Welcome to the Microbiology Information

Onchocerciasis is an infection caused by Onchocerca volvulus, a parasite nematode worm transmitted to humans by a species of black fly of the Simulium genus whose larvae develop in fast-flowing rivers.

Infected subjects suffer not only from severe skin lesions but also eye damage that can lead to irreversible of−loss of sight, hence the name ‘river blindness’. A huge majority (99%) of the 37 million people
infected by the parasite live in SubSaharan. Ivermectin, a medicine capable of killing the parasite
embryos (the microfilariae) circulating in the organism of patients and temporarily interrupting the nematode’s reproduction, is the only treatment used for onchocerciasis control.

Since 1995, the African Programme for Onchocerciasis Control (APOC) has been covering 19 of the
continent’s 28 countries hit by the disease. Access to this treatment is possible for 70 million people and has
significantly diminished the onchocerciasis-induced morbidity. However, the doubling of cases of infection in
certain communities of Ghana between 2000 and 2005, in spite of annual treatments, created fear of the emergence of ivermectin-resistant strains. Such apprehension appears particularly justified in that a high degree of therapeutic cover is achieved during mass distribution campaigns and hence only a tiny part of the parasite population targeted remains unexposed to drug treatment pressure.

Since 1994, a team of IRD researchers, working jointly with Cameroon researchers and others from McGill University of Montreal, has been monitoring a cohort of Cameroon patients benefiting from repeated treatments with ivermectin. Regular parasite sampling from these subjects was performed over a 13-year period in order to determine the changes in the genetic structure of Onchocerca volvulus
populations. Each occasion involved measurement of the genotype frequency of heterozygotes and homozygotes for the gene coding β-tubulin, a protein involved in the organization of the parasite’s cells. The team focused on this particular gene because it acts as a marker of resistance to ivermectin in other nematode species parasitic on cattle. As a control, they monitored the changes in genotype frequency
of two other genes, known for their high evolutionary stability over time. The proportion of homozygotes and heterozygotes for these two genes remained stable throughout the investigation, but the situation was
completely different for the β-tubulin gene.

Between 1994 and 1998, the percentage of parasites showing a genotype homozygous for this gene fell from 79 to 31% in subjects receiving quarterly treatment with ivermectin. At the same time, the proportion of heterozygous genotypes changed in the opposite sense, rising from 21 to 69%. These results could be the sign of adaptation of nematode worm populations to repeated treatments using this drug. The research team inferred that the parasites showing a genotype homozygous for β-tubulin are more susceptible to
it. As courses of treatment progressed, they would therefore gradually disappear, to the benefit of the more resistant heterozygous strains. Ivermectin’s effect on microfilariae, other than its direct one, is to prevent them from leaving the uterus of adult worms, for several months after treatment: this is its embryostatic effect. Post-treatment, there were more microfilariae in the uterus of homozygous female parasites than in those of heterozygous females.

This could mean that, in the latter, the microfilariae succeed in leaving the uterus, as they usually do in the absence of treatment, and therefore that the embryostatic effect of ivermectin would be diminished. Contrary to the effect anticipated, the repeated exposure to treatments could in this way select those worms more able to keep up the production of new generations. Nevertheless, the drug’s direct action on the moment, there is no reason to call into question the current control strategy against the disease based on annual treatments with ivermectin.

Affirmation of the results requires further investigations1, starting from new cohorts subjects infected by Onchocerca volvulus who have not yet been treated with ivermectin. This type of approach should bring more information on the risks of the parasite’s resistance to this drug. If such risks were confirmed, then the whole onchocerciasis control strategy would probably have to be revised. Nevertheless, for many years to come, ivermectin could well remain the sole drug applicable for mass treatment in measures to control river blindness.

An eight hour listeria test is what DuPont Qualicon has just annouced.

The new test is genetic-based and allows food companies to detect Listeria on environmental surfaces in only eight hours.

A spokes person for DuPont Qualicon says the new assay “is the first commercial application of Reverse-Transcriptase PCR for bacterial testing in food.” It is part of a suite of BAX(R) system products.

“This flexible test can give food companies clear, precise results at the end of a shift,” said Kevin Huttman, president of DuPont Qualicon. “With fast, accurate detection of Listeria, even at low concentrations, food processors get the information they need to take action sooner and release product faster.”

Listeria is found in many kinds of foods and us usually killed with proper cooking. Ready-to-eat products, such as hot dogs and deli meat, can become contaminated between cooking and packaging, however. The infection Listeriosis is caused by eating food contaminated with pathogenic Listeria monocytogenes. This illness is especially risky for pregnant women and immuno-compromised individuals. DuPont Qualicon said.

Applications

The BAX® system detects all species of Listeria, even at very low concentrations (101 cfu/mL).

With reverse-transcriptase PCR, samples do not require the usual 24-48 hour enrichment in nutrient brotoh. Instead, Listeria cells are resuscitated by heating in the collection buffer solution for four hours, providing a jump-start to the process.

Validation studies on stainless steel using both the classic and Q7 models have shown that the BAX® system detected more positive results on spiked samples than the reference USDA FSIS culture method. In a panel of 58 strains across 7 species of Listeria and 52 strains of non-Listeria, the assay demonstrated 100% inclusivity/exclusivity.

Approvals

The BAX® system 8-hour Listeria assay will be submitted to AOAC-RI for Performance Tested Method approval.

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Helmholtz Association of German Research Centres - Science Daily — A German-American research team of biologists and geochemists has discovered hitherto unknown anaerobic bacteria in marine sediments which need only propane or butane for growth, as recently reported by the scientific journal “Nature.”

The hydrocarbons ethane, propane and butane — as well as the main component, methane — are the major constituents of natural gas.

Biological processes may lead to the degradation of these hydrocarbons in underground petroleum reservoirs and other geological habitats.

Heinz Wilkes, a leading biogeochemist at GeoForschungsZentrum Potsdam (GFZ), points out: “The bacteria isolated here for the first time from marine sediments use sulphate instead of oxygen for respiration and utilize propane and butane as their sole source of carbon and energy. These organisms are tough specialists that have become adapted to strictly utilising only these and no other substrates.”

The investigations showed that the bacteria employ an unprecedented biochemical mechanism for transforming what are essentially unreactive hydrocarbons into reactive metabolites which may then be further oxidised to carbon dioxide.

The findings concerning this reaction mechanism are an important step in designing new synthetic methods for selectively producing chemicals from hydrocarbons.

The effort to find preserved samples of the 1918 influenza virus has been a pursuit of both historical and medical importance.

The influenza pandemic in 1918 was the most devastating single disease outbreak in modern history, and examining the virus that caused it may help prepare for, and possibly prevent, future pandemics. When the complete sequence of the 1918 virus was published in 2005, it represented a watershed event for influenza researchers worldwide.

An article in the journal Antiviral Therapy, scientists at the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, narrate the story of how scientists discovered samples of the 1918 strain in fixed autopsy tissues and in the body of a woman buried in the Alaskan permafrost.

The article places this discovery in the context of decades of research into the cause of pandemic influenza, and the authors detail the strange convergence of events that allowed them to recover and sequence the virus in the first place. Its genetic material is so fragile that it should not have survived for days, let alone decades.

In a mass grave in a remote Inuit village near the town of Brevig Mission, a large Inuit woman lay buried under more than six feet of ice and dirt for more than 75 years. The permafrost plus the woman’s ample fat stores kept the virus in her lungs so well preserved that when a team of scientists exhumed her body in the late 1990s, they could recover enough viral RNA to sequence the 1918 strain in its whole entirety. This remarkable good fortune enabled these scientists to open a window onto a past pandemic. It could also help mankind gain a foothold for preventing a future one.

On the morning during August, several students from Northern Lehigh High School showed symptoms of staphylococcus infections or possibly respiratory “walking pneumonia.”

Later in the day, Principal Aileen Yadush wrote a letter to parents and had it posted on the school district’s Web site under a bold red link reading, “Alert!: Staphylococcus Infection Letter.”

The letter mentions the source of the infections was unclear but they narrowed it down to the school’s field house weight room.

The field house was closed and a professional cleaning crew was hired to scrub every surface and every piece of equipment.

The letter explained what type of bacteria it is - staphylococcus aureus, how to look for symptoms and what to do in case something unusual is found on students’ bodies.

The letter also assured parents and students “we will take every possible precaution in maintaining their safety and health.” which is a bold statement.

In a recent environmental survey conducted by University of Arizona researchers, surfaces in teachers’ classrooms came in as the Number 1 workplace for germs which is nearly 20 times higher than those found in lawyers’ offices, and seven times higher than doctors’ offices.

With over 2,000 parents questioned in the survey, 14 percent said they send their children to school despite running a fever higher than 100 degrees.

Educating children on proper hand washing and taking basic sanitation measures could hold down the germ level.

Bethlehem Health Bureau Director Judy Maloney says the bureau and local schools work clean-hand in clean-hand using a program called Germ City: Clean Hands, Healthy People.

The bureau also mailed a letter to principals at elementary and middle schools.

That letter urges schools to contact parents and let them know how important it is to keep sick children home.

Dr. Bonnie Coyle, director of St. Luke’s Hospital’s Community Health Department in Fountain Hill, says direct education programs are recommended by the Centers for Disease Control and Prevention to corral germs.

“If there is a child that has a disease that is a community health threat,” she says, “we get involved.”

In New Jersey, Mary Van Horn, supervisor of the Warren County Board of Health in Washington, says, “My department focuses on flu and pneumonia immunization, but good hand washing is so important.”

Coyle ventures one reason why.

“I think we’re seeing more emerging infectious disease threats,” Coyle says. “As the world becomes smaller through international travel, we’re seeing more drug-resistant tuberculosis. Then there are the things that have always been there (flu, staphylococcus, meningitis and other infectious diseases.)”

Coyle also says that since the 9/11 terrorism attacks, bioterrorism is becoming an issue.

“It’s certainly not a crisis,” she soothes, “but it’s something schools need to keep in mind.”

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New Zealand with only a population of 6 million people is a nation of food worriers after a 750 people survey found some interesting data on their views of food and food borne pathogens.

Interestingly, scientists believe people may be anxiously worrying over small issues that pose little risk to their health.

In the phone survey conducted for the New Zealand Food Safety Authority (NZFSA), they found that salmonella was the worst food fear, with 77 per cent being “very concerned” about it.

In addition, an antibiotic in meat was next with 67 per cent and campylobacter with 63 per cent.

But scientist Dr Donald Campbell said people were missing the three biggest threats to life, the amount of salt, fat and sugar in their diet.

Interestingly, people were more concern about eating at local buffets, food halls and ethnic restaurants than food made at home in an unhygienic way.

Campbell, the NZFSA principal adviser of public health, was surprised salmonella was the most feared.

“I would have expected campylobacter to be higher than salmonella,” he said.

Campylobacter had a greater impact on the community than salmonella. There were generally 10 times as many cases of campylobacter in a year than salmonella, said Campbell.

New Zealand had a 15 per cent rise in notified campylobacter cases last year to 15,873, compared with 1335 cases of salmonella.

Both are food-borne illnesses that have been associated with chicken and raw meats, and can cause symptoms of diarrhea, abdominal pain, nausea and headache.

Canterbury medical officer of health Alistair Humphrey put campylobacter high on his list of concerns.

But he said many other bugs lurked in food, including norovirus which causes gastroenteritis’s of which there had been outbreaks in Christchurch.

Antibiotics used in animals for therapeutic purposes and to prevent disease may scare consumers towards vegetarianism, but “the evidence is of it being a very low risk,” Campbell said.

Listeria was a rarer food-borne illness (19 cases nationally last year) but could have devastating consequences, he said. At least half of cases occurred in pregnant women and one in four of their babies have died.

Listeria is linked to deli meats, poultry products, smoked seafood’s, soft cheeses and pre-cooked sausages. However stronger regulations have forced many food manufacturers to comply with strict hygiene.

Participants were more spooked about the use of pesticides in food production and additives.

More than 60 per cent of participants were “very concerned” about their potential effects.

Campbell said these were more “perceived risk” than actual risk, as pesticides and additives were covered by regulations.

The authority commissions the surveys every few years to gauge public feeling and tailor its food safety messages. “We eat at least three times a day, so it matters to us all,” Campbell said.

Genetically modified food greatly concerned 56 per cent of respondents, about the same as in two previous years, whereas a new category, food from cloned animals, worried 54 per cent.

“There is such a small use of genetically modified food. I would not put them as high on the list,” said Campbell.

Food allergies and irradiated food brought up the rear, with 47 per cent and 41 per cent respectively.

Following an inquest into the deaths of 3 people from the Legionella bacteria, it may now become compulsory for results of cooling towers to be made available to health officials.

According to Canterbury’s medical officer of health, Alistair Humphrey who told an inquest looking into three deaths from legionella in winter 2005 says that New Zealand should adopt a compulsory regime on testing and reporting of legionnaire’s disease.

All 3 deaths were part of an outbreak of 19 cases clustered in the southwest of Christchurch, Dr Humphrey told Southland-Central Otago coroner Trevor Savage at the inquest, which is likely to last two days.

“It is appropriate that New Zealand moves to adopt a compulsory regime,” Dr Humphrey said. “It will in my view minimise the risk of another outbreak and will be likely to save lives.”

Attention has centred on the cooling tower at the Ravensdown plant in the suburb of Hornby as a possible source, and the company had lawyer Robert Osborne at today’s hearing.

He asked about gaps in the testing of cooling towers, and reporting of results under the present voluntary regime, and Dr Humphrey agreed it was possible that none of the cases came from the Ravensdown cooling tower.

But Dr Humphrey also said: “Our view is that there is no way you can say none of them came from that point source. Everything pointed to a cluster in the southwest of Christchurch around the plant we are talking about, with what we found to be genetically identical species of legionella.”

He agreed with Mr Osborne that the strain was the ubiquitous Christchurch type of the disease.

Inquiries by health officials during the outbreak turned up 141 cooling towers. Some of the owners or those leasing the buildings had not co-operated by testing and providing results and had to be visited by officials.

It meant there were gaps in the knowledge of what was happening during the April to August outbreak. When tests were done it was not known how many had already used biocide to kill organisms in the cooling systems — a call made by health officials to contain the outbreak.

The inquest is hearing evidence on the deaths of Ross Hern 56, Peter Jones, 48, and Valmai Finlayson, 87, who died of legionnaire’s disease at Christchurch Hospital.

Legionella species are widely found in lakes, rivers, groundwater and soil. The hearing was told it was “generally benign” until it was turned into a mist and spread. This could be through hot water systems, air cooling systems, cooling towers, water spraying devices, water sprinklers, demisters, and spa pools. An Auckland outbreak had been traced to a high pressure hose used in a boat washing operation.

When Ravensdown tested its tower in April, it was found to have a high level of 2400 colony-forming units of legionella. Biocide was used and a later test showed the level was down to 260 units.

Ravensdown provided its results to the health authorities.

Dr Humphrey suggested four changes were needed to tighten testing and reporting procedures for legionella, consistent with requirements in New South Wales, Victoria, and now being considered by South Australia.

He wants local bodies to maintain a register of cooling towers, evaporation condensers, and scrubbing towers. In the 2005 outbreak it took health officials about two weeks to gather information on all these installations from Christchurch City Council records.

He also wants compulsory testing by owners and operators, and compulsory disclosure of the results to local authorities and medical authorities.

He also wants a consistent testing regime between commercial and industrial properties.

Giving evidence this afternoon, a senior technical adviser to the Department of Building and Housing, Bruce Trevor Klein, told the coroner that since 2004 all new buildings with water cooling towers required a building compliance certificate.

Owners were required to test their systems regularly for bacterial organisms.

Cooling towers under the 2004 Act had to be sited away from building air conditioning intake systems.

Building owners must furnish annual documents showing the cooling towers had been tested monthly for legionella bacteria.

Legislation required owners or operators of cooling towers showing a level of legionella bacteria exceeding 1000 colony-forming units (cfus) should notify a medical officer of health within 48 hours.

Test results had to be retained for two years.

Questioned by Mr Savage, Mr Klein said his department would need to investigate whether it would support the mandatory reporting of all water cooler test results to health authorities.

He cautioned against Canterbury Medical Officer of Health Alister Humphrey’s earlier assertion that New Zealand should adopt Australia’s reporting system.

Mr Klein said he understood the Ministry of Health was investigating adopting a system that would require the mandatory reporting of high legionella bacterial counts.

As the law stood now, building owners, cooling tower operators and laboratories had no onus to make such reports available despite having to test regularly and retain results.

Questioned by Donna Blandford, niece of the late Mr Hern, Mr Klein said under the Building Act, cooling tower owners or operators faced fines of up to $200,000 for non-compliance.

He was unaware of any prosecutions.

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The Food and Drug Administration (FDA) and the USDA have extended GRAS (Generally Recognised as Safe) Approval for LISTEXâ„¢ to all Food Products.

In the fight against Listeria, one of the most dangerous food pathogens, US food processing companies can now apply a novel yet natural tool: LISTEXâ„¢ bacteriophages. The FDA and USDA have approved this
product from The Netherlands as GRAS, based on extensive safety and efficacy data and organoleptics tests confirming that LISTEXâ„¢ is safe and has no impact on taste, smell, colour, and other physical properties of treated products.

Bacteriophages or phage are some of the most abundant micro-organisms on earth. Fresh water and seawater can contain as many as 1 billion phages per ml, while in fresh and processed meat and meat products, more than 100 million viable phages per gram are often present. Phages are harmless to humans, animals and plants, and target only bacterial cells. They are extremely specific in regard to the bacteria they recognize.

The LISTEXâ„¢ bacteriophages target only Listeria bacteria (leaving desirable bacteria in place), and are easy to apply in the environmental areas of the production processes or even within the process.

In October 2006 the FDA had already proclaimed GRAS for LISTEXâ„¢ against Listeria in cheese. The extension to all products susceptible to Listeria, opens the door for the meat and fish industry to apply LISTEXâ„¢.

Earlier this month, the Dutch designated inspection office SKAL confirmed the ‘organic’ status of LISTEX™ under EU law, as a result of which it can be used in the EU in regular and organic products.

EBI Food Safety’s CEO, Mark Offerhaus: “Food Safety now tops the agenda of US food processing companies and consumers, who are insisting on ‘green’ solutions, rather than chemicals. Natural bacteriophages prove to be a unique solution, where increased safety does not come at the expense of product characteristics. US food processors can now benefit from LISTEX™, like their European counterparts.”

According to the World Health Organization (WHO), Listeriosis, the disease caused by Listeria monocytogenes, is one of the most severe food borne infections, with a mortality rate of 30%. It can take weeks after exposure before an infection becomes apparent. The US Food Safety and Inspection Service maintain a zero tolerance policy for the bacterium, which grows at refrigeration temperature and is omnipresent.

Researchers from the University of Sheffield have received joint funding from the Engineering and Physical Science Research Council (EPSRC) and the Ministry of Defence (MoD) to develop an innovative sensor to detect bacteria. The new method will use a polymer which will give a fluorescent signal when it encounters bacteria, allowing scientists to easily identify infected wounds much earlier than using conventional methodologies.

The new technology will be of immediate benefit to healthcare industries in general, as well as those involved in detecting infection in battlefield conditions and bacterial contamination, whether accidental or deliberate.

Currently identifying bacterial infection takes several days and requires swabbing and culturing of bacterial swabs as well as the use of specialist bacteriology laboratory facilities.

By combining polymers, which change shape when they encounter bacteria, and developing a light signal through fluorescence non radiative energy transfer (NRET), the researchers will be able to detect early stages of bacterial contamination.

Being developed by a multi-disciplinary team of researchers from the University’s Departments of Chemistry, Engineering Materials and the Dental School, the sensor will have widespread applications beyond the initial project.

Dr Steve Rimmer from the University’s Department of Chemistry, said: “The project is a great example of progress that can be achieved at the life sciences/physical sciences interface and we hope the project will deliver technology of real importance.”

The multi-disciplinary team will be led by Dr Steve Rimmer of the Department of Chemistry and consists of Dr Linda Swanson (Chemistry) Professor Sheila MacNeil (Engineering Materials) and Dr Ian Douglas (Clinical Dentistry).

The project received £670,000 funding jointly from the Engineering and Physical Science Research Council and the Defence Science and Technology Laboratory - an agency of the Ministry of Defence over three years and started in December 2006.

Pink slime at the surface of water trickling through an old mine in California is proving to be a haven for researchers in their quest to learn more about how bacterial communities co-exist in nature.

A letter published in Nature shows that it is possible to follow what micro-organisms are doing in their natural environment by identifying the range of proteins that they produce. The technique, utilized in a microbial community thriving in battery acid-like streams underground at Richmond Mine near Redding, California, combines recently developed ways to sequence microbial genes with methods to identify the range of proteins from specific microbial members.

Researchers from Oak Ridge National Laboratory and UC Berkeley discovered that Leptosprillium group II bacteria in these streams are exchanging large blocks of genes. While scientists have seen extensive gene transfer in bacteria, this is the first observation of exchange of huge genomic blocks in a natural microbial community.

“Consequently, this provides important information about the conservation of genetic resources to enable life to survive and thrive,” said ORNL’s Bob Hettich, a co-author and member of the Chemical Sciences Division. “Ultimately, the basic knowledge gained from this research will lead to a greater understanding of genetic diversity in related organisms and should lead to developments in human health
and bioremediation.”

The combination of mass spectrometry support from ORNL researchers with extensive reconstruction of genomes from community genomic data at UC Berkeley was a key component to this work, said Jill Banfield, who led the project. Banfield, a professor in UC Berkeley’s Department of Environmental Science, Policy and Management, expects this to have far reaching implications.

“More important perhaps is the demonstration of our ability to simultaneously identify a large fraction of an organism’s proteins and to distinguish them from proteins derived from quite closely related organisms,” Banfield said. “This opens the way for detailed studies of how a wide range of microbial communities are structured and how they function.” Hettich agreed that today’s powerful molecular tools are playing a vital role in investigating the complexity of how bacterial consortia cooperate and compete in nature. In fact,
ORNL mass spectrometry provided the ability to resolve and differentiate peptides that differ by as little as one amino acid.

Nathan VerBerkmoes of the lab’s Chemical Sciences Division was instrumental in designing the experiments and acquiring the mass spectrometry data while Manesh Shah of the Biosciences Division provided the bioinformatics horsepower to sort through the massive datasets.

“A key aspect of this paper is the ability to get proteome information on organisms that do not directly have complete genome sequencing information,” VerBerkmoes said. “As a result we could study organisms related to those completely sequenced - such as the bacterial clades, or ‘cousins,’ that are likely to exist in natural environments”.

“This also might have implications into helping study human proteomics because not everyone’s individual genome will be sequenced.”

The pink microbial biofilm communities found in the mine runoff provide perfect research specimens because they have fewer organisms than most communities found in nature. The reason, Hettich noted, is that these environmental conditions - a low pH of 0.8 are way too extreme for most organisms to survive. A pH level of 7 is considered neutral and most proteins prefer pH levels between 5 and 7. In addition, the water from the mine often exceeds 120 degrees Fahrenheit. Because of their simpler makeup, the Banfield Laboratory established these communities as a model system in the mid 90s.

This latest publication builds upon research that was published in May 2005 by Science. In that paper, Banfield, Hettich and colleagues at ORNL describe the bacteria community that thrives in what amounts to sulphuric acid. Their work set the stage for the latest development because it provided the first large-scale proteome dataset for a real life microbial community with a limited number of members.

Of particular interest to DOE is how this effort relates to its Genomes to Life program, which is focused on identifying and characterizing the molecular machines of life. This study helps extend the initial studies of microbial isolates growth in carefully controlled laboratory settings to more real-world complicated microbial communities.

Funding for this project, which is in the second of five years, is provided by DOE’s Office of Science, Office of Biological and Environmental Research and by the National Science Foundation. UT-Battelle manages ORNL for DOE.