Friday, 14 December 2012

Newsbite: Terbinafine Offers Benefits for Avian Aspergillosis

Aspergillosis is one of the most difficult diseases to treat successfully in avian species. Terbinafine  offers numerous potential benefits over many common antifungals for treatment of this disease. This paper explores the pharmacokinetics of nebulized terbinafine in Hispaniolan Amazon parrots (Amazona ventralis).more...

Thursday, 13 December 2012

Common Misconception Refuses to Go Away

This recent article from Ireland  states that work has been halted on the building of a new hospital in the Mid-West of Ireland because of fears of infection by the 'virus aspergillosis'

Galway builders JJ Rhatigan & Company have pulled around 30 workers off its construction site in Dooradoyle, and closed it until the HSE acts to install filters, and seal up windows to prevent the Aspergillosis virus getting on site.
Ger Mullane, of JJ Rhatigan, says it is the HSE’s responsibility to install the filters, not his company’s.
The condition is carried by dust in the air. Common when demolitions are taking place, if building workers inhale the spore, it can cause a range of illnesses from coughs and fevers to chills, delirium, blood clots and failure of vital organs.
This is of course incorrect as people with a healthy immune system have little to fear from inhaling the amounts of fungal spores normally present in the air, indoors and out. Our lungs are populated with plentiful neutrophils which destroy the fungus before it can do any harm.

The people at risk from building works close to hospitals are not the construction workers (other than those allergic or asthmatic). Those at risk are the patients who are suffering from illnesses that cause problems with their immune system (e.g. neglected diabetes, HIV) or who are being treated with drugs that suppress our immune systems (corticosteroids, some drugs used to help transplant recipients) or who have had their immune system removed for a short time while undergoing treatment for some cancers.
There is also another category of people at risk that includes those who suffer from severe asthma with fungal sensitivity (SAFS) and allergies.

This point is made by the hospital spokeman later in the article in question
“When you carry out demolition works, you obviously create dust. The dust can, and usually does contain an organism called aspergillosis. When you seek excavation, or do demolition, you release this, and it can be contagious. People who have lung problems or breathing difficulties are susceptible to inhaling that spore. If you are working in a hospital environment, you will seal up the windows and the fans, and put in better filters, meaning the spore will not get into the hospital,”
Ironically Ireland is one of the few countries in the world that have a written protocol for precautions to take when running a hospital close to building work, so this is one subject we could expect the Irish media to get right! Oh! and while they are at it they might remember that aspergillosis is caused by Aspergillus, a fungus, not a virus.

Tuesday, 11 December 2012

Newsbite: 5 Million ABPA Sufferers Globally

New research released by the National Aspergillosis Centre estimates the total number of people in the world likely to be suffering from Allergic Bronchopulmonary Aspergillosis (ABPA) to be nearly 5 million people, 400 000 of these will develop the more invasive Chronic Pulmonary Aspergillosis (CPA) as a complication more...

Monday, 10 December 2012

UK Lung Disease Reorganisation Criticised By Doctors


1000 National Health Service (NHS) doctors have signed a letter to the government expressing serious misgivings about the dissolution of NHS regional boards. Regional boards plan services and training for employees of the NHS professionals.

 The current UK government heavily criticised the existing regional structure and in part of the political manifesto on which it was elected it opted to abolish many of the powers of the regional boards and replace them with a national independent body which will act through regional boards, claiming this to be a more efficient, streamlined system.

Unfortunately the regional boards seem to have been credited with vastly improving the standard of care for lung diseases in the UK and many doctors don't want to lose this organisation. The letter says:
"The respiratory improvement programme started by the Department of Health just two years ago is starting to make real progress in improving respiratory care, whilst also saving the NHS money. "Yet the support and funding for all this work is being withdrawn from April 2013, just at the point when patients are about to really benefit. "We are concerned that patients living with respiratory disease will be left behind in the new NHS."
The NHS is having to absorb many significant cuts as part of the need to reduce national dept incurred after the credit crisis in 2008. The new national board will be charged with making many of those savings and has the power to decide on staffing and service levels. There is thought to be potential for local needs to be ignored and this protest may well be part of the many protests designed to prevent service reductions in what doctors see as important areas to maintain.

Thursday, 6 December 2012

Mouldy Bread a Thing of the Past?


Bread is one of the major reasons for food waste in many countries of the world - in the UK a third of all bought bread is thrown away due to becoming mouldy. The average family in the US for example throws away 40% of its food. Much of this discarded bread is perfectly edible, it has not dried out and gone stale but has become mouldy.

This is thought to be partly because bread is kept moist using plastic bags for storage as the moisture that is trapped encourages the growth of the principle common bread mould Rhizopus stolonifer and any other moulds that may land on the bread.

 If we could sterilise the bread after enclosing it in its plastic bag the chances are that the bread will be edible for some time.

Research carried out by a group at the american company MicroZap have developed a technique to achieve just that using a variant of the microwave technology we use to heat food up. A treatment of just 10 seconds destroys all mould spores without heating the bread. Bread treated in this way lasts for 60 days without getting mouldy (and presumably with the plastic container bag not having been opened), potentially allowing us to radically reduce waste.

Once opened though I would imagine that the bread would still be vulnerable to spores in the air landing on it and germinating so bread moulds may not be completely eradicated.

 The designers of the sterilising machine also mention that the use of this machine might enable bread manufacturers to reduce the amount of preservative added to bread that some people may find unpalatable. BBC News story

Wednesday, 5 December 2012

Genome Mining - Visualisation

Researcher surrounded by data
Genome mining is a new technique that is leading to the efficient and rapid identification of useful new microbial gene products (See the last blog for new antifungals identified using this technique) by directly analysing the product and 'reverse engineering' the molecular structure to give us the genes that are producing the product via the genome DNA sequence of the organism concerned. This includes research on people in order to improve our understanding of how our bodies respond to disease and what influence our genes have  in the outcome of infections.

One difficulty with this type of research is the sheer amount of data that is generated. A human genome contains 25 000 genes and a lot more DNA besides. How do scientists effectively work with such a huge amount of data? We know that pictures relay vast amounts of information very efficiently and this company are maximising the use of that principle. Research data is projected on all surfaces of a specialised viewing room and the researcher can interact with the computer using arm and hand movements.

Together with specialised software to highlight groups of genes on demand (not that dissimilar to the ways we carry our searches on massive datasets using Google search engine) this might be one helpful way genomes and their transcriptional data can be navigated in the future.

Tuesday, 4 December 2012

New Antifungals From Bacteria

Current antifungal drugs useful to treat aspergillosis fall into four main classes; polyenes, azoles, echinocandins and a pyrimidine analogue (Full list). All have strengths and weaknesses (some are very effective but are expensive and inconvenient to give, requiring hospital visits) and in all cases there is the potential for resistance to develop in fungal isolates, eventually rendering them useless.

 There is therefore a clear need for the continued development of new antifungal drugs. There have been several recent stories about new strategies to find new 'targets' in the fungus to attack with new drugs (1, 2) but a new source is now being reported in the media. In the history of the development of antibiotics (i.e. drugs that will kill bacteria) fungi are well represented, indeed the first antibiotic (penicillin) was discovered when a fungus started growing on Alexander Flemings' bacterial culture plates and started killing off the bacteria. We now know that many micro-organisms produce toxins though to be designed to kill off competitors for food or other valuable resource.

Bacteria can also produce powerful toxins to kill off fungi and a recent study has identified one such group of  new antifungal chemicals that they have named jagaricin. This bacterium normally lives off fungal material and is known as a 'soft rot' disease of commercial mushrooms so it was a clear candidate for the identification of chemicals that might be able to kill (and eat) fungi.

In the past researchers may have screened many strains of the bacterium and then tried to isolate the antifungal substances, identify them and subsequently isolate the genes. In the 1950's and 60's they may well have had to hunt for natural strains that produced lots of antifungal activity and then find ways to cultivate it in such a way as to enable large quantities of the new drug to be produced and purified. This was very time intensive and quite a hit or miss procedure.



 This modern research group have used techniques that are revolutionising how we can find new drugs. We can now quickly analyse an interesting new substance produced by a bacterium and 'read' its genetic structure using a Mass Spectrometer. Once we have a good idea of the genetic structure of the gene that produces the protein we can easily find it in the bacterium's genome as it ia easy to read all of the DNA in a bacterium, analyse all of the genes it contains. The gene can then be easily manipulated to produce large amounts of the interesting new gene product e.g. a new antifungal drug - a technique known as genome mining.

This revolutionary approach is already impacting many areas of drug development (and any other applicable research field including fuel production, food production etc.) and excitingly this includes  new antifungal drugs.

Friday, 30 November 2012

Newsbite: How the Cause of the US Meningitis Outbreak was Solved

For those following the recent story of the outbreak of fungal meningitis caused by contaminated injectable steroid solution, this is an interesting news article giving some perspective on how difficult it is to detect and treat Aspergillus & other fungal infections more...

Thursday, 29 November 2012

Caution! Nature's Genetic Engineers at Work

There have been many critics of the use of genetic engineering techniques to transfer genetic material from on species to another as the process is viewed as potentially dangerous, changing some modified organisms in ways that were impossible by natural processes and thus generating organisms that may be harmful to the environment in some way.

However it is becoming increasingly clear that although natural mechanisms that pass genetic material from one generation to the next i.e. sexual or asexual reproduction remain by far the most common, there are natural mechanisms that pass genetic material - in some cases containing many genes - to and  from species between which sexual reproduction is not thought possible.

We have been aware of horizontal genetic transmission for many years but it had been assumed that it was rare and limited in cope - we have noticed it happening in bacteria and viruses. A recent research paper suggests that that view should be changed. Antonis Rokas, assistant professor of biological sciences at Vanderbilt and research associate Jason Slot found that a large piece of DNA containing 23 genes had transferred from Aspergillus nidulans to Podospora anserina or vice versa at some point in evolutionary history millions of years ago.

Finding evidence for horizontal transfer of quite large gene clusters between eucaryotic organisms that are far more complex than bacteria & viruses is quite a surprise and suggests that this process is far more widespread than we thought even a few years ago, and changes the way we should now think of what defines a species and how genes can potentially be transferred between any living organism. This paper suggests that fungi can pass between them 'cassettes' of DNA containing many genes that can work together to allow the fungus to exploit a new advantage - in this case produce a toxin that would give it a competitive advantage when growing under certain conditions in the wild. In some ways this is similar to one workman lending his specialised tool to another so that he can carry out a task more efficiently.

This may well account for some of the versatility of ability of fungi to live on a huge range of foods and substrates, producing a massive range of metabolites.

How such substantial gene transfer happened remains something of a mystery as known mechanisms tend to provide ways to transfer much smaller pieces of DNA compared with this finding.

Perhaps then nature has been carrying out its own genetic engineering for millions of years, predating human efforts by a very long time!

Wednesday, 28 November 2012

Take Care When Picking Wild Mushrooms

Aspergillus is not a fungus that produces large fruiting bodies above group that most would recognise as a mushroom, but many fungi do reproduce in this way. Just as some species of Aspergillus can produce toxins under some growth conditions, so can some other species of fungus - thus some fruiting bodies (referred to as mushrooms and toadstools in many countries) are also toxic.

 Four people have died after one of the victims made soup out of a mushroom that contained deadly toxins. This unfortunate incident emphasises that it is very important that anyone collecting wild mushrooms must be familiar with what dangerous mushrooms are likely to look like & where they grow.

This US government advice page is useful and so is this UK resource but different countries may have other species of harmful mushrooms or certain types may be more common in some areas of the world - always check local information.

Tuesday, 20 November 2012

Ash Tree Dieback Fungal Disease - Why Now?

The news channels in the UK have recently carried several stories on the newly identified fungal disease of Ash trees caused by the fungus Chalara Fraxinea. The main thrust of the stories is that this heralds the arrival of a new fungal disease in the UK which will cause the demise of one of our most common trees in a similar way to that seen 30-40 years ago when Dutch Elm Disease reduced another of our native tree species from a huge tree that dominated our landscape to what is now generally growing as a small hedgerow bush. Incidentally this nicely illustrates the power of a fungus to change our landscape even today as Dutch Elm Disease is caused by the fungus Ophiostoma ulmi.

Dutch Elm Disease was naturally spread by an insect that was probably imported into the UK on a load of imported timber whereas the new Ash fungal pathogen seems to have arrived in the UK via a wind dispersal mechanism as infected imported stock had been destroyed, but this conclusion remains in some doubt as prior to being detected in the UK the fungus is not known to have travelled more than 20km via wind - and the UK is more than 20km distant from the continent!

Why do we suddenly get such hugely destructive invasions of plant pathogens? Again the story of Dutch Elm disease provides useful information. The fungus that causes Dutch Elm Disease is known to have been in the UK for many years prior to the death of all of our Elms. Our native strain of Ophiostoma ulmi was however  quite a mild pathogen and seemed mainly responsible for killing a few branches of an infected tree rather than killing the whole tree. It was the arrival of the highly virulent strain from North America that caused destruction on a large scale, and that arrival was caused by human intervation in the form of the international trade in timber.

Likewise Ash dieback has been caused by the arrival of a highly virulent strain of Chalara Fraxinea against which our native Ash trees have few defences. The isolation of our island has probably protected our native trees up until now but it is as yet unclear if human intervention was again the cause of the spread or if some unknown natural dispersal mechanism bridged the English Channel. Nonetheless this is an unusual situation and it will rapidly resolve as trees (the host) and pathogen (the fungus) interact  over the next few years - most probably leading to the demise of most of our Ash trees.

Pathogen and host usually exist side by side in a relatively benign 'war of attrition'. The fungus will have limited ability to attack the host and will not usually be able to kill it - otherwise the pathogen would quickly run out of hosts and die out itself! Each will slowly attack and defend from the other. It is only when neither has come into contact with the other that we get these spectacular die-off events and we regularly find that human activities are the cause.

What will happen to our Elm & Ash trees now? More than likely resistant strains of the host will grow out eventually and in time may repopulate the countryside, though there is a possibility that will not happen for many years. This is a completely natural process and once set in motion there is not much that we can do to stop it. Sadly Constables landscapes will not be the same again for many years.

Monday, 19 November 2012

Aspergillus awamori as a Beneficial Food for Chickens

It may seem odd that after regular stories are published about birds suffering from aspergillosis that we now find an article talking about using Aspergillus awamori as a food for broiler chickens in the press. The article is summarising a published research article that carried out an experiment whereby small amounts of A. awamori were fed to chickens and their weight monitored.

A. awamori is in fact in widespread use in the food industry in eastern countries such as Japan, known as koji. The strains tend to have been 'in captivity' in human hands for thousands of years (e.g. Tea fermentation) and are thought to be quite harmless to humans.

The experimenters found that the use of Aspergillus increased the amount of meat produced when the amount of food uptake by the chickens actually fell. This surprising result suggests that the fungus may help the chickens digest their food, but it is also suggested that chicken muscle tissue growth is also encouraged.


Friday, 9 November 2012

Winners of 'Funky Fungi' Art Competition Announced


Over 300 million people are acutely or chronically infected by fungi, leading to death, long term illness, blindness, psychological problems and reduced work capacity. Many recent improvements in diagnostics and treatment have not reached treating clinicians in all countries, and access to appropriate diagnostics and simple antifungal agents is far from universal. This needs to change.
LIFE ran an art competition for age 13 - 18 in the North West of England and North Wales running from late 2011 until May 2012, engaging thousands of schools throughout the area in an attempt to improve awareness of fungal diseases by the use of the creative arts

Project LIFE 2012 Theme: "Funky Fungi"


Fungi are beautiful and fascinating they are essential to our ecosystem in the carbon and nitrogen cycles, and are valuable in commerce as many industries require fungal activity eg. alcohol, bread and cheese making.


You will be familiar with  mushrooms and toadstools which are types of fungi, but the ones which cause disease are nearly invisible except with a microscope.

But some fungi can also cause human diseases. Fungal diseases are mostly hidden and diagnosis is often missed, around 300 million people worldwide are affected, in many different forms of illness, some of which are deadly.

The challenge was to design a piece of artwork using this as a theme. With more than 350 entries that met the challenge, these were judged by an independent panel to be the winners:


Overall Winner: Sophie Wills, Millom School, Cumbria

Judges comments: "Strength of message, strong story and deceptive naivety"


Second place: Erica Inglis, Stockport College (Ink and paper)
Judges comments: "Sensitivity, observation, insidious danger within the beauty. Beautiful image masks and invasive threat"


Third place: Jason Rhodes, Stockport College


Judges comments: "We are constantly reminded of danger - red figure, red immune system afloat in a world of hidden threats"

Congratulations to all 3 winners and the schools particularly Stockport College who had many strong, varied entries in the shortlist and finished with 2 in the top 3.



Tuesday, 6 November 2012

Bitter Tastes Initiate Our Immune System Response

It has long been suspected that we evolved to taste bitter substances and generally reject them in order to be able to identify foods that had 'gone off' after being infected with micro-organisms, but does it go further than that?

Researchers have discovered that when we eat bitter substances it can actively initiate our immune response in our upper airways, and those who taste bitterness particularly well also fight off infection of our upper respiratory tract (upper throat and  sinuses) particularly well. The infecting agents in this study were bacteria but foods spoiled by fungi are likely to have a similar bitter taste.
About 25% of us cannot taste bitterness  very well and it follows that these people may not fight off infection efficiently and thus be prone to chronic sinusitis.



Quoting from the Penn University News Report:

They found that one of the bitter taste receptors that functions in upper airway cells, known as T2R38, acts as a type of “security guard” for the upper airway by detecting molecules that a certain class of bacteria secretes.  “These molecules instruct other bacteria to form a biofilm, which helps harbor the bacteria. From previous work, we know that these biofilms spur the immune system to mount an over-exuberant inflammatory response that can lead to sinusitis symptoms.  When the T2R38 receptor detects these molecules, it activates local defensive maneuvers to increase mucus clearance and kill the invading bacteria. It’s really like modern warfare – intercept the enemies’ early communications to thwart their plans and win the battle,” Cohen said, who is also the director of the Rhinology Research Lab at Penn.
Through the cultures, the research team demonstrated that super-tasters detect very small concentrations of the offending molecules, while non-tasters and the middle-ground individuals require 100 times more of the molecule for detection.  The research team also examined the patients that the original sinus tissue samples were collected from. They found that none of the super tasters were infected with the specific type of bacteria that are detected by the T2R38 receptor, known as a gram-negative bacteria.
“Based on these findings, we believe that other bitter taste receptors in the airway perform the same “guard duty” function for early detection of attack by different types of bacteria, and we hope to translate these findings into personalized diagnostics for patients with chronic rhinosinusitis,” Cohen says.


News report at Penn University

Friday, 2 November 2012

Manchester Entrepreneur joins Rebranded Fungal Infection Trust

During the Manchester Science Festival, The Fungal Research Trust announced that Peter Folkman, a successful Manchester entrepreneur was joining the Board and The Trust was changing its name to the Fungal Infection Trust.

Peter Folkman is a graduate of Oxford University and the Wharton School of the University of Pennsylvania. His background is in technology and venture capital. Peter served on the Council of The University of Manchester and several Boards as a non-executive Director including Manchester Science Park, Manchester Technology Fund and University Hospital of South Manchester NHS Foundation Trust. He is currently Chairman of Nowgen, a centre of excellence in public engagement, education and professional training in biomedicine, primarily related to genetics.

The Fungal Infection Trust will take forward the 21-year charitable legacy of the Fungal Research Trust, with a broader remit to be more inclusive of public and health professional education and awareness of fungal diseases. The Trust was set up in 1991 and since then has distributed in excess of £3,500,000 in research grants resulting in more than 145 research publications on clinical and scientific aspects of fungal infection. It has contributed to the postgraduate training of more than 25 scientists and doctors in the UK and overseas.

The announcements by Dr Geoff Scott, Chairman, were made at the Funky Fungi exhibition held in the Manchester Science Festival showcasing art and fungi. The Project LIFE competition winners were teenagers from the North West of England and North Wales who created inspiring, fantastic art work related to fungi. The Fungal Research Trust supports the encyclopaedic Aspergillus Website at www.aspergillus.org.uk.

As well as being a key resource for clinicians and researchers, the website also devotes several sections to patients and relatives to help them understand more about aspergillosis. In a recent quarter Google searches picked up the The Aspergillus Website 2,800,000 times and there are 33,930 links to the Website from other domains. The Fungal Research Trust has also supported the development of LIFE (Leading International Fungal Education) a new initiative to make the subject of fungal infection more accessible for doctors and other health professionals. LIFE is linked to a growing advocacy movement for fungal diseases which are not recognised or supported by major health agencies internationally.

Thursday, 1 November 2012

Your Help Needed: Please Report all Antifungal Drug Side Effects

Side Effects of drugs are vitally important to identify and assess. Problems occur with new drugs because in testing only the new drug is taken by people assessing them for side effects. As we all know it is more usual for ill people to take more than one drug per day!

Different drugs can interact and cause new side effects so it is especially important to keep track of side effects of new drugs - and 'real' patients are the experts we need to consult for this research.

Many of those reading this blog may well take antifungal drugs, some of which are relatively new so we are especially encouraging everyone who takes antifungal drugs (old or new) to record all the side effects they experience using this new website set up by the Medicines and Healthcare products Regulatory Agency in the UK. The system has been in place for some time but recently it has been redesigned to allow & encourage use by members of the public rather than just doctors.

The general idea is that if a side effect is consistently reported by several different people and/or it occurs in combination with a particular drug then it will be flagged up by the system to pharmacists who will be able to adjust advice given to doctors and the public about the use of those drugs.

Please help us complete this vital work for everyone who has to take antifungal drugs by recording all the side effects you experience when taking antifungals on this website: http://yellowcard.mhra.gov.uk/ NOTE: this website is for side effects experienced in the UK only.

US patients can submit adverse drug reactions here: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053074.htm

Friday, 26 October 2012

Systematic Failings Ruling Over Aspergillosis Case

A recent coroners court case found that a 68 year old man died following a lack of precautions taken to protect him from infections including aspergillosis. Extra precautions are not usually necessary following a bowel operation such as that undertaken on Mr Michael Meek in January 2009, but in this case there were several extenuating circumstances:

  1. the  patient had had a transplant operation prior to the bowel operation and as such was presumably in an immunosuppressed state as is normal to prevent rejection of the transplanted organ (in this case a kidney).
  2. At the time of the operation there had been, or there were ongoing building works in the hospital, generating dust and dirt known to increase the risk from aspergillosis
  3. Mr Meek was moved into wards where no protection was in place to prevent infection without consultation with the hospital infection prevention team
  4. Mr Meek was housed in a ward where other patients were suffering from C. difficile infection, known to be infectious and especially so in this case due to Mr Meek's reduced immune status
The coronor ruled that these amounted to systematic failures that led to the death of Mr Meek while suffering  from invasive aspergillosis (which caused severely debilitating injury) and C. difficile infection.

If any one of these circumstances had been different Mr Meek may have been less likely to have become infected. This case illustrates how carefully hospitals must manage buildings work and the identification of individuals vulnerable to infection, particularly where aspergillosis is a risk for the patient.



Thursday, 25 October 2012

GSK Increase Transparency of Drug Testing

There is an accusation regularly levelled at companies that design and manufacture medicinal drugs that they lack transparency when it comes to releasing their own experimental results after they have tested their own drugs. Drug companies are under no obligation to release all of their results and some assume that results that cast their new products in a bad light are ignored and remain unpublished.

In particular clinical trials are crucial to demonstrate the effectiveness of a new drug and billions of dollars of investment can rest on each trial result - there is certainly a lot of financial pressure for each new drug to succeed though many do not and some fall at this last, most expensive hurdle.

In the US the distrust between pharmaceutical company and consumer has reached a peak for one company as it has been fined $3 billion after being found guilty of misleading the US government over the usefulness of  its drugs and in a watershed decision the company (GlaxoSmtihKline) has agreed to release details of all of its trials for peer assessment in publically available journals - both positive and negative results. This is a first for a pharmaceutical company but the likelihood is that others will follow.

It is hoped this move will allow greater scrutiny of all new drugs (or all new purposes for older drugs), increasing transparency and rebuilding trust in the proof of efficacy of the next generation of medications.

Wednesday, 24 October 2012

Newsbite: Fungal Meningitis Outbreak: Protective Antifungals?

There are up to 14 000 people in the US suspected of having been exposed to the contaminated steroid injection solution that has so far been detected in 300 people. Questions are being asked about whether or not those suspected of being exposed should be given protective antifungal medication even if they are showing no signs of illness. Unfortunately giving antifungal medication is not to be taken lightly as it has many side effects, even risks to health for some people so indiscriminate dosing is not recommended at this stage. more...

Tuesday, 23 October 2012

Newsbite: Open Access to Medical Mycology Case Reports

This week is Open Access week (22nd-28th October) and the publishers would like to take this opportunity to thank all the authors who have published their research in the recently launched journal Medical Mycology Case Reports. We now have over 25 papers available online which are helping to shape the journal into a valuable collection of fungal cases with clinically important information for healthcare professionals, researchers and the wider public. more...

Monday, 22 October 2012

Flax Contains Natural Antifungals

New Zealand flax
A team of researchers in New Zealand is working on the fibres of the flax plant, traditionally used throughout the world to provide thread and fibres capable of being woven into cloth (linen). Linen and flax fell out of favour when synthetic fibres became popular but now may well come back into favour as synthetic fibres made out of unsustainable oil reserves inevitably become more expensive and less available over time.

In the meantime the New Zealand research group are looking for new applications for New Zealand flax (or harakeke as it is know in New Zealand) and the realisation that it has antifungal properties mean that it could be used in situations where spoilage by fungi is a problem e.g. storage of spoilable foods. It is also of course a natural, sustainable, biodegradable material so is ecologically beneficial where used especially when used to replace synthetic materials.

Friday, 19 October 2012

Bioplastic Aspergillus 'Bullets' Fight Aflatoxins

Aspergillus growing out of a bioplastic pellet
The USDA has developed an efficient method of 'packaging' biocompetative strains of Aspergillus for use to introduce strains of Aspergillus that do not produce dangerous aflatoxins onto crops that are at risk from growth of strains of Aspergillus that do produce mycotoxins - it is established that the non-producers can outgrow the aflatoxin producing strains in the field while crops are growing and thus reduce the amount of aflatoxin contaminating the crop.

'Bioplastic bullets' made out of cornstarch and vegetable oil are effective at containing the 'non-producer' fungus for dispersal and subsequently allow good growth of the fungus. This method of packaging has improved properties for stable storage of the mold compared with the earlier methods involving the used of grain coated in fungal material, and the bioplastic is a lot less attractive to animals that eat seeds & grain so losses are reduced (as well as reducing the health risk to the animals presumably). Bioplastic degrades naturally once scattered onto the field.

For full story click here.

Monday, 15 October 2012

Another Mechanism Suggested for Mould Toxicity in the Home

Trichoderma longibranchiatum
The debate on whether or not the toxins produced by moulds is a contributory factor to the illnesses claimed by many when living in a home with increased levels of moulds caused by dampness continue. Proponents of the theory in the US (where most of this information seems to come from) highlight many perfectly reasonable research studies showing the well characterised toxicity of mycotoxins, volatile chemicals, ozone and many others (see Sick Building Syndrome). Much time has been spent trying to prove that enough of any one of those irritants may come into contact with the occupants of a building to cause health problems.

Those who oppose (and those who consider the principle unproven as yet)  point out that although there are many potential toxins in the indoor environment we are yet to be able to demonstrate convincingly how enough toxin could enter our bodies to cause health problems. Perhaps low doses of several toxins have health effects we do not yet understand?

A recent paper from a research group in Finland outlined a 'new' type of toxic peptide that might be prevalent in the damp indoor environment - trilongins. Up to 2.6% of the mycelial mass of the common fungus that produces them is made up of various types of trilongin, and different types of trilongin are shown to act synergistically to inhibit mitochondrial activity in mammalian cells. The suggestion is that this is a source of toxin that is plentiful and is a candidate for one cause of health problems in damp homes. We are still lacking quantitative estimate of the amount of trilongin produced in a 'sick' home and the suggested mode of  ingestion so doubts remain about the effect on human health as it is difficult to estimate dose but the case for the presence of multiple sources of toxin which can interact to increase toxicity in a damp home is strengthened by this paper.

Friday, 12 October 2012

US Genomic Sequencing Laws to Strengthen Privacy



The US Presidential Commission for the Study of Bioethical Issues has this week published a report entitled 'Privacy and Progress in Whole Genome Sequencing'






Quoting from the introduction of the report:

Over the course of less than a decade, whole genome sequencing has progressed from being one of our nation’s boldest scientific aspirations to becoming a readily available technique for determining the complete sequence of an individual’s deoxyribonucleic acid (DNA)—that person’s unique genetic blueprint. With this tremendous advance comes the accumulation of vast quantities of whole genome sequence data and complex questions of how—across a multitude of clinical, research, and social environments—to protect the privacy of those whose genomes have been sequenced. Collections of whole genome sequence data have already been key to important medical breakthroughs, and they hold enormous promise to advance clinical care and general health moving forward. To realize this promise of great public good ethically, individual interests in privacy must be respected and secured.  The report identifies several instances where processes to ensure confidentiality or privacy needed to be clarified and strengthened. Some of them have been discussed before in this blog - for example there are legal differences depending on whether the tissue sample taken for sequencing was taken by your doctor or a researcher - but others are more obscure;

Another quote from the report:

Another privacy concern associated with whole genome sequencing is the potential for unauthorized access to and misuse of information. For example, in many states someone could legally pick up a discarded coffee cup and send a saliva sample to a commercial sequencing entity in an attempt to discover an individual’s predisposition to neurodegenerative disease. The information might then be misused, for example, by a contentious spouse as evidence of unfitness to parent in a custody case. Or, the information might be publicized by a malicious stranger or acquaintance without the individual’s knowledge or consent in a social networking space, which could adversely affect that individual’s chance of finding a spouse, achieving standing in a community, or pursuing a desired career path.  

The report recommends procedures & laws for the protection of privacy are consistent across all possible sampling entities, all sequence data must be stored anonymously and protected to a high  degree of security. Those who's DNA is being sequenced should remain in control of its use and steps are to be taken to promote all that is learned from the data to the widest possible audience, in the public interest.

Thursday, 11 October 2012

Aspergillus Meningitis Outbreaks Spreads - Officials Fight Back

Map of Healthcare Facilities which Received Three Lots* of Methylprednisolone Acetate (PF) Recalled from New England Compounding Center on September 26, 2012
The past week has seen a developing disaster in the US involving Aspergillus. As we know infection of people who have normal, fully functional immune systems is rare and is mainly confined to the lungs and sinus' when conditions exist that provide a 'toehold' for the fungus to evade our normal immune response to their presence. Favourable conditions include damage caused by other infections and overproduction and lack of drainage of mucus (e.g. in the airways of cystic fibrosis sufferers and in the inflamed sinus).

However, if Aspergillus can find a way past our skin - occasionally via a wound or after surgery - it can sometimes infect parts of the body that seem less well defended and it can be difficult to diagnose as it resembles other much more common infections so precious time when the patients could be receiving antifungal medication is lost. Once established it can be difficult to treat.

The first news reports emerging last week (reported in this blog here) focussed around 12 cases reported in a small area which is a highly unusual event. At that time we speculated that this outbreak would be due to a failure in the medical care systems - in particular the use of non-sterile equipment or solutions.

Tragically there has now been 137 people effected and 12 deaths so far due to a contaminated solution of steroid being distributed and used widely in the US (see map above). As this is a preparation designed for injection it has no preservative added to it which might have prevented contamination. Those who have been injected directly into the spine would be most vulnerable to a rapid onset as the fungus can grow more quickly in that location, especially as steroids can act locally to reduce the bodies immune response which would normally fight the infection. Injections into other sites of the body may also be infected - anyone who is concerned is being advised to contact their doctor immediately.

Chances are there will be more infected people found in the weeks to come as Aspergillus does not always cause symptoms immediately but the rapid detection of the source of the infection and efficient recall of infected medication  should minimise the number of further cases as far as is possible.

News report
CDC statement 

Wednesday, 10 October 2012

Identify Common Pills Using Mobile Phone

For people who have to take several different medications and for those who have to hand out many different pills (e.g. hospital staff, nursng home staff, relatives) identification of each pill is important and can be quite difficult as many pills look very similar despite having completely different contents. There are only a small number of shapes and colours available to pill manufacturers!

Mistakes can have serious consequences and are not uncommon. Referred to as medicine-related problems (MRP's) symptoms often include

  • excessive drowsiness
  • confusion
  • depression
  • delirium
  • insomnia
  • Parkinson’s-like symptoms
  • incontinence
  • muscle weakness
  • loss of appetite
  • falls and fractures
  • changes in speech and memory.


This article in the New Scientist Journal describes a new 'App' (a computer program that runs on a smartphone or tablet computer) that allows the user to identify most common pills (568 currently tested)  from their shape and colour just by taking a photo of the pill using a phone camera. The App should be available soon.


Tuesday, 9 October 2012

Newsbite: 15 ALLFUN Fellowships for Young European Scientists

On behalf of Prof. Romani, I'm glad to inform you that, within the next Gordon Research Conference that will be on January 13-18, 2013, there are 15 fellowships available on a first come basis for European postdocs and students that attend the GRC. They are available through ALLFUN grant. Information can be found at: http://www.allfun-fp7.eu/training_dissemination.html

Monday, 8 October 2012

Human Lung Regrowth - Is It Possible?

Mouse lung tissue regrowing after 'flu
There are many groups of patients with respiratory disease (including aspergillosis) who have severely damaged lungs, the worst affected of whom are dependent on a lung transplant for long term recovery. Even for those least effected by lung damage replacement of damaged lung tissue could greatly improve their quality of life.

Recent research has found stem cells capable of regrowing lung tissue - something I mentioned in a talk I gave to our Patients support group and the National Aspergillosisi Centre, UK. Boston University has a research group led by Dr Darrell Kotton which demonstrated convincingly that lung tissue could be rebuilt and regrown in a mouse experimental model system, opening the way for many more researchers to work on how to get this to happen in humans.

When reporting on this work in an earlier blog we noted that some of the results suggested that our lungs may contain 'natural' stem cells which were capable of carrying out lung tissue repair without any intervention by doctors - in other words our own lungs had some capacity to repair themselves. This sounds absurd, after all if this were possible why would we have illnesses such as tuberculosis and chronic pulmonary aspergillosis where there are large areas of lung that are completely destroyed and never seem to recover?

However - absurd as it might be there is now solid evidence that in one case at least, regeneration of lung tissue has been precisely tracked and recorded. The authors of this paper in the New England Journal of Medicine describe a patients losing a large part of their lung as part of their treatment for lung cancer. Lung capacity was not surprisingly markedly reduced, but more surprisingly over the next 15 years a steady increase in capacity was noticed.
CT scans showed an increase in the size of the lung and careful testing with an MRI scanner revealed evidence for an increase in the number of lung alveoli - the lung was literally growing back!

Although not a common event this case proves unequivically that lung tissue can grow back once damaged.  Further research is needed to detect why this happened in this patient in the hope of making it a more common event but the potential is clearly there.

Thursday, 4 October 2012

Newbite: Allergy to Fungi Can Indicate Lower Risk of Glioma in Women

Allergy to common allergens (e.g. pet dander, pollen) including some fungi has been systematically compared with risk of developing glioma in nearly 600 cases. Remarkably it has been found (confirming some earlier simpler studies) that women who tend to have high IgE levels to common allergens have a significantly lower risk of developing glioma compared with those who have low levels of IgE, even when the IgE tests were carried out at least 20 years before the patients developed glioma.
This correlation does not hold for men. more...

Wednesday, 3 October 2012

ISHAM Committee launched on Nomenclature of Clinical Fungi

Reproduced from ISHAM publication:

On 12 and 13 April, 2012 the CBS Spring Symposium was held in Amsterdam, The Netherlands and was devoted to fungal nomenclature. It was entitled “One Fungus = Which Name”, being an extension of the 2011 workshop “One Fungus = One Name”. These symposia will have a strong impact on nomenclature of medically significant fungi, and therefore it is important that we as ISHAM implement a democratic procedure to achieve a stable result which will be adopted quickly by the entire community. Your  cooperation and input is therefore explicitly requested.

In essence, changes involve the abolishment of Art. 59 of the Code of Nomenclature, which previously allowed separate names for sexual stages and different asexual stages of one and the same fungus. From 1 January 2013 onwards this will no longer be allowed. The question now is which name of polymorphic fungi has priority and should be used in the future. Nomenclature has always been a very formal process on the basis of strict rules in the Code of Nomenclature, but with the Amsterdam symposia there was a consensus for a much more practical approach, taking the needs of the user as a starting point.

This has led to some suggestions outlined below.

Concerning name changes of pleomorphic fungi:


  •  We, the community of medical mycologists, first have to decide which names we want to keep above all doubt. For example: Candida albicans and Aspergillus fumigatus should be maintained,and we wish to use Trichophyton rather than Arthroderma. Probably there are many other classical pathogens and opportunists that we wish to keep. This list of names can be proposed for conservation.
  •  An important criterion for choice of a name will be how frequently names have been used.  But“commonly used” is an unclear criterion; for each of the names the reasons for proposed conservation should be specified. For example: how to establish whether Scedosporium is more current than Pseudallescheria?
  •  If no single name is strongly favoured, the oldest name (anamorph or teleomorph) has priority. For example: names of Aspergillus are older than Neosartorya, and therefore the Neosartorya species will be Aspergillus in the future.


Concerning name changes due to reclassifications of fungi:


  •  Taxonomic methods are not regulated by the Code, so these may be classical phenotypic, or molecular phylogenetic. Phylogenetic criterion of a group (“genus”) is the monophyletic clade. The clade determines the genus name. Preferably the oldest name available for that group is used, see the example of Aspergillus.
  •  New molecular taxonomy may reveal groups where all experts agree that they are clearly monophyletic and may share essential characteristics such as pathogenicity or antifungal susceptibility. This may be the case in the yeasts.
  •  But there are also groups where so many new data – often of environmental relatives – are added, that the phylogeny is highly unstable. For example, black yeast taxonomy develops rapidly. We may propose that for the time being we just leave the names as they are, even if form-genera are polyphyletic.
  •  Ancient, poorly differentiated genera, such as Acremonium today may be highly polyphyletic, and thus have become ambiguous. There was a proposal to abandon such genera at all, but an alternative option would be to redefine them in a modern sense on the basis of accessible type material.

What’s next

The community of medical mycologists including the ISHAM membership is requested to propose lists of preferred on the basis of the above criteria. Many fungal pathogens have an ancient history and have become source of confusion over the years. We therefore urge taxonomists, if necessary, to (re)define the groups of fungi they are working with by the deposition of (new) type material; the procedures are> outlined in the Code of Nomenclature. (http://ibot.sav.sk/icbn/main.htm).

Proposals for preferred names will be submitted to the International Commission of the Taxonomy of Fungi (ICTF, http://www.iums.org/ICTF) for approval. An ad hoc commission (below) will provide a list of fungal names in current use based on the Atlas of Clinical Fungi for the ISHAM membership to send any kind of comments to de.hoog@cbs.knaw.nl.

We hope to have active involvement of many medical mycologists.

Best regards,
Sybren de Hoog, Vishnu Chaturvedi (reporters)
Teun Boekhout, Walter Buzina, Heide-Marie Daniel, Marizeth Groenewald, Wieland Meyer, Richard
Summerbell

Tuesday, 2 October 2012

Aspergillus Meningitis Cluster Reported in Tennessee, USA

Tennessee Department of Health official have revealed that there have been an unusually high number of fungal meningitis infections at two surgical centres in Tennessee and North Carolina. 12 patients have become infected and two have died as a result of this serious infection of the central nervous system.

As yet the cause of this cluster of infections is unknown but all those infected had undergone a lumbar epidural steroid injection.

Aspergillosis infections are not passed from person to person (unlike meningitis caused by viral infection (viral meningitis) or bacteria (bacterial meningitis)) so that can be ruled out as a cause. More likely routes of infection are use of a non-sterile batch of instruments/medical solutions, badly contaminated environment where the procedure was carried out or poor procedure/human error.

This type of infection is extremely rare amongst people who do not have a compromised (suppressed) immune system as there is no 'way in' for the infecting fungus to exploit in order to infect - our skin and highly effective immune systems usually prevent infection even when hundreds of fungal spores are breathed deep into our lungs.
However once past the barrier of our skin the fungus has a much better chance of surviving within our bodies (though it is still only a very slim chance) so doctors take precautions to prevent infection such as ensuring the injection site is sterile and obviously the needles, catheters and solutions used are sterile. If either becomes contaminated there is a small chance that infecting spores can be pushed deep into our bodies.

In these cases there is an added risk factor as the steroid used can aid infection if spores have been introduced into the injection site - they tend to locally suppress immune response.

The outbreak was detected by vigilant doctors quickly and correctly diagnosing this infection which is difficult to positively identify as it mimics other types of infection. Further infections have undoubtedly been prevented by their professionalism.

Both clinics are closed until the cause has been detected.

Further Information & References

Post-operative Aspergillosis
Aspergillus Website article

Social Media and Medical Care

Not so long ago people were being warned off reading medical information on the worldwide web (WWW) as much content was untrustworthy or information was unsuitable for the untrained eye.

A lot has changed. There is still a need for high quality information resources to be clearly distinguished from less useful or even damaging content (HonCode) but overall there is considerably more good trustworthy content than there was 5 years ago - in the UK we have the NHS hosting its own content and other high quality medical services do the same e.g.(Mayo Clinic, Great Ormond Street, Drugs.com).

It is a good thing that availability of high quality information is becoming the norm as a recent Price Waterhouse Cooper survey found that:
According to HRI’s survey, 42% of consumers have used social media to access health-related consumer reviews (e.g. of treatments or physicians).

Andrew McCracken  takes a closer look in his recent article for the Royal College of Physicians. In particular the ability of Twitter to promote and support rapid 'conversations' online are mentioned. In one example someone uses Twitter to send a quick question to NHS direct (a phone based health information resource used by UK government to provide information to patients) which was relied to quickly, saving a phone call and time on both sides of the conversation.

An example in the PwC report is of a patient in a waiting room sending a message to Twitter (known as Tweeting) complaining that they had not yet been seen while others that came into ER (known as A&E in UK) had already passed through. The Twitter was read by a member of staff and they responded by coming to explain to the patients why they were waiting. This can only have been possible if the ER ran and monitored its own Twitter account and the patient had Tweeted to that account, or mentioned the hospital directly.

There are possibilities for the use of this technology that may be attractive to the patient (i.e. getting attention quickly) but any advantages would quickly lost if the care provider was unaware and failed to monitor the tweets constantly. It also has limitations as Twitter only accepts 140 characters per message and conversations are made public.
Used incorrectly or without great thought it is hard to see how this is going to save much money for those that pay for healthcare yet (paid staff may well be needed to monitor Twitter) and not many doctors are going to have time to constantly reply.

  • Is there an advantage to the public asking questions on Twitter? Yes - it is free of charge whereas phonecalls are not. 
  • Is there an advantage to the provider answering questions on Twitter? Fewer, shorter interactions are possible but then the phonecall charges presumably go towards providing the service.
  • Is there an advantage to having all conversations made public on a website with facilities to search? Yes as earlier answers can be found easily thus potentially avoiding the need for another Twitter/call. This cannot happen with phonecalls.
  • Can Twitter conversations reduce the numbers of appointments needed with GP's much like it is hoped NHS Direct phone lines do? Possibly yes - NHSDirect are already hosting & monitoring Twitter and the NHSDirect service is ever expanding in response to demand - we can only assume that translates into less need for a GP appointment.

Perhaps this is the future of healthcare advice in the UK - NHSDirect are effectively constructing a new model for providing healthcare information in just the same way as they did when setting up the original phone service.

Monday, 1 October 2012

US Doctors TV Show Mold Guidelines


“Mold can also be completely harmless, but in some situations, it can be truly deadly,” E.R. physician Dr. Travis Stork says.

“One study found a child’s risk of asthma can double from simply smelling mold,” pediatrician Dr. Jim Sears says.

“Pregnant women fall into the [compromised immune system] category,” Dr. Lisa says. “They can get really sick from respiratory infections, however no studies have shown that mold causes birth defects.


more...

Wednesday, 26 September 2012

Preventing Cold Housing Can Cause Mould in the Home

Housing authorities and governments over the last 40 years have gone to great trouble to improve the standard of housing in their countries by installing insulation, better heating and removing draughts - this news article from New Zealand is typical and many homeowners speaks of the potential benefits of a warmer home with less condensation.

Unfortunately after a short period of improvement in living conditions as more heat is retained within living areas we have found that condensation is far from 'cured'. The amount of moisture in the air can rise as warmer air can hold more water than cold air, but ultimately moisture must be exhausted out of the property somehow otherwise it will inevitably reappear, especially during the night as the heating goes off and air cools. Once moisture starts to settle on walls and furnishing moulds will quickly follow as it is not warmer air that prevents moulds growing - it is the absence of moisture.

If all draughts are plugged and ventilation grids are blocked up, including old chimney's then there is nowhere for all the moisture generated in a building by its occupants (washing, clothes drying, breathing) to go. Installation of insulation has to be done so as to retain ventilation, insulating materials must not be biodegradable (shredded paper, sheep's wool) and the occupants need to be made aware of the potential problems with mould if they do not change the way they live a little - a warm home comes with responsibilities! Ventilation that ensure good flow of fresh air into a house must be installed if not present - and their are devices which will retain most of the heat in a house as damp air is removed.

The Institute of Specialist Surveyers and Engineers (ISSE) and the National Aspergillosis Centre, Manchester, UK are investigating a partnership to help prevent moulds growing in homes and other properties. There is to be a series of qualifications to help train building inspectors and remediators with damp as a main focus, and a national awareness campaign to help educate all interested parties.

Tuesday, 25 September 2012

Newsbite: Aflatoxin Widespread in US Mid West Drought

This year has been one of very little rain in the American MidWest (64% of the lower 48 states are in serious drought - a new record (U.S. Drought Monitor)), promoting growth of Aspergillus. As crops dry out (mainly corn/maize) the plants become highly stressed in the dry heat and are vulnerable to infection. Once the crop is infected Aspergillus itself becomes stressed as moisture is short and it starts to defend itself by producing mycotoxins which contaminate the crop. If the contamination exceeds 20 parts per billion it cannot be used for human or dairy cattle consumption. Consequent shortages effect both human food needs and food needed for cattle. more...

Monday, 24 September 2012

Newsbite: Rarity of Aspergillosis Claims Another Victim

Invasive aspergillosis is so rare (especially in people with healthy immune systems) there are many doctors who have never seen a case. Aspergillosis is also good at mimicking other types of infection so accurate diagnosis is difficult and tends to be slow, leading to a poorer outcome. We have already reported in this blog several fatalities caused by these problems (1, 2, 3, 4, 5) and this case is another - the lead surgeon had never seen a case in 25 years of practice. The only solution for this will be to increase awareness of aspergillosis and to improve diagnostic tools.
In addition NOTE that this case was only uncovered after an autopsy was performed - this vital learning tool is underused as discussed in an earlier blog more...

Friday, 21 September 2012

Europe Dominates World Research into Fungi

The online journal and European news journal Lab Times periodically releases analyses of the citation ranking of countries of the world in order of the number of publication that are referred to by other researchers in a particular field.
Citations are a form of performance measurement for academics as arguably the number of times a research paper is cited by other authors reflects its importance in that field more accurately than simply counting the number of papers published by a researcher or research group.

This is because some research papers are more important than others. Those which are amongst the first to describe a finding will be cited by all of those following and will get a high number of citations. Those that merely make a minor point in an already established field of research will attract relatively few citations.

Citation indexes are routinely collated and used by journals as a measure of their importance and are included as one factor in calculating impact factor.

 Lab Times calculates a citation 'league table' for scientists in each field of research - effectively a league table of importance of each researcher in each field of research.

Their most recent analysis is for the field of fungal research and interestingly it shows that Europe dominates the world in this category, particularly powered by major fungal research centres in Germany, Holland and England, closely followed by France and Spain. Taken together the EU claims nearly twice as many citations as the US and nearly ten times as many as Japan.

Within Europe Germany dominates closely followed by Holland but it might be worth noting that the UK is divided up into its component countries. If this had not happened UK might well edge out Germany for first place as there are prolific centres of excellence in fungal research in both Scotland (currently led by Aberdeen University) and Wales (Cardiff University).

This success is said to largely reflect the size of the CBS Fungal Biodiversity Centre  in Holland, the Pasteur Institute in France as well as multiple smaller Universities throughout Europe but perhaps most remarkable is the research prominence of the University of Manchester in this field. Professors David Denning and Stephen Oliver are placed first and third in the league table for authorship of papers and both work in Manchester.

Thursday, 20 September 2012

Newsbite: First Recorded Case of Antifungal Resistant Aspergillus Strain Originating in the Environment

Recent studies have shown that antifungal-resistant strains of Aspergillus can be found outside of hospitals and other non-clinical environments. It is assumed that agricultural use of antifungal azole drugs (very similar to those used to treat infected patients) could be promoting the development of these resistant strains and it has been suggested that some of the resistant organisms found in clinical samples may be the result of a patients breathing in resistant Aspergillus. The first case where it has been proven that a resistant clinical specimen has originated in the environment has now been published more...

Wednesday, 19 September 2012

Newsbite: Fungal Paper Celebrates Rare 10,000th Citation

Scientific papers are carefully managed as much rests on their impact. A paper that is referred to in another publication (cited) is clearly important or significant enough for another research group to quote its findings. Most scientific papers might be cited 10 - 100 times. The paper memorably entitled "Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics" recently achieved the rare accolade of being cited over 10 000 times more...

Tuesday, 18 September 2012

Aspergillosis and the Role of Misdiagnosis in Morbidity and Mortality

A recent US study systematically surveyed 31 reports giving a total of nearly 6000 autopsies. Of these cases anything from 6 - 100% showed evidence of misdiagnosis - indicating that the doctors diagnosed and treated incorrectly, presumably often contributing to death (mortality).
28% of all autopsies revealed evidence of at least one missed diagnosis and 8% evidence of a Class I (Goldman criteria) error which means that the misdiagnosis could have contributed to or directly caused death (the most common of which were heart attack, pulmonary embolism, artery blockage in the lungs, pneumonia and aspergillosis).

About two thirds of all missed diagnoses are thought to have not contributed to death

This is clearly a serious issue and as a result of this study an estimate for the United States is that 40 500 deaths occur in intensive care units every year as a result of misdiagnosis. Given that aspergillosis is one of the most common of these (up to 30% of Class I misdiagnoses - though the paper isn't clear on this) this could account for up to 13 000 deaths a year. For a rare infection such as aspergillosis that represents a substantial increase in the number of recorded fatal infections per year.

Why so many? What can we do about it?

The report mentions several factors involved and many are mentioned in this slide presentation by the author (Winters suggested hospitals consider employing intensivists to monitor their ICUs, as well as improving nurse-to-patient ratios) but a major factor is the lack of autopsies now carried out to discover the true cause of death. In the US and throughout the EU the rate of autopsies has been falling for years, consequently doctors can no longer learn from comparing what they diagnosed with what actually killed a patient - or at least they can do far less than they used to. Under-representation of aspergillosis as a cause of death is one consequence.

Monday, 17 September 2012

Fungi are Effective at Helping Make a New Generation of Stradivarius Violins

Physisporinus vitreus
One of the most famous and sought after musical instrument over the last few years has been one of the violins made by Stradivarius in his workshops in Italy in the late 1600's and early 1700's. Enthusiasts declare that those violins have no equal and modern attempts to replicate those instruments can never quite meet the sound produced by a Stradivarius. Consequently they sell for many millions of dollars.

Theories abounded as to what was special about this instrument - ranging from the blend of woods to special treatments applied to the wood but essentially it seems to have been concluded that the key is a specific batch of wood that he used. Grown during a particularly cold spell in the 1650-1750's the wood was less dense than normal - but such wood is no longer available.

It should be mentioned that there has been great difficulty measuring much difference between a Stradivarius and more modern violins - even when panels of human experts are tried they often fail to identify the right instrument. Nevertheless they are still highly prized.

Insofar as I have been able to understand the low density of the wood allows the sound to travels through the wood easily, while at the same time its stiffness produced the tone. Modern woods are denser than those picked by Stradivarius but perhaps they could be lightened?

xylaria longipes
In his after dinner speech at the 1st ECRC "Franz-Volhard" Symposium of the Max Delbrück Center for Molecular Medicine (MDC) and Charité -- Universitätsmedizin on Sept. 7, 2012 in Berlin-Buch, Professor Francis W. M. R. Schwarze (Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland) reported that he had treated modern wood with two types of fungus (Physisporinus vitreus and Xylaria longipes) and that the slow digestion of the wood by these fungi had adequately replicated the wood used by Stradivarius.

Tests of violins made with this wood failed to distinguish the new violin from the old (though we know that even with a non-treated violin that is far from easy). Enthusiasts claim that this may make the sound quality of a famous classical instrument accessible to far more people, and encourage young musicians by working with better instruments.

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