Article: FDA draws criticism after U-turn on antibiotics in animal feed

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2012 set to see some heavyweight M&A activity? Definitely, say leading food market analysts

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Article: Giant Microbes Christmas Ornament Sets

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Article: USDA Announces Zero Tolerance E. Coli Policy

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Article: CFIA issues warning to consumers of jalapeno peppers

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Article: Recalled Eclectic Institute Supplements May be Tainted with Salmonella

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Article: E. coli 0157:H7 Infections possibly tied to romaine lettuce

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Article: FDA Issues New Safety Rules for Beef

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Article: Cargill Resumes Ground Turkey Production After 2 Salmonella Incidents

Cargill Resumes Ground Turkey Production After 2 Salmonella Incidents - The Huffington Post

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Article: Review: HandSan

Review: HandSan - Confessions of a Psychotic Housewife

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Article: William Marler: The Twelve Days of Food Safety Christmas

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Article: Beautiful, but deadly to salmonella

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Article: Eggs now considered safe beyond their 'best before' dates

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Article: Selfridges' raw milk dispenser 'contravenes food hygiene regulations'

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Article: Alarm as Dutch lab mutates killer virus

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Article: E. coli outbreak in raw cookie dough explained

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Article: Cilantro Recall in Indiana

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Article: How Salmonella forms evil twins to evade the body's defenses

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Article: FDA says it's OK to turn bad food into sellable stuff

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Article: Norovirus present in 76% of British oysters, research finds

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Article: Culprit in 2009 cookie dough E. coli outbreak could be raw flour

Culprit in 2009 cookie dough E. coli outbreak could be raw flour - The Sacramento Bee

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A Proposal of Genomic Analytical Workflow in a Bacterial Pathogen Outbreak Investigation : Nature Precedings

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Article: St. Louis-based produce company recalls grape tomatoes due to possible salmonella contamination

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Article: Orange Peels In Cattle Feed May Help Fight Foodborne Illness

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Article: Do you own your germs? My new piece for the New York Times on micro-bioethics | The Loom

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Article: New FSA research identifies norovirus levels in oysters

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Article: Trans-Ocean Products Recalls Certain Smoked Salmon Lots Due To Listeria Risks

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Food Safety and Quality Information - FoodHACCP.com

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Article: Whittington's beef jerky may be contaminated with Salmonella

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Article: Turkish pine nuts recall

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Article: The raw milk revolution

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Article: Cause of antibiotic-resistance found

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Article: Salmonella Outbreaks in many states

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Article: Pasteurized Shell Eggs Give Consumers Safe, Salmonella-Free Option During Holiday Meal Season

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Article: Raw milk in E. coli recall in Calif.

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Article: Ready Packed Salad Product Recalled By Ready Pac Foods Due To E. Coli

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Article: More tests for raw milk dairy after E. coli illnesses

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Article: AvidBiotics' Targeted Antibacterial Proteins Show Potential to Address Food-Borne Bacterial Infections, Provide Antibiotic Alternative

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Article: CFIA recalls ginger beef sold at Costco

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Article: Smucker's recalls 300 cases of peanut butter for possible Salmonella

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Article: USDA to enforce regulation of Shiga toxin-producing E. coli

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Article: Local organic raw milk, butter, cream, colostrum & qhephor recalled

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Article: An 'Operating System' That Runs on Cells Could Create Whole New Life Forms | Popular Science

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Article: Health warning: Pine nuts may contain salmonella bacteria

Health warning: Pine nuts may contain salmonella bacteria - BayToday.ca

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Health warning: Pine nuts may contain salmonella bacteria By Kate Adams BayToday.ca Saturday, November 05, 2011 Canadian Food Inspection Agency News Release  ********************* OTTAWA - The Canadian Food Inspection Agency (CFIA) and David Roberts Food Corporation are warning the public not to consume certain David Roberts brand and Sysco brand pine nuts, described below, because the products may be contaminated with Salmonella. The following pine nuts products are affected by this alert: Sysco Plastic bag 1.5 kg 00734730026268 Lot 1323  David Roberts Plastic tubs 90 g 0 67261 24656 1 Lot 1323 Best Before Aug 17, 2012  David Roberts * Plastic bags 1.5 kg None Lot 1323  None* Plastic tubs Variable 90-100 g None Pack date: AU 17, 2011  * Sold only at David Roberts Food Corporation retail store: 426 Watline Avenue, Mississauga, ON. These products have been distributed to food service accounts in Ontario and sold at the David Roberts Food Corporation retail store located at 426 Watline Avenue, Mississauga, ON. There have been no reported illnesses associated with the consumption of these products. Food contaminated with Salmonella may not look or smell spoiled. Consumption of food contaminated with this bacteria may cause salmonellosis, a foodborne illness. In young children, the elderly and people with weakened immune systems, salmonellosis may cause serious and sometimes deadly infections. In otherwise healthy people, salmonellosis may cause short-term symptoms such as high fever, severe headache, vomiting, nausea, abdominal pain and diarrhea. Long-term complications may include severe arthritis. The importer, David Roberts Food Corporation, Mississauga, ON, is voluntarily recalling the affected products from the marketplace. The CFIA is monitoring the effectiveness of the recall. For more information, consumers and industry can call one of the following numbers: David Roberts Food Corporation at 905-502-7700; CFIA at 1-800-442-2342 / TTY 1-800-465-7735 (8:00 a.m. to 8:00 p.m. Eastern time, Monday to Friday). For information on Salmonella, visit the Food Facts web page at: http://www.inspection.gc.ca/english/fssa/concen/cause/salmonellae.shtml For information on all food recalls, visit the CFIA�s Food Recall Report at: http://active.inspection.gc.ca/eng/corp/recarapp_dbe.asp. To find out more about receiving recalls by e-mail, and other food safety facts, visit: www.foodsafety.gc.ca. Food and consumer product recalls are also available at http://www.healthycanadians.gc.ca. ********************* Print View | Send to a Friend News Response | Sports Response

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Article: Number of confirmed St. Louis area E. coli cases rises to 27

Number of confirmed St. Louis area E. coli cases rises to 27 - STLtoday

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Are Gut Bacteria In Charge? - Discovery News

http://news.discovery.com/human/gut-bacteria-obesity-111026.html

Are Gut Bacteria In Charge?

27 October, 2011 4:07:00 AM

Jessica Marshall)

The bacteria in our gut may be controlling our lives more than we ever realized.

In the latest findings, published today in Nature, researchers report a link between gut bacteria and the development of multiple sclerosis in mice. Studies in mice have also examined gut bacteria in relation to obesity, depression and much more.

More human studies are emerging hinting at the role the bacteria in our guts may play well beyond helping us to digest our food.

NEWS: Is Obesity A Disease?

"What has been observed in humans with regard to obesity is that there seems to be a difference in the number of kinds of bacteria in the gut," said Rob Knight of the University of Colorado, Boulder. "That number is much lower in obese people than in healthy people."

Researchers have also seen differences in bacteria between mice bred to be obese versus those of normal weight. In one experiment, researchers found that an obese mouse's gut microbes extracted more of the calories from a given parcel of food than did those of non-obese mice.

This caused the obese mice to gain more body fat than the non-obese mice did.

But even stranger, in a type of mouse with a different mutation that leads to obesity, transferring gut microbes from the obese mice into other mice led the non-obese mice to eat more.

"They're not any better at extracting energy from the food. They're just hungrier apparently," Knight said. "There are more microbial cells in your body than there are brain cells. They may be outvoting you when it comes time to order (at the restaurant)."

If gut microbes can tell mouse brains to eat more, could they have other effects on the brain? Researchers are finding that the answer is yes.

"We're now starting to see direct impacts of the gut microbial community on host behavior," Knight said.

Experiments have shown that mice with no gut microbes show differences in how much they move and in their anxiety-like behavior than mice with normal gut bacteria. Mice treated with "probiotic" Lactobacillus bacteria showed a different gene expression in the brain, reduced anxiety behavior and stress hormone levels than untreated mice.

The effects may extend to diseases that are seemingly unrelated to the digestive system. In the work published today, researchers studied mice bred to develop a disease similar to multiple sclerosis.

Those raised in an environment with no bacteria never developed symptoms. Once typical gut bacteria were introduced, the mice began to show signs of the disease.

"I think what our study really shows is the importance of the gut microbiota in the initial phase of the disease," said Gurumoorthy Krishnamoorthy of the Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany who led the study with colleague Hartmut Wekerle.

Of course, it's impossible for humans to live a microbe-free lifestyle, but the findings suggest the microbial community may play a role in human multiple sclerosis. The team will now look for specific microbes that may be responsible for triggering symptoms.

NEWS: Animals Getting Fatter, Too

If a healthy gut microbial community proves important for different aspects of our health, what could we do to encourage the bacteria that would prevent obesity or disease?

One option might be to take probiotics, eat a particular diet, or minimize antibiotic use, Krishnamoorthy said.

But others are investigating transferring gut bacteria from the other end-through "fecal transplants" from healthy people to those with illness. "The potential is very high, but the actual amount of research is relatively low," Knight said.

In trials of patients with Clostridium difficile infections -- a gut-wrenching intestinal problem -- more than 90 percent of patients have been cured, and their microbial communities restored to normal.

In preliminary work with huge public health implications, a study last year showed improved insulin sensitivity among patients with metabolic syndrome who received stool transfers from lean individuals.

"Then the question is which other conditions are there that could also benefit from stool transplants," Knight said.

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Article: FDA to launch major Salmonella screening of pet foods in 2012

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Article: Recalls & Withdrawals

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Article: FDA begins testing pet food products for salmonella

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ABCNews.com: St. Louis E. Coli Probe Focuses on Grocery Salads

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Article: E. coli outbreak in Missouri investigated

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Article: And Now, an E. coli Bacterium That's Fifteen Feet Long

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Article: States vary widely in reporting foodborne illnesses

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Article: US food store recalls pine nuts

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Article: Salmonella Outbreak Forces Recall of Pine Nuts

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Article: New Liquid Crystal-Based Technology Rapidly Detects Multiple Pathogens in Food

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Article: German E. coli outbreak: Closer look at bacterium's new strain

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Article: Fridge Salad Drawers May Contain 750 Times More Bacteria Than "Clean" Level, Research Shows

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Article: Yale Innovates New E. Coli Test That Could Save Thousands Of Lives

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Article: Death toll from tainted cantaloupe jumps to 18, at least 100 sickened

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Article: FDA: Cantaloupe Listeria Outbreak Not Over Yet

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Article: Listeria found in cantaloupe has killed at least 13; number is expected to grow

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Article: The Microbial Immune System Can Be Likened To A Vaccination Program

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Article: Michele Bachmann's Latest Job Creation Idea: Less Food Safety Regulation, More E. Coli

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Biomedical Literature Search Tools

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Article: BioMed Central | Full text | Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella

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Article: Recall expanded for walnuts over possible E. coli contamination

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Article from Science News: Mind-Altering Bugs...

I thought you might be interested in this article from Science News:

Mind-Altering Bugs

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Article: Ground turkey salmonella toll climbs to 111

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Article: Battle of the Bacteria: Genetically Modified E.coli vs. P.aeruginosa

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Article: E. Coli Found In Strawberries At Oregon Farm

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Article: Turkey recall raises U.S. food safety questions

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Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4 — NEJM

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Microbial Genomics and Infectious Diseases — NEJM

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Article: University of Maryland School of Medicine Institute for Genome Sciences Cracks Genomic Code of Deadly German E. coli Outbreak

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Article: Recall Notification Report 056-2011 | USDA Food Safety and Inspection Service

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Article: As E. Coli Sequencing Data Accumulates, Teams Disagree on Evolutionary Origins of Outbreak Strain

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Article: Only 1 deadly strain of E. coli is illegal, but that may change

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Article: Early IV reduces renal risk after E. coli

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Software for Genomics, Proteomics, Metabolomics & Transcriptomics: Genedata AG

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Article: Space shuttle may have planted seed for MRSA, salmonella vaccines

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Article: AP Exclusive: US victim of German food poisoning outbreak describes '30 days of hell'

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Article: Bill Marler To Sprout Industry: Face Reality, Sprouts Can Sicken and Kill

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Article: Seattle Lab Finds Tainted Grocery Store Chickens

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Article: Spanish eggs linked to salmonella outbreak

Spanish eggs linked to salmonella outbreak - The Daily Mirror

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Article: Neogen Corp. (NEOG) Reports E. coli Detection Breakthrough for NeoSEEK

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Combating E. Coli: Can a Peptide Block the Bug?

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Article: The end of E. coli | Thoughtomics, Scientific American Blog Network

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Article: Five Experiments Underway in Space

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Article: China dogged by ongoing food safety breaches

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Article: In final mission, space shuttle Atlantis carries vaccine research

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A Parallel Clinical Pattern to O104:H4

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Two Studies Analyze the Unusually Deadly Outbreak of E. Coli in Germanty - - TIME Healthland

http://healthland.time.com/2011/06/24/why-the-german-e-coli-outbreak-was-so-deadly/

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Pacific Biosciences Contributes Whole Genome Sequence Data for German E. Coli Outbreak Strain and 11 Related Strains for Comparative Analysis - MarketWatch

http://www.marketwatch.com/story/pacific-biosciences-contributes-whole-genome-sequence-data-for-german-e-coli-outbreak-strain-and-11-related-strains-for-comparative-analysis-2011-07-06?reflink=MW_news_stmp

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Article: The 2011 E. Coli Diagnostics Market: US, Europe, Japan - Test Volume and Sales Forecasts by Country Profiles Leading Suppliers and Recent Market Entrants

The 2011 E. Coli Diagnostics Market: US, Europe, Japan - Test Volume and Sales Forecasts by Country Profiles Leading Suppliers and Recent Market Entrants - FinanzNachrichten

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Article: A food safety ‘who done it'

A food safety 'who done it' - The Globe and Mail

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Article: Final space shuttle to carry five CU-Boulder-built payloads

Final space shuttle to carry five CU-Boulder-built payloads - Physorg

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Article: Phage on the Rampage

Phage on the Rampage - Cornucopia Institute

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Article: E. coli bacteria ehec traced to Sweden

E. coli bacteria ehec traced to Sweden - Stockholm News

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Article: Budget cuts threaten testing of produce for pathogens

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'Megapixel' DNA replication technology promises faster, more precise diagnostics

http://www.sciencedaily.com/releases/2011/07/110703133842.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29&utm_content=Google+International

Article: The 15 Most Terrifying Food Scares

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Article: Cornell gets grant to start food safety training

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NGSLeaders :: Blogs

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Article: China wrestles with food safety problems

China wrestles with food safety problems - Los Angeles Times

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Article: Human Belly Button Is Home to Hundreds of Never-Before-Seen Species

Human Belly Button Is Home to Hundreds of Never-Before-Seen Species - Popular Science

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Article: A Decade of Inaction at USDA on Non-O157 E. coli

A Decade of Inaction at USDA on Non-O157 E. coli - www.foodsafetynews.com

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Article: France E. coli outbreak: One dead

France E. coli outbreak: One dead - BBC

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Article: Under pressure, Idaho producer recalls sprouts

Under pressure, Idaho producer recalls sprouts - San Francisco Chronicle

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Article: Update On E. Coli O104 Outbreak In Germany And Cluster Of Cases In France

Update On E. Coli O104 Outbreak In Germany And Cluster Of Cases In France - Medical News Today

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Article: Irradiating organic food would save lives - health - 28 June 2011 - New Scientist

Irradiating organic food would save lives - health - 28 June 2011 - New Scientist - www.newscientist.com

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Article: Bill Marler To Sprout Industry: Face Reality, Sprouts Can Sicken and Kill

Bill Marler To Sprout Industry: Face Reality, Sprouts Can Sicken and Kill - PRWeb

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Article: New salmonella-based 'clean vaccines' aid the fight against infectious disease

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Article: EU investigating if Egypt seeds common link in E. coli outbreak in Germany and France

EU investigating if Egypt seeds common link in E. coli outbreak in Germany and France - The Washington Post

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Article: Decoding Genomes Of Microbe Ecosystems Could Deliver Untold Benefits

Decoding Genomes Of Microbe Ecosystems Could Deliver Untold Benefits - Fast Company

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Article from Science News: Mutated Bacteria Drives Scarle...

I thought you might be interested in this article from Science News:

Mutated Bacteria Drives Scarlet Fever Outbreak

http://news.sciencemag.org/scienceinsider/2011/06/mutated-bacteria-drives-scarlet.html?ref=wp

---

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Article: Alfalfa Sprouts Salmonella Risk Warning Issued By FDA

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Article: Understanding the E. coli outbreak part four

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Article: The long and winding road to a PhD [infographic] - Holy Kaw!

The long and winding road to a PhD [infographic] - Holy Kaw! - holykaw.alltop.com

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Article: Tyson Bribery Case Reveals Gaps in Meat Inspection Policy, White Collar Crime Law

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Article: Epidemiology and social media: conference fail : Aetiology

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Article: The E. coli O104:H4 Outbreak Gets More Confusing--and Potentially More Disturbing

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Article: Understanding the E. coli outbreak part three

Understanding the E. coli outbreak part three - Examiner

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Article: French E.coli Strain Is The Same As Germany's

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Article: Spoonful of Medicine: As E. coli continues to claim lives, new approaches offer hope

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Article: Will budget cuts spell the end for "Team D"?

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Article: France halt sales of 3 seed types linked to British vendor after E. coli outbreak

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International Activities > Foreign Food Inspection Program Questions and Answers

FDA list of high risk food.

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Article: Sickening Shopping Carts

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Article: E. coli: Some Answers, Many Questions Still

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The Tree of Life: Fun with Ligercat: pubmed word clouds

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Article: Gangrenous Bowel Shows Deadly Risk of German Bug, Study Says

Gangrenous Bowel Shows Deadly Risk of German Bug, Study Says - Business Week

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From Foodborne Pathogen Team Kwan Lab CUHK--German outbreak strains: Alignment-free whole-genome phylogeny suggested that EAEC 55989 is a close relative but not a direct parent

German outbreak strains: Alignment-free whole-genome phylogeny suggested that EAEC 55989 is a close relative but not a direct parent

Introduction:

Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 9 outbreak isolates against existing E. coli genomes using the alignment-free feature frequency profile (FFP) method (Sims et al. 2009).

Datasets:

1. Genome sequences of 30 E. coli isolates from NCBI, and

2. Genome sequences of 9 outbreak isolates, TY2482 from BGI, LB226692 from Life Technologies, 5 isolates from HPA, and 2 isolates from Göttingen.

Method:

1. Genome sequences were converted into an RY (purine/pyrimidine)-coded form.

2. Overlapping features, l-mers of length 24, were counted over each of the whole genomes.

3. Forward and reverse complement features were considered equivalent.

4. Only core features which were present in all 39 isolates were extracted.

5. Features occurring more than 3 times in any of the isolates were removed.

6. Simple cumulative distances were calculated among all feature states in an unordered manner.

7. A neighbor-joining tree was plotted with the resulting distance matrix using MEGA5.

For details, please refer to Sims & Kim (2011).

Results:

The following is the phylogenetic tree produced using the current alignment-free method. Outbreak isolates were highlighted in red.

Our tree generally agrees with that reported by Konrad Paszkiewicz & Kat Holt built using a SNP-based approach, both revealing a high similarity among the outbreak isolates and 55989 being the most closely related isolate sequenced thus far. However, we should note that the genetic difference between 55989 and the outbreak isolates in our FFP tree is greater than that in the tree built based on SNPs. 

Linear phylogenetic inference of bacteria might be problematic due to horizontally transferred elements. While Kat Holt tried to remove obviously horizontally transferred DNA by removing SNP calls in genes annotated with keywords like "phage" and "transposase", we removed features likely to be associated with mobile or repetitive DNA by filtering out features with high frequencies and used an unordered character state model to reduce the effect of lateral transfer signal. Both methods seem to work well.

Concluding remarks:
To sum up, using an alignment-free phylogenetic approach, we further confirm 55989 being the most closely related isolate to the outbreak isolates sequenced thus far, again showing an EAEC-origin of the outbreak isolates. However, the genetic difference suggested that 55989 is not a direct parent of the outbreak isolates.

References:

Sims GE, Jun S-R, Wu GA, Kim S-H (2009) Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. PNAS 106:2677-2682.

Sims GE, Kim S-H (2011) Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). PNAS 108:8329-8334.

Prepared by Simon CHEUNG, Wenyan NONG,  Lei LI & H.S. KWAN

Eurosurveillance editorial on E. coli outbreak credits crowdsourcing « bacpathgenomics

Eurosurveillance editorial on E. coli outbreak credits crowdsourcing « bacpathgenomics

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Article: Hog roast salmonella investigated

Hog roast salmonella investigated - BBC

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WHO/Europe | EHEC outbreak: Update 22

http://www.euro.who.int/en/what-we-do/health-topics/emergencies/international-health-regulations/news/news/2011/06/ehec-outbreak-update-22

Table copied from WHO report linked above:

"
The table shows the reported cases of and deaths from HUS and EHEC infection as of 22 June at 15:00 CET.

Country	HUS		EHEC		Comments
	Cases	Deaths	Cases	Deaths
Austria	1	0	3	0
Canada	0	0	1	0
Czech Republic	0	0	1	0	A tourist from the United States who had travelled in Germany
Denmark	9	0	13	0
France	0	0	2	0
Germany	823	29	2865	13
Greece	0	0	1	0	A German tourist
Luxembourg	1	0	1	0
Netherlands	4	0	5	0
Norway	0	0	1	0	Contact with a German in Norway
Poland	2	0	1	0
Spain	1	0	1	0
Sweden	17	1	33	0
Switzerland	0	0	5	0
United Kingdom	3	0	3	0
United States of America	3	0	2	0	3 HUS cases (all confirmed) and 2 EHEC cases (one confirmed and one suspected)
Total	864	30	2938	13

Note. There are 3802 HUS and EHEC cases in total, including 43 fatalities.




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CIDRAP >> German E coli outbreak kills 3 more, reaches 3,800 cases

http://www.cidrap.umn.edu/cidrap/content/fs/food-disease/news/jun2311ehec.html

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Article: Salmonella 'superbug' threat from intensive pig farms

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Article: New device promises quick testing for food-borne pathogens

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Article: E. coli's sticky secret revealed in medical journal

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Article: Scarlet-fever scare

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Article: Unusual Traits Blended in Germany E. Coli Strain - NYTimes.com

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Article: Hemolytic uremic syndrome (HUS) in history--part 3

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Article: A New Way to Combat Antibiotic-Resistant Bacteria

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Article: Cornell researchers tackle containment of E. coli

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Article: Omics! Omics!: E.coli Outbreak Genomics

Omics! Omics!: E.coli Outbreak Genomics - omicsomics.blogspot.com

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Article: Nature News Blog: The German E. coli outbreak: 40 lives and hours of crowdsourced sequence analysis later

German E. coli Crowdsourcing is reported in Nature News Blog.

Nature News Blog: The German E. coli outbreak: 40 lives and hours of crowdsourced sequence analysis later - blogs.nature.com

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Article: GMO Pundit a.k.a. David Tribe: Complete map of German E. coli O104 (Acronym STpEAEC) genome released

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Article: Hemolytic uremic syndrome (HUS) in history--part 2

Hemolytic uremic syndrome (HUS) in history--part 2 - Aetiology

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