LOOKING TO CURE ANTIBIOTIC RESISTANCE

FROM:  NATIONAL SCIENCE FOUNDATION
Researcher studies how to prevent antibiotic resistance
Solution could be in bacterial protein called UmuD

The widespread and indiscriminate use of antibiotics has prompted many bacteria to mutate, an adaptation that often renders the drugs useless. The increasing threat of resistance worries infectious disease experts who fear that the era of public health successes brought by the introduction of antibiotics in the 1940s is seriously eroding, or soon even may be at an end.

But what if science could improve existing antibiotics in such a way as to not only destroy bacteria, but prevent them from mutating?

At least one research team, in seeking to better understand bacterial mutation, may provide scientific answers that ultimately could lead to thwarting the organisms' ability to mutate, thus blunting the increasing threat of antibiotic resistance.

"The idea would be a one-two punch," says Penny Beuning, an associate professor of chemistry and chemical biology at Northeastern University's college of science. "We need a good therapeutic target that will both kill the bacteria and prevent mutagenesis."

To be sure, the approach almost certainly is years away. Still, the National Science Foundation (NSF)-funded scientist thinks it may be possible. She and her colleagues are studying an important bacterial protein known as UmuD that regulates mutagenesis and may provide important clues about how to stop the process that eventually results in antimicrobial resistance.

Using the bacterium E. coli as a model, she has learned that UmuD interacts with the machinery that replicates DNA, and, when altered, may provide the switch that triggers mutation. UmuD exists in two forms, a full length version when first expressed, and later, if DNA is damaged, a much shorter form. It is this shorter version that allows bacteria to mutate.

Once there is DNA damage, "there is an SOS response, and the levels of some specific proteins go up," she says. "There is a massive stress response, and UmuD responds by cutting its arms off."

In cells where only the full-length version of the protein is present, the bacteria cannot mutate. "But when it forms its shorter self, the cells are mutable," she says.

The fact that UmuD is not present outside bacteria makes it a viable antibiotic target.

"The hope would be to find something that targets UmuD together with an existing antibiotic to prevent bacteria from mutating and developing a resistance to that particular drug," she says. "Among the things we have been looking at: how does UmuD work, and what controls the cleavage of the arms?"

Beuning is conducting her research under an NSF Faculty Early Career Development (CAREER) grant awarded in 2009 under the American Recovery and Reinvestment Act. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organization. NSF is funding her work with $994,655 over five years.

Beuning specifically is looking at the cleavage process of UmuD using gel electrophoresis, which separates proteins according to size.

"UmuD is a small protein--139 amino acids--which loses 24 amino acids from the arm. So it goes from 139 to 115," she says. "We can observe this difference with electrophoresis, allowing us to determine how different conditions or other proteins might affect UmuD cleavage."

The team is studying different UmuD protein interactions in the lab, using biochemistry to see when and how different proteins bind to one another. Essentially "we light up the proteins and measure how they change when other proteins bind, using a method called FRET, which stands for fluorescence resonance energy transfer," she says.

"This measures energy transfer between two proteins using light emission," she adds. "The proteins have to be close to each other for energy transfer to occur, so it's a way of detecting whether two things bind to each other. People often call the technique a molecular ruler, because it can be used to measure precise distances, but we use it simply to measure proximity."

Using FRET, they discovered that UmuD prevents specific protein interactions in the replication process. That is, it stops or slows down replication by keeping two proteins that need to interact for replication from binding to each other. "Protein-protein interactions are generally hard to target with drugs, but the approach has some potential," she says.

They also use another technique that measures how floppy or flexible proteins are by putting them in heavy water and measuring how much heavier the protein gets as it trades its regular hydrogens with heavy hydrogens from the heavy water. "The floppier parts swap out the hydrogens faster than the less floppy parts," she says.

As part of the grant's education component, she has up to ten undergraduates--as well as local high school students and teachers--working in her research lab. Several students have worked in her lab as part of Northeastern's signature co-op program, in which students work full-time for six months in positions related to their career goals.

Also, she teaches an upper level chemical biology class to undergraduates, and created a lab research project for the students that takes place during half of the semester that actually involves them directly in her mutagenesis research.

"A lot of these students had not yet conducted any research, so they were really motivated by the idea of doing something that someone would use as part of a bigger project," she says. "Particularly at Northeastern, where co-op is such a large part of the culture, it is fun to take advantage of the laboratory as the ultimate in experiential education.”

-- Marlene Cimons, National Science Foundation
Investigators
Penny Beuning
Related Institutions/Organizations

NSF ARTICLE: TESTING FOR PATHOGENS

FROM:  NATIONAL SCIENCE FOUNDATION 

Testing for pathogens

Innovation Corps researchers focus on medical applications rather than food safety in response to customer needs

When Sunny Shah and his research colleagues at the University of Notre Dame developed a new diagnostic tool for detecting the presence of bacteria, viruses and other pathogens, they assumed that the food industry would be the perfect market.

It made sense, particularly amid ongoing concerns over food safety. The test could identify, among other things, E. coli 0157, which has caused a number of deadly outbreaks in the United States, as well as the bacterium responsible for brucellosis, a disease caused by eating undercooked meat or unpasteurized dairy products.

Their test was accurate and inexpensive. It just wasn't fast enough.

"Even though we could provide a cheaper test than what is already available, they said they would be willing to pay more for a faster test," Shah says, referring to his conversations with representatives from food processing plants, health agencies and food testing labs. "They said we needed to produce results within two hours, not two days, because they wouldn't be able to ship anything out, and had to pay for refrigeration, while waiting for test results."

So the National Science Foundation (NSF)-funded scientist switched his focus--he likes to call it a "pivot"--from food safety to medical applications. In addition to food-borne bacteria, the test also can recognize the virus that causes Dengue fever, potentially valuable for surveillance activities both here and abroad, and human papillomavirus (HPV), which is linked to cervical and oral cancers.

Shah, who also is assistant director for the ESTEEM graduate program, which exposes those with STEM (science, technology, engineering, and mathematics) backgrounds to business and entrepreneurial courses, received $50,000 in 2013 from NSF's Innovation Corps (I-Corps) program. I-Corps helps scientists assess how, and whether, they can translate their promising discoveries into viable commercial products.

The award supports a set of activities and programs that prepare scientists and engineers to extend their focus beyond the laboratory into the commercial world, with the idea of providing near-term benefits for the economy and society.

It is a public-private partnership program that teaches grantees to identify valuable product opportunities that can emerge from academic research, and offers entrepreneurship training to student participants.

Although things did not turn out as originally planned in this case, Shah's experience nevertheless actually embodies the I-Corps philosophy, since one of its major goals is to mentor scientists in ways that allow them to evaluate the commercial potential of their discoveries, and send them in different directions if necessary to ensure their research ends up in the best possible place to do the most good at an affordable price.

"It doesn't matter what we, as researchers, think is the value of our technology," Shah says. "It's what the customer thinks that is important and the only way to identify this customer need is by getting out and interviewing them."

NSF also earlier supported the research that developed the test in 2011. Shah's research colleagues on this project include Hsueh-Chia Chang, professor of chemical and biomolecular engineering, Satyajyoti Senapati, research assistant professor, and Zdenek Slouka, postdoctoral associate in the Chang group. For the I-Corps grant, Kerry Wilson, managing director of Springboard Engineers, played the role of the business mentor, while Shah was the entrepreneurial lead

The test uses a biochip that can detect the DNA or RNA of a particular pathogen.

"Every pathogen has a unique biomarker, and what we do is put a probe on our biochip that captures that biomarker," Shah says. "If the sample has that particular pathogen, then its biomarker will bind to this probe and give us a signal. There are changes in the electrical properties, so it gives us a visual electrical signal that can easily be translated into a target present/absent signal."

Each chip is programmed for a specific pathogen, "but in the future we hope to develop what we call a multiplex biochip that can detect numerous pathogens all on the same device," Shah adds.

The plan now is to develop the tool for future use by dentists to test their patients during office visits for early detection of HPV-related oral cancer before there are visible signs of disease.

"Usually dentists now just examine you visually for lesions, but this would be a sample swab that could give you advance warning," he says.

The test also might be useful as a diagnostic tool for food-borne disease after infection, that is, in testing an already ill patient's blood, he says.

The team recently received a National Institutes of Health grant to study a possible future surveillance role for the test in screening mosquitoes for the presence of Dengue Fever.

"This is not a huge problem for the United States, although there have been a number of cases in parts of Florida in recent years, but it is an issue in South America, Brazil and India, and other areas, " he says.

The impact of I-Corps allowed Shah to make the transition. "Knowing the market and the customer early is extremely important in the technology commercialization process," he says. The program helped him to "quickly assess a particular market to identify customer need and be ready to pivot from one market to another, if needed."

-- Marlene Cimons, National Science Foundation
Investigators
Sunny Shah
Li-Jing Cheng
Hsueh-Chia Chang
Satyajyoti Senapati
Related Institutions/Organizations
University of Notre Dame

COMPLAINT FILED AGAINST MICHIGAN CHEESE FACTORY FOR DISTRIBUTING ADULTERATED CHEESE PRODUCTS

FROM:  U.S. JUSTICE DEPARTMENT 

Friday, August 8, 2014

United States Files Enforcement Action Against Michigan Cheese Company and Owners to Stop Distribution of Adulterated Cheese Products

A civil complaint was filed today in federal court in Michigan against S. Serra Cheese Company of Clinton Township, Michigan, and its owners, Stefano and Fina Serra, to prevent the distribution of adulterated cheese, announced Assistant Attorney General Stuart F. Delery of the Justice Department’s Civil Division.

S. Serra Cheese Company manufactures and distributes several varieties of Italian cheeses, such as ricotta, provolone, mozzarella and primo sale.  The complaint alleges that the company’s Italian cheeses are manufactured in insanitary conditions, and that the company’s procedures are inadequate to ensure the safety of its products.  The department filed the injunction action in the Eastern District of Michigan at the request of the U.S. Food and Drug Administration (FDA).

“The presence of potentially harmful pathogens in food and processing facilities poses a serious risk to the public health,” said Assistant Attorney General Delery.  “The Department of Justice will continue to bring enforcement actions against food manufacturers who do not follow the necessary procedures to comply with food safety laws.”

According to the complaint, two FDA inspections performed in 2013 revealed that the company’s cheese is adulterated within the meaning of the Food, Drug and Cosmetic Act because it is prepared, packed or held under insanitary conditions in which it may have become contaminated with filth or rendered injurious to health.  The complaint alleges, for example, that the company repeatedly failed to reduce the risk of contamination from two potentially dangerous types of bacteria: Escherichia coli (E. coli) and Listeria innocua (L. innocua).

Although the strains of E. coli found in cheese samples collected from the company’s facility were n on-pathogenic, their presence indicates that the facility is insanitary and contaminated with filth.  In addition, t he presence of L. innocua indicates insanitary conditions and a work environment that could support the growth of L. monocytogenes, an organism that poses a life-threatening health hazard because it is the causal agent for the disease listeriosis, a serious encephalitic disease.  The presence of L. innocua in the company’s facility demonstrates the potential for the presence of L. monocytogenes in the same processing environment.

According to the complaint, the FDA’s most recent inspection in November 2013 revealed insanitary conditions, including the presence of generic, non-pathogenic E. coli and L. innocua and the absence of effective monitoring and sanitation controls in accordance with the current Good Manufacturing Practice requirements for food under federal law.  For example, cleaning and sanitizing operations for utensils and equipment were not performed in a manner that protects against contamination of food and food contact surfaces.

FDA previously inspected the facility in January 2013.  According to the complaint, at that time, FDA inspectors discovered a number of Good Manufacturing Practice deficiencies.  For example, FDA inspectors noted that the facility was not constructed in such a manner as to allow floors to be adequately cleaned and to be kept clean and in good repair.  The FDA inspectors also observed that the company failed to store raw materials in a manner that protects against contamination.

The government is represented by Trial Attorney Dan Baeza of the Civil Division’s Consumer Protection Branch and Assistant U.S. Attorney Peter Caplan for the Eastern District of Michigan, with the assistance of Assistant Chief Counsel for Enforcement Christopher Fanelli of the Food and Drug Division, Office of General Counsel, Department of Health and Human Services.

A complaint is merely a set of allegations that, if the case were to proceed to trial, the government would need to prove by a preponderance of the evidence.

SWIMMING POOL OR TOILET? YOU DECIDE

Photo Credit:  Wikimedia.

FROM: CENTERS FOR DISEASE CONTROL AND PREVENTION

CDC study finds fecal contamination in pools
A study of public pools done during last summer’s swim season found that feces are frequently introduced into pool water by swimmers. Through the study, released today by the Centers for Disease Control and Prevention (CDC), researchers found germs in samples of pool filter water collected from public pools.

CDC collected samples of water from pool filters from public pools and tested the samples for genetic material (for example, DNA) of multiple microbes. The study found that 58 percent of the pool filter samples tested were positive for E. coli, bacteria normally found in the human gut and feces. The E. coli is a marker for fecal contamination.

Finding a high percentage of E. coli-positive filters indicates swimmers frequently contaminate pool water when they have a fecal incident in the water or when feces rinse off of their bodies because they do not shower thoroughly before getting into the water. No samples tested positive for E. coli O157:H7, a toxin-producing E. coli strain that causes illness.

Pseudomonas aeruginosa, whichcan cause skin rashes and ear infections, was detected in 59 percent of samples. Finding Pseudomonas aeruginosa in the water indicates natural environmental contamination or contamination introduced by swimmers. Cryptosporidium and Giardia, germs that are spread through feces and cause diarrhea, were found in less than 2 percent of samples. The tests used in the study do not indicate whether the detected germs were alive or able to cause infections. Indoor and outdoor public pools were sampled.

The study did not address water parks, residential pools or other types of recreational water. The study does not allow CDC to make conclusions about all pools in the United States. However, it is unlikely that swimmer-introduced contamination, or swimmer hygiene practices, differ between pools in the study and those in the rest of the country.

"Swimming is an excellent way to get the physical activity needed to stay healthy," said Michele Hlavsa, chief of CDC’s Healthy Swimming Program. "However, pool users should be aware of how to prevent infections while swimming. Remember, chlorine and other disinfectants don’t kill germs instantly. That’s why it’s important for swimmers to protect themselves by not swallowing the water they swim in and to protect others by keeping feces and germs out of the pool by taking a pre-swim shower and not swimming when ill with diarrhea."

This study is presented in recognition of Recreational Water Illness and Injury Prevention Week, May 20–26, 2013. The goal of the prevention week is to raise awareness about healthy swimming, including ways to prevent recreational water illnesses (RWIs). Germs that cause RWIs are spread by swallowing, breathing in the mists or aerosols from, or having contact with contaminated water in swimming pools, water parks, hot tubs, interactive fountains, water play areas, lakes, rivers, or oceans.