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What is genomics? How will it affect our lives? In this primer on the genomics revolution, entrepreneur Barry Schuler says we can at least expect healthier, tastier food. He suggests we start with the pinot noir grape, to build better wines.

Melioidosis is a severe disease affecting humans and animals in the tropics. It is caused by the bacterium Burkholderia pseudomallei, which lives in tropical soil and especially occurs in southeast Asia and northern Australia. Despite the recognition that melioidosis is an emerging infectious disease, little is known about the habitat of B. pseudomallei in the environment.

Researchers from Menzies School of Health Research in Darwin, Australia have found that the soil bacterium Burkholderia pseudomallei, which causes the emerging infectious disease melioidosis in humans and animals, is associated with land management changes such as livestock husbandry or residential gardening. They performed a survey in the Darwin area in tropical Australia, screening 809 soil samples for the presence of these bacteria using molecular methods. The study sheds light on the environmental occurrence of this bacterium in the soil.

B. pseudomallei lives in tropical soil and is endemic in southeast Asia and northern Australia, where it can be a common cause of fatal community-acquired bacterial pneumonia. In predisposed hosts such as those with diabetes, it can also lead to systemic sepsis, with mortality rates over 50 percent. Through a large survey in the tropical Darwin area of Australia, the authors found that environmental factors describing the habitat of these bacteria differed between environmentally undisturbed and disturbed sites. At undisturbed sites, B. pseudomallei was primarily found in close proximity to streams and in grass- and roots-rich areas. In disturbed soil, B. pseudomallei was associated with the presence of animals, farming or irrigation. Highest B. pseudomallei counts were retrieved from paddocks, pens and kennels holding livestock and dogs. This study contributes to the elucidation of the habitat of B. pseudomallei in northern Australia. It also raises concerns that B. pseudomallei may spread due to changes in land management.

These findings raise concerns that B. pseudomallei may spread due to the influence of land management changes. This would increase the risk of human and livestock exposure to these potentially deadly bacteria which are transmitted by contact with contaminated soil or surface water through cuts in the skin or inhalation. In-depth analysis of the influence of anthropogenic factors upon B. pseudomallei and further studies in other endemic areas are needed to confirm the results of this study.

Landscape Changes Influence the Occurrence of the Melioidosis Bacterium Burkholderia pseudomallei in Soil in Northern Australia. PLoS Negl Trop Dis 3(1): e364

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• Glanders and Melioidosis – coming soon to a crowded shopping centre near you?

Bees are important contributors to the economies of many countries, but as Travis Glare and Maureen O’Callaghan discuss in this article in Microbiology Today, they are many threats to the survival on the humble bee, including the risk of disease from micro-organisms:

There are many threats to bee survival, including the risk of disease caused by micro-organisms. The vast majority of our knowledge of bee diseases focuses on the honey bee, Apis mellifera, although there are actually over 20,000 species, both stingless and stinging, from those with solitary lifestyles to complex societies such as honey bee hives. Viruses, fungi, protozoa and bacteria are all known to cause infections in bees, sometimes leading to collapse of colonies, and causing serious threats to the bee-keeping industry. Bees have two distinct life forms, brood (egg, larva and pupal stages which develop within the hive) and adult. Most diseases are specific to just one of these life stages. While the list of diseases is quite long, only a few are of serious concern to apiculturists.

Read more

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• Colony Collapse Disorder
• The great bee swindle – colony collapse disorder

A decade ago, a new variant form of Creutzfeldt-Jakob disease was identified. The emergence of this prion disease in humans was the consequence of the zoonotic transmission of bovine spongiform encephalopathy through dietary exposure. Since then, the control of human exposure to prions has become a priority, and a policy based on the exclusion of known infectious materials from the food chain has been implemented. Because all investigations carried out failed to reveal evidence of infectivity in milk from affected ruminants, this product has continuously been considered as safe. In this study, researchers demonstrate the presence of prions in colostrum and milk from sheep incubating natural scrapie and displaying apparently healthy mammary glands. This finding indicates that milk from small ruminants could contribute to the transmission of prion disease between animals. It also raises some concern with regard to the risk to humans associated with milk products from ovine and other dairy species.

Prions in Milk from Ewes Incubating Natural Scrapie. 2008 PLoS Pathog 4(12): e1000238
Since prion infectivity had never been reported in milk, dairy products originating from transmissible spongiform encephalopathy (TSE)-affected ruminant flocks currently enter unrestricted into the animal and human food chain. However, a recently published study brought the first evidence of the presence of prions in mammary secretions from scrapie-affected ewes. Here we report the detection of consistent levels of infectivity in colostrum and milk from sheep incubating natural scrapie, several months prior to clinical onset. Additionally, abnormal PrP was detected, by immunohistochemistry and PET blot, in lacteal ducts and mammary acini. This PrPSc accumulation was detected only in ewes harbouring mammary ectopic lymphoid follicles that developed consequent to Maedi lentivirus infection. However, bioassay revealed that prion infectivity was present in milk and colostrum, not only from ewes with such lympho-proliferative chronic mastitis, but also from those displaying lesion-free mammary glands. In milk and colostrum, infectivity could be recovered in the cellular, cream, and casein-whey fractions. In our samples, using a Tg 338 mouse model, the highest per ml infectious titre measured was found to be equivalent to that contained in 6 µg of a posterior brain stem from a terminally scrapie-affected ewe. These findings indicate that both colostrum and milk from small ruminants incubating TSE could contribute to the animal TSE transmission process, either directly or through the presence of milk-derived material in animal feedstuffs. It also raises some concern with regard to the risk to humans of TSE exposure associated with milk products from ovine and other TSE-susceptible dairy species.

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BBC News reports that Britain is running out of mycologists. There were 32 in the 1990s, but just eight now. Scientists say we should be worried as, without a British research base, other countries could stand to make lucrative fungi-based discoveries in everything from medicine to engineering.

10 things fungi have done for us

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• MicrobiologyBytes: Mycology

Unbelievable as it sounds, leaf-cutter ants developed the secret of agriculture over 50 million years ago. In this article in Microbiology Today, Garret Suen and Cameron Currie describe how freshly-cut leaves are incorporated into gardens for the growth of a specialized fungus that the ants use for food:

Until about a decade and a half ago, research on fungus-growing ants focused primarily on the ants and their foraging behaviour. It wasn’t until the early 1990s that this focus shifted to the fungus gardens and their associated microbial communities. Since the ant gardens are maintained in soil chambers, they are routinely exposed to a number of potential pathogens that could infect and overtake a garden. In fact, many of the ant colonies do become overgrown by fungal pathogens, often resulting in the death of the colony. Intensive sampling of the fungal communities within the gardens revealed that a specialized microfungal pathogen selectively attacks the gardens of the fungus-growing ants.

Read more

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• Wolbachia
• MicrobiologyBytes: Fungi

The UK commercial poultry industry is an important industry to the British government, the consumer and farmers alike. Worth an estimated £3.4 billion at retail value, producing over 174 million birds for consumption per year, poultry diseases are of widespread interest, both from the point-of-view of understanding different poultry farming methods, and in terms of studying the potential impact of different diseases on poultry. However, our knowledge of how poultry farms in the UK are connected to each other by the movement of people and equipment is more limited. This is essential for effective prevention and control for potential outbreaks of diseases transmitted by the movement of people and equipment between farms within the commercial poultry industry. Diseases spread in such a way include avian influenza viruses (AIV), Newcastle disease virus, Salmonella and Campylobacter species.

An epidemic of any poultry disease with high mortality or which is zoonotic, such as AIV, would result in the culling of significant numbers of birds, as seen in the Netherlands in 2003 and Italy in 2000. Such an epidemic would cost the UK government millions of pounds in compensation costs, with further economic losses through reduction of international and UK consumption of British poultry. In order to better inform policy advisers and makers on the potential for a large epidemic in the UK, we investigate the role that interactions amongst premises within the British commercial poultry industry could play in promoting an AIV epidemic, given an introduction of the virus in a specific part of poultry industry in the UK.

Poultry premises using multiple slaughterhouses lead to a large number of premises being potentially connected, with the resultant potential for large and sometimes widespread epidemics. Catching companies can also potentially link a large proportion of the poultry population. Critical to this is the maximum distance traveled by catching companies between premises and whether or not between-species transmission could occur within individual premises. Premises closely linked by proximity may result in connections being formed between different species and or sectors within the industry.

Even quite well-contained epidemics have the potential for geographically widespread dissemination, potentially resulting in severe logistical problems for epidemic control, and with economic impact on a large part of the country. Premises sending birds to multiple slaughterhouses or housing multiple species may act as a bridge between otherwise separate sectors of the industry, resulting in the potential for large epidemics. Investment into further data collection and analyses on the importance of industry structure as a determinant for spread of AIV would enable us to use the results from this study to contribute to policy on disease control.

Contact structures in the poultry industry in Great Britain: Exploring transmission routes for a potential avian influenza virus epidemic. BMC Vet Res. 2008 4: 27

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Leptospirosis is a relatively rare bacterial disease in humans but also affects a wide range of animals, including mammals, birds, amphibians and reptiles. It is caused by infection with Gram-negative spirochaete bacteria of the genus Leptospira.

The infection is usually transmitted to humans when fresh water that has been contaminated by animal urine comes into contact with unhealed breaks in the skin, eyes or the mucous membranes. In the UK, leptospirosis is most frequently associated with rat urine, but a wide range of other mammals including dogs, deer, rabbits, hedgehogs, cows, sheep and even marine mammals are also able to carry and transmit the disease. The causative bacteria are likely to be found on muddy riverbanks, ditches, gullies, and muddy livestock rearing areas which wild or farmed animals use regularly. There is a direct link between the amount of rainfall and the incidence of leptospirosis, making it a seasonal disease in temperate climates and year-round in tropical climates. The incubation period can be anywhere from 4 to 14 days and in humans the symptoms include high fever, severe headache, chills, muscle aches, and vomiting, and may include jaundice, red eyes, abdominal pain, diarrhea and a rash. Weil’s disease, a term which has often been used for leptospirosis in general, is reserved for severe multisystem disease with severe jaundice and impaired kidney function.

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It has recently been reported that a 56-year-old British woman has died from leptospirosis after being scratched by a wild rat that had been trapped in a wire bird feeder in her garden. The woman was injured while trying to free the animal. In fact, leptospirosis is an uncommon disease in the UK with a total of 15-30 cases reported yearly. 18 fatal cases were reported in England and Wales between 1988 and 2006. The disease occurs sporadically throughout the world, but a recent public health warning about leptospirosis was issued in Thailand after an outbreak involving 2030 cases and 46 deaths in the northeastern region of the country. This outbreak occurred as a result of heavy flooding across Thailand during September and October 2008.