 2014. Dairy products and pancreatic cancer risk: pooled analysis of 14 cohort studies. Ann Oncol 25: 1106-15.
7 Jiang W et al. 2014. Dairy food intake and risk of Parkinson’s Disease: a dose response meta-analysis of prospective cohort studies. Eur J Epid 29:613-9.
8 Nogarol C et al. 2013 Continue reading

2014 molecular microbiology meeting

Molecular Microbiology Meeting, Waterview, Sydney, 5-6th March, 2014.

As is often the case with specialist national conferences, the recent Molecular Microbiology Meeting was an exceptional opportunity to share ideas and learn from others working in the same field.  The choice of which four talks to review was a difficult one, particularly for the MicroGnome, who took notes from dawn to dusk on both conference days. Topics covered by the speakers ranged across all the main categories of infective agent, through diagnosis, antimicrobial resistance and molecular epidemiology, to emerging biotechnology and clinical pathology lab administration. With a tight timetable, speakers were notably disciplined in keeping to schedule, which allowed plenty of time for questions.


Here is a taste of what you missed:

Whole genome sequencing for bacteriology, S Bentley, Cambridge

Molecular microbiology methods are being used increasingly in laboratory diagnosis, detection of antimicrobial resistance, in outbreak investigation and to investigate vaccine escape. The impact of bacterial whole genome sequencing (WGS) is being felt in analysis of mutations, single nucleotide polymorphisms, and of gene presence/absence. WGS applications in bacteriology include identification, assessment of virulence, antimicrobial resistance, potential vaccine coverage and phylogenetic relationships. Challenges of translation of WGS into clinical applications include integration into the clinical laboratory, infection control practice which requires, in turn data interpretation, reporting and database management, linked to what the physician user wants. Notable examples include:

  • MRSA transmission pathway mapping, which is more discriminating by WGS than by MLST. Potential cost savings by application of WGS to infection control.
  • XDRTB where continued spread may occur due to the length of time required to culture then analyse the bacteria. Faster detection of XDRTB can inform treatment decisions.

Carbapenemase-producing Enterobacteriaceae, GM Rossoline, Siena

Several distinct families of carbapenemases have emerged. These are transferable, in high risk bacterial lineages that retain their virulence. They include three main types; KPC, OXO-48-like and the metallobetalactamases (MBL), IMP, VIM & NDM. The KPC form of resistance arrived in Italy in 2008 and has since spread widely so that it was common by later 2013. It is also widespread in Greece. Treatment options are limited and suboptimal, so that there is increased risk of treatment failure. There is newly emergent Colistin resistance in these bacteria, which removes one of the last remaining effective antibiotics. Selection of stable Colistin resistance in the absence of the antibiotic has occurred, with stepwise increase in resistance. Colistin should therefore not be used alone for treatment of KPC+ Klebsiella pneumoniae infections. CPE remain in the intestine for prolonged periods and thus remain a risk to the patient and their contacts. New antimicrobial agents are being assessed including combinations with betalactamases inhibitors. But for the meantime, we will have to rely on combination antimicrobial therapy, infection control and antibiotic stewardship.

Vancomycin resistant Staphylococci, B Howden, Melbourne

MRSA first came to attention in 1961 and has since become a recognised cause of high mortality infection. In 1991 an ability to form a Vancomycin high MIC subpopulation was noted, and subsequently referred to as heteroresistance. The evolution of high MIC Vancomycin resistant S. aureus (VRSA) was demonstrated in 2009 as a result of a chimeric plasmid containing elements of enterococcal origin. Transcriptional analysis demonstrates key differences in bacterial capsule, protein A and aspartate synthesis. Changes in a two component system affect bacterial cell wall metabolism and are associated with increased cell wall thickness. In a hollow fibre infection model run over 10 days, variable vancomycin doseage was associated with changes in the genes coding for the two component system. Serial passage of the bacteria showed reduced fitness. Tracking the evolution of S.aureus during the course of prolonged systemic infection, small colony variants were seen to emerge with time. These observations may explain why rifampicin resistance emerges quickly when given simultaneously with Vancomycin.

Bacterial detection and dynamics in sepsis, Westmead group, Sydney

The key problem for the clinical laboratory in sepsis is that culture takes 24-48 hours to generate useful results and nucleic cid amplification tests still take 12-18 hours, when critical results are needed within 5 hours. In a study that used 16s DNA targets to identify the bacteria responsible for DNAaemia in sepsis, results were available in a few hours. Satisfactory explanations were available for the few initially discordant results. For Gram negative species, DNA positive results persisted for up to 3 days, but Gram positive cocci subsided in most cases by 24 hours. Although there are hundreds of Gram negative antibiotic resistance genes, a much smaller selection can be used to predict the majority of clinically important resistance types. Optimal choice of anticoagulant is needed for the blood sample tube. Higher bacterial counts in severe sepsis and septic shock make detection easier in these patients.