This is the time of year when we reflect on the event of the past year and prepare for what might be coming over the horizon. 2011 was a year of steady progress in the field of infectious diseases, with notable milestones in all of the big three and some game-changing developments for other infections.

The MicroGnome has picked a handful of achievements for this 2011 MicroGnome review that should inspire anyone with an interest in infection. If you have been living under a stone all year, maybe you should try the coffee zone for a less demanding read.

• Malaria: progress made on a malaria vaccine that works

Reporting the preliminary results of a phase three trials of the RTS,S vaccine candidate in neonates and infant groups from seven African countries over 14 months, the authors of a November paper in the New England Journal of Medicine reported a halving of malaria, and a 45% reduction in severe malaria cases. While these effects are far less than routinely used childhood vaccines, they raise hopes for development of a mortality-reducing malaria vaccine.

• Tuberculosis: working out rapid molecular tests for TB in low income countries

Promising early performance studies prompted the World Health Organisation and other donor agencies to equip clinical laboratories in resource-poor countries with rapid molecular screening tests for pulmonary tuberculosis. In a useful review of this application of molecular microbiology, Carlton Evans explains the need for caution in the introduction of this technology to low and middle income countries.

• HIV/AIDS: antiretroviral therapy has a primary preventive effect

There is a growing awareness of the potential for antiretroviral agents in a preventive role. In a mathematical model of the cost effectiveness and impact of different strategies, an international group showed that effective preventive pre-exposure prophylaxis of the uninfected partner could be more effective than commencing ART earlier in the infected partner.

• Septicaemia: MALDI-TOF speeds up bacterial identification in septicaemia

The application of mass spec-based methods for identifying the contents of blood cultures has been gathering pace in Europe for several years, and has started to spread to other parts of the world. While some clinical laboratory directors might have their heads stuck in the sand, there are plenty of pathologists who would give an arm and a leg for equipment that can trim around 24hr or more off the time to identification of bacterial causes of septicaemia. Klein and colleagues are one of many groups working out how to implement this emerging technology in a busy clinical laboratory service.

Influenza: working out why the vaccine had adverse effects

the adverse effects of Australian produced vaccine are thought to have been due to suboptimal virus splitting by a deoxycholate-based procedure. Benefits of vaccination still outweigh the risk of adverse effect.

• Dengue fever: vaccine trials promise improvements in dengue control

A phase three trial of a tetravalent live attenuated vaccine against dengue virus is now under way. Once industrial production of this promising candidate has been established, its efficacy confirmed and administration optimised, it will be of considerable interest to many parts of the tropics where dengue is a substantial burden on the public health.

So what’s in store for 2012, apart from more of the same?

At a guess, it looks like we’re going to drill deeper into severe sepsis, see an expanding series of field studies and continue our peripatetic investigation of tropical infectious diseases. The language of infection series is set for significant expansion in support of teaching and training activities. One outcome of our 2011 MicroGnome Review was to recognise the need for an expanded writing team. The group sends you their best for 2012, and will now pause briefly to welcome in the New Year.

The Lab Without Walls project is ready to move up a gear, now that we have successfully completed an overseas deployment in a needy part of our region.

The following posts will show you what progress we’ve made already. They may give you some idea how you could help.

• Introduction
• Lab Without Walls in East Timor
• Opening the box
• When do we return?
• Operating on a mine site
• Thinking more widely

Lab Without Walls must now look closely at where the priorities lie.

• Where do we need to concentrate our efforts?
• What diseases should we target?
• Which patient groups are most urgent?
• What outcomes will we use to measure success?
• How best can we keep operating costs down? 

These questions will inform the foundational stages of our organisation.

A few things are certain:

• Our principal aim will be to improve the level of support for front line clinicians making point-of-care decisions about potentially life-threatening infections. 
• We will function as a not-for-profit agency, supporting other agencies whose primary role is the provision of a clinical service.
• Much of what we do will be to act as pioneers, blazing a trail for others to follow.

This won’t always be easy, but people have said repeatedly that what we set out to do couldn’t be done. It might be true that it won’t be done if we stick with the time-honoured methods. But we have shown several times over that it can be done. New and emerging technology, a clear set of clinical lab objectives and good logistic support can deliver accurate data on specific infections in places where little or no clinical microbiology service previously existed. To coin a phrase: Yes, we can!

Clearly, the places where the greatest gains will be made are where the biggest burden of disease coincides with the most under-resourced health service. Sadly, not all of these places are in developing countries overseas. There is a pressing need to use the insights we’ve gained from overseas lab deployments to meet the diagnostic support needs of remote area medicine in rural and regional Australia. We previously demonstrated advanced health threat assessment capability on a mine site in tropical Australia. Is it too much of a stretch to imagine Lab Without Walls modules operating in health centres on industrial sites, remote clinics and regional hospital labs?

The centralised service operated from a small number of clinical labs in urban centres has its merits, but falls a long way short of the point-of-care testing front line clinical staff are looking for. Recent infectious disease tragedies in nearby regional centres are confronting for those who have the imagination to see how things could improve. Lab Without Walls wants to close the gap between where we are now to where we need to be in the early and accurate diagnosis of infection.

Beware!  We had little warning. The Stafinator is here; scourge of staphylococci, decoloniser par excellence. If it needs antibacterial armour, he’ll put the tanks on the streets. If you have an exotic microbe lurking under cover, he’ll be onto your case. And as for the Resistance, he’ll be only too HAPI to make life difficult for them.

Crazy bug hunters are skeptical.  Fascinellas are laying low. The μgnome is quaking in his boots.

The μgnome scurried out of his burrow yesterday to make a few points about applied cell biology for microbiologists. The main thrust of his argument was that as we have the technology at hand, the question is no longer ‘can we do it?’ It’s a matter of practical application – what can be done with the technology, what specific applications are chosen, when these should be used and what should be done with the results.

The μgnome suggested a short list of potential clinical microbiology applications:

• attribution of a causal role to a given priobe or causal agent
• prediction of the likely course of infection
• targeting of early antimicrobial interventions
• guidance on the efficacy of public health control measures

The μgnome highlighted the possible role for advanced microscopy tools with two cases of ophthalmic infections; one parasitic, the other fungal.

Key microscopic methods demonstrated were:

• confocal microscopy (Acanthamoeba, mycorrhizal fungi)
• high resolution scanning electron microscopy (black & white images with subtitles!)
• whole slide scanning

Other methods discussed were

• flow cytometer analysis of fluorescent live/dead labelled bacterial cells
• small animal imaging for fluorescent probes
• image based reporting for parasites, fungi and mycobacteria

Asked to predict where this was likely to make a difference in clinical practice, the μgnome predicted that it would be image-based reporting of early growth bacteria in blood cultures and other sterile fluids, and possibly targeted live/dead cell analysis of drug-bug combinations to provide an early guide to antibiotic efficacy.

μgnome, 26th March