Bug decoding: By sequencing the genomes of numerous samples of the drug-resistant bacterium MRSA (shown here in yellow), scientists have confirmed where and when the superbug emerged. Credit: CDC, Janice
Haney Carr, Jeff Hageman, M.H.S.
Analysis of MRSA starts to reveal its journey around the globe–and within a hospital.
MIT Technology Review, February 2, 2010, by Emily Singer — By sequencing the entire genome of numerous samples of the notorious MRSA (Methicillin-resistant Staphylococcus aureus) bacteria–a drug-resistant strain of staph responsible for thousands of deaths in the United States each year–researchers at the Wellcome Trust Sanger Institute in the United Kingdom have gained clues as to how the superbug travels both around the globe and in local hospitals. Scientists say the approach will shed light on the epidemiology of the troublesome bacteria and help public health programs target their prevention efforts most effectively.
The research, which would have been impossible just two years ago, was enabled by fast and inexpensive sequencing technology from Illumina, a genomics company based in San Diego. “The work demonstrates the value of applying high-resolution sequencing technology to public health problems,” said Caroline Ash, a senior editor at the journal Science, where the research was published, at a press conference on Wednesday. “Potentially the technology could pinpoint the origin of the outbreak and the origin of its spread.”
About 30 percent of people carry Staphylococcus aureus bacteria on their skin, often harmlessly. But for some people, the microbes can cause severe problems, including serious skin infections, sepsis, and death. Antibiotic-resistant strains of the virus emerged in the 1960s, and these now account for more than half of all hospital-acquired infections in the U.S.
In the current study, researchers sequenced 63 MRSA samples, some collected from across the globe during a 20-year period, and some from a single hospital in Thailand over 20 months. While standard analysis methods, which analyze only a small portion of the microbes’ DNA, classified each isolate as being of the same subtype, sequencing the whole genome allowed scientists to identify very small genetic differences between the microbes.
The researchers constructed an evolutionary tree for the microbes and confirmed that MRSA likely first emerged in Europe in the 1960s, coinciding with the growing use of antibiotics to treat staph infections. The tree also showed that the superbugs evolved drug resistance multiple times over the past 40 years. “That demonstrates there is immense selective pressure caused by antibiotic use worldwide,” said Simon Harris, the lead author on the study, at the press conference.
The researchers also analyzed minor genetic differences in MRSA samples collected in a much more localized setting–a single hospital in Thailand–and discovered greater than expected diversity among the microbes. That suggests that patients were infected by new strains coming into the hospital, rather than patient-to-patient transmissions, says Harris. That finding might affect control measures. “If you institute infection control settings in this hospital, it will only have limited success because, in this case, it looks like patients appear to be getting the infection from other sources,” said Sharon Peacock, a clinical microbiologist at the University of Cambridge who also participated in the research, at the press conference.
(The analysis will not affect how individual patients are treated, because all variants of MRSA are treated the same. Tests that classify subtypes of the bacteria are used to track the spread of infection, rather than to make treatment decisions.)
It’s not yet clear how the technology might be incorporated into standard public health efforts to track and control MRSA infections. “I believe this approach will expand our understanding of the evolution of MRSA, but I don’t think it will catch on right now in hospitals,” says Dan Diekema, a physician and epidemiologist at the University of Iowa, who was not involved in the study. “I think most hospitals find our current typing methods to be adequate in helping to guide prevention efforts. It’s not exactly clear to me how having a finer-grained look would impact prevention efforts.”
Peacock aims to address that question with ongoing studies. “We hope to clearly define through prospective studies of this tool what its value is and how to incorporate it into a hospital setting,” she said. The technology would need to undergo some major changes to transform from research tool to standard surveillance measure. “Before being adopted in standard clinical practice, the technology needs to be adapted so that it can be used in any major laboratory,” said Peacock. “We want the readout not in terms of sequencing but in what potential virulence it carries, and what its origins might be.”
Currently, sequencing a MRSA genome takes four to six weeks and costs about $300. “Even though turnaround time has been dramatically reduced from years to weeks, it’s still not a practical timescale for use in clinical settings,” said Stephen Bentley, senior author on the study. “But I expect that with third-generation sequencing technology, the turnaround time could be reduced to hours and the per sample cost might be reduced to the £20 mark [about $30].”
The project is part of a growing trend that capitalizes on increasingly affordable sequencing technologies to track the origins, evolution, and migration of human pathogens. “It’s going to require scientists to do some real innovative thinking to fully explore the potential of this technology,” said Bentley. Researchers at the Sanger Institute have already applied it to a number of other infectious organisms, including those responsible for tuberculosis, pneumonia, and meningitis.
Prepregnancy screening: To determine the risk of passing rare inherited diseases to their offspring, prospective parents spit in a tube (shown here) and then send the sample to Counsyl, a California-based startup. The company screens the sample for genetic mutations linked to more than 100 diseases.
Startup aims for routine preconception genetic testing
MIT Technology Review, February 3, 2010, by Emily Singer — Counsyl, a Stanford startup based in Redwood City, CA, has developed a genetic test for prospective parents that determines their risk for passing more than 100 different genetic diseases on to their child. The test, which costs $349 and is already covered by some major insurers, could rapidly expand preconception screening for rare inherited conditions. For most people, screening recommendations are currently limited to the chronic lung disease cystic fibrosis, with broader testing offered to some ethnic groups.
While the genetic culprits for more than 1,000 rare inherited diseases have been identified, screening for them has been limited, largely due to cost. The comprehensive nature of Counsyl’s test and its reasonable price tag reflect rapid advancements in screening technologies. “When cystic fibrosis testing first started in the early ’90s, it cost on the order of $350,” says Philip Reilly, a clinical geneticist, now with Third Rock Ventures, a Boston-based investment firm. “Now [Counsyl] is offering to test for 100 disorders for the same price, and it will fall lower.” In the late 1990s, Reilly, who is not involved with Counsyl, launched a similar company, which he says failed partly because testing was still too expensive.
Counsyl’s test detects genetic variants linked to rare inherited conditions such as cystic fibrosis, Tay-Sachs disease, and Pompe disease, a metabolic disorder featured in the new film Extraordinary Measures. (Counsyl, which until recently was operating in stealth mode, appears to have pegged its public debut to the film’s release.) While individuals carrying a single copy of the mutation for such diseases are typically healthy, those who inherit two copies, one from each parent, are guaranteed to develop it. Many of these diseases are incurable and have devastating consequences, including early death.
The rate of single-gene disorders in the United States is estimated at about 0.3 to 0.5 percent of live births. According to Counsyl, about 35 to 40 percent of people who have taken its test are carriers for at least one disease in the test. Both prospective parents carry the mutation about 0.6 to 0.8 percent of the time. Those couples would have a 25 percent chance of having a child with the disease, thanks to a 50 percent chance of inheriting the disease variant from each parent.
The genetic variants screened in Counsyl’s test themselves aren’t new–all can be tested for individually or as part of other screens. (Ashkenazi Jews, for example, often undergo screening for a handful of inherited disorders that occur more frequently in that group.) The novelty in Counsyl’s test comes in grouping together such a large number of conditions–the company’s founders say it can detect several hundred variants responsible for more than 100 different genetic diseases.
If parents discover that they both carry risk variants for the same disease, they can choose to undergo in vitro fertilization and have embryos screened for the disease prior to being implanted in the womb. Or the woman can choose to get pregnant the normal way and then they can have the fetus screened during pregnancy.
Testing is likely to lead to an increase in techniques such as in vitro fertilization and preimplantation genetic diagnosis, which together cost about $12,000 to $17,000. But that figure is still drastically lower than the hundreds of thousands to millions of dollars it can cost to take care of a child with a severe genetic disorder. “That’s why we got insurance coverage so rapidly, which is extremely unusual for a new diagnostic test,” says Balaji S. Srinivasan, chief technology officer at Counsyl.
In addition to getting the test through fertility clinics, consumers can order it directly through the Internet, similar to services provided by startups 23andMe, Navigenics, and DecodeMe. While these companies have largely pioneered the concept of direct-to-consumer genetic testing–and garnered extensive media attention doing so–their goal is much different than Counsyl’s. Their screens are designed to detect common genetic variants that have a fairly minor impact on an individual’s risk for a number of common diseases, while Counsyl’s test detects rare genetic variants linked to serious diseases in people carrying two copies of it.
Reilly predicts other companies will soon follow suit. “I think there will be lots of other groups offering similar tests in the future,” he says. “There’s no reason why 23andme couldn’t do this, or Navigenics or Baylor or the Mayo clinic.”
Counsyl uses a technology called a molecular inversion probe array, which can capture small, select pieces of DNA and allow them to be analyzed with high accuracy. Srinivasan says the company will publish details of the method as well as its accuracy in a peer-reviewed journal this week. He says the company also plans to change its screening methods in the near future, using gene sequencing technology, which determines every letter of the selected genes.
The test is not foolproof. It doesn’t detect a number of genetic and environmental factors that can affect a healthy pregnancy. In addition, many of the mutations underlying the conditions encompassed by the test have not yet been discovered, meaning someone may still be a carrier
Boosting blood vessels: Exposing human embryologic stem cells to a small inhibitor molecule dramatically boosts production of endothelial cells (green), which form the inner lining of blood vessels. The bottom image shows a culture of cells exposed to the inhibitor, while the cells in the top image were not. Credit: Daylon James
Scientists find a better way to make more of the cells that make blood vessels.
MIT Technology Review, February 2, 2010, by Jennifer Chu — An efficient new method of making endothelial cells, which give rise to blood vessels, could prove a huge boost for tissue engineering and regenerative medicine. By first finding a way to effectively tag endothelial cells, researchers at Weill Cornell Medical College developed a simple way to increase production of these cells by more than 30-fold. The cells might one day by used to create blood vessels in engineered tissue or administered to patients directly to repair injury after heart attack or stroke, resupplying blood to damaged organs.
“[Eventually], we want to be able to inject slurries of these cells into people who have suffered heart attacks, and allow those tissues to recuperate by renewed blood flow,” says Daylon James, assistant research professor in the department of reproductive medicine at Weill Cornell Medical College, who led the research.
Our bodies house billions of endothelial cells, which line the interior of blood vessels. This vast network is responsible for maintaining vascular health, controlling blood pressure, managing clotting, and giving rise to new blood vessels. While researchers already knew how to turn embryonic stem cells into endothelial cells, the challenge has been a matter of commitment and scale. Once stem cells turn into endothelial cells, it’s difficult to make them stay that way. Getting endothelial cells to expand to numbers great enough to engineer functional artificial blood vessels has been another major roadblock.
While previous methods produced about 0.2 endothelial cells for every embryonic stem cell, James and his colleagues have found a much more efficient way to make committed endothelial cells. The new technique yields seven endothelial cells for every stem cell, according to research published in the advanced online edition of the journal Nature Biotechnology. When these differentiated cells were injected into mice, they formed tiny, capillary-like structures.
To create the new method, the team first developed a way of identifying endothelial cells among cultures of differentiating embryonic stem cells. James recognized a gene called VE-cadherin that only appears in endothelial cells, making it an ideal marker. He then genetically engineered a green fluorescent protein to turn on in embryonic stem cells only when VE-cadherin is expressed, signaling in real time that the stem cell has differentiated into an endothelial cell.
Researchers then looked for molecular triggers that ramp up endothelial differentiation and production. Shahin Rafii, a professor of medicine at Weill Cornell Medical College, and a Howard Hughes Medical Institute investigator, carefully selected various drugs and small molecules, and tested their effects in cultures of embryonic stem cells. Rafii found one candidate in particular that significantly boosted the yield of differentiated, committed endothelial cells.
This molecule, which goes by the technical label SB431542, is known to inhibit TGF-beta, a protein involved in cell differentiation and proliferation. Researchers found they were able to get the highest yield of endothelial cells when they first allowed TGF-beta to act uninterrupted, then introduced the inhibitor molecule to turn off TGF-beta at just the right time. Properly timed exposure to the TGF-beta inhibitor boosted production of endothelial cells 36-fold.
That increase could have real clinical significance, says Joseph Wu, assistant professor of medicine and radiology at Stanford University School of Medicine. “This new protocol is a significant advance, and a very good amplification process, because in order to translate therapy to humans and animals, you have to scale up the numbers,” says Wu, who was not involved in the research. Heart grafts to treat cardiovascular disease, for example, would likely require 20 million to 50 million cells, he says.
The researchers now plan to determine whether the cells can actually restore blood flow to damaged tissue by injecting them into injured animals. The group is also working to grow engineered endothelial cells into functional blood vessels in vitro, on three-dimensional scaffolds that simulate the real conditions in the body. Sina Rabbany, a bioengineering professor at Hofstra University, is designing polymeric scaffolds, and growing endothelial cells on grafts of smooth muscle cells.
“Almost every body part requires a vascular supply, and endothelial cells are the building blocks of that supply,” says Rabbany. “So now that we can make these cells, how can we make them grow in a 3-D setting and make conduits that carry blood, and can provide oxygen and nutrients to other cells? [Because] whether you want to grow a pancreas for diabetes, or help treat Parkinson’s disease, every cell in the human body is next to an endothelial cell.”
The New York Times, by Nicholas Bakalar — Dental cavities are not good news, but when it comes to preventive oral health, they may be among the smaller problems.
The advice is familiar: brush and floss regularly, use fluoride mouthwash, limit snacks and sweet drinks, visit the dentist twice a year. Good suggestions, even if not everyone follows them: by age 12, 50 percent of children have cavities. But there are two much more serious problems, common dental diseases that can lead not only to loss of teeth but also to loss of life: periodontal disease and oral cancer.
Periodontal disease — a chronic bacterial infection of the gums that destroys the bone and tissues that hold the teeth — is the leading cause of tooth loss in adults. Some people are genetically susceptible, and the problem can be aggravated by smoking, taking certain medications, stress and other factors.
Several studies have found that gum disease is associated with an increased risk for heart attack. “It isn’t nailed down yet,” said Dr. Martin J. Davis, professor of clinical dentistry at the College of Dental Medicine at Columbia, “but there seems to be a link between the inflammation of gums and the inflammatory markers of heart disease.”
It may be that oral bacteria enter the bloodstream, attach to fatty plaques in the coronary arteries and cause clots to form. Or maybe inflammation itself increases plaque buildup. A 2007 study showed that periodontal disease increased the risk of heart disease in men by one third and doubled it in women, even after controlling for smoking.
Studies also suggest that gum disease is associated with the risk for stroke, altered glycemic control in people with diabetes and adverse pregnancy conditions like pre-eclampsia (pregnancy-induced high blood pressure), low birth weight and preterm birth. When periodontal disease is treated by reducing inflammation and lowering the quantities of harmful bacteria in the mouth, it can have a major impact on inflammation in the rest of the body.
Oral cancer is the second serious dental problem. It afflicts about 34,000 people a year and kills 8,000. Dr. Michael Kahn, a professor of oral pathology at Tufts University, compares oral cancer with the 11,000 cases of cervical cancer that are detected by the 60 million pap smears administered every year. “A person dies every hour around the clock from oral cancer,” he said, “yet it’s a struggle to get insurance to cover any of the new screening tests. It causes at least twice as many deaths as cervical cancer, but we’ve paid for pap smears — which have reduced cervical cancer by 90 percent.”
Smoking and alcohol abuse are the major causes, but 25 percent of oral cancers appear in people who have never smoked or drunk to excess. The suspected cause of at least some of these cancers is human papillomavirus, or H.P.V., the same sexually transmitted virus that causes most cervical cancers, which can invade the mouth during oral sex. “Some are already hypothesizing that if kids are inoculated against H.P.V.,” Dr. Kahn said, “there will be a turnaround in the oral cancers caused by H.P.V., too.”
For now, prevention, screening and early treatment are crucial to lowering the death rate.
The first sign of oral cancer is often a tiny white or red spot in the mouth, but the disease can be detected before a sore appears. In the last two or three years, manufacturers have produced noninvasive devices for detecting abnormal tissue that may be invisible to the naked eye, and some dentists are beginning to use them, even though their effectiveness remains controversial.
“The literature says they work,” Dr. Kahn said. “Some would like more or stronger evidence, but for others, they’re convinced. In dentistry, you don’t have much time to look. The theory is that if you use one of these devices, it gives you some additional help.” If a dentist finds a suspicious lesion, Dr. Kahn recommends referral to an oral pathologist as the next step.
There is more to good oral health than conscientious brushing and flossing, even though they remain important. “You have to take care of your mouth like any other part of the body,” Dr. Davis said, “because it’s linked to the rest of the body.”
Nano pyramid: Gadolinium ions (green) are chemically linked to the surface of a nano diamond to form an MRI contrast
A nano diamond agent is 15 times more sensitive.
MIT Technology Review, February 3, 2010, by Corinna Wu — Magnetic resonance imaging (MRI) has become an indispensable medical diagnostic tool because of its ability to produce detailed, 3D pictures of tissue in the body. Radiologists often inject patients with contrast agents to make certain tissues, such as tumors, stand out more on the final image. Now, researchers have synthesized an MRI contrast agent that is 15 times more sensitive than the compounds currently used. This could allow less contrast agent to be used, thus reducing the potential for harmful side effects.
The researchers created the new compound by chemically linking gadolinium ions to nano diamonds–tiny clusters of carbon atoms just a few nanometers in diameter. Gadolinium, a rare-earth metal, is used in MRI contrast agents because of its strong paramagnetic properties (magnetism in response to an applied magnetic field). But alone, gadolinium is toxic, so it has to be bonded to other, biocompatible molecules to be used clinically. Many groups have been trying to improve the properties of gadolinium-based contrast agents by attaching the metal to a variety of materials, ranging from large organic molecules to nanoparticles.
“We’ve done this with many classes of nanoparticles and have never seen this extraordinary increase in sensitivity,” says Thomas J. Meade, the Eileen M. Foell professor of chemistry and director of the Center for Advanced Molecular Imaging at Northwestern University. He and his colleagues published their findings online in Nano Letters last month.
Meade collaborated with Dean Ho, assistant professor of biomedical and mechanical engineering at Northwestern, and his group, which has been studying nano diamonds as vehicles for drug delivery. Unlike some carbon nanomaterials, Ho says nanodiamonds are well-tolerated by cells and do not change gene expression in adverse ways. The researchers coupled the nano diamonds to gadolinium and tested the properties of the resulting complex to assess how good of an MRI contrast agent it might be.
MRI works by surrounding a patient with a powerful magnetic field, which aligns the nuclei of hydrogen atoms in the body. Radio wave pulses systematically probe small sections of tissues, knocking those atoms out of alignment. When they relax back into their previous state, the atoms emit a radio frequency signal that can be detected and translated into an image.
Because of its strong paramagnetic properties, gadolinium alters the relaxation of hydrogen atoms when it’s nearby. Contrast agents containing gadolinium can be designed to collect preferentially in tumors, thus enhancing the contrast between the tumor and the surrounding tissue. The contrast agent’s ability to alter the relaxation of hydrogen atoms is expressed as “relaxivity”, which accounts for the relaxation time and the concentration of gadolinium in the tissues.
The high relaxivity of the gadolinium-nano diamond compound can be partly attributed to its ability to attract water, which helps boost the MRI signal. “If you look at the shape of a nano diamond, it’s like a soccer ball but more angular around the faces,” Ho says. “It’s not totally round.” The different faces have alternating positive and negative charges, which helps to orient water molecules in such a way that they create a tight shell of water around the nanodiamond.
The researchers tested the gadolinium-nano diamond on different types of cells in the lab and did not find evidence of toxicity. The next step, Ho says, is to test the compound’s safety and effectiveness as a contrast agent in animals. “We’re excited to see what kind of increased performance we can get,” Ho says.
“I think it’s a very interesting system,” says Kenneth N. Raymond, professor of chemistry at the University of California at Berkeley. “They’ve obviously got a one order of magnitude increase in relaxivity that’s quite significant.” Many researchers have tried to attach gadolinium ions to high molecular weight compounds, like proteins and dendrimers, he says. “The little nano diamond, as far as I know, is quite novel, and, I think, a very clever thing to do.”
Currently, radiologists need to inject what amounts to several grams of gadolinium into a patient to get good contrast on an MRI. By increasing the sensitivity of the contrast agent ten-fold, “you could use one-tenth as much gadolinium,” Raymond says. “There’s a lot of concern in the clinic for certain classes of patients about gadolinium toxicity. Toxicity is very closely connected to dose.”
Harvard Medical School, February 3, 2010 — Change is an important part of living with heart disease or trying to prevent it. A jump in blood pressure or cholesterol earns you a lecture on healthy lifestyle changes. Heart attack and stroke survivors are often told to alter a lifetime of habits.
Some people manage to overhaul their exercise pattern, diet, and unhealthy habits with ease. The rest of us try to make changes, but don’t always succeed. Instead of undertaking a huge makeover, you might be able to improve your heart’s health with a series of small changes. Once you get going, you may find that change isn’t so hard. This approach may take longer, but it could also motivate you to make some big changes.
Here are 10 small steps to get you on the road to better health in 2010.
1. Take a 10-minute walk. If you don’t exercise at all, a brief walk is a great way to start. If you do, it’s a good way to add more exercise to your day.
2. Give yourself a lift. Lifting a hardcover book or a two-pound weight a few times a day can help tone your arm muscles. When that becomes a breeze, move on to heavier items or join a gym.
3. Eat one extra fruit or vegetable a day. Fruits and vegetables are inexpensive, taste good, and are good for everything from your brain to your bowels.
4. Make breakfast count. Start the day with some fruit and a serving of whole grains, like oatmeal, bran flakes, or whole-wheat toast.
5. Stop drinking your calories. Cutting out just one sugar-sweetened soda or calorie-laden latte can easily save you 100 or more calories a day. Over a year, that can translate into a 10-pound weight loss.
6. Have a handful of nuts. Walnuts, almonds, peanuts, and other nuts are good for your heart. Try grabbing some instead of chips or cookies when you need a snack, adding them to salads for a healthful and tasty crunch, or using them in place of meat in pasta and other dishes.
7. Sample the fruits of the sea. Eat fish or other types of seafood instead of red meat once a week. It’s good for the heart, the brain, and the waistline.
8. Breathe deeply. Try breathing slowly and deeply for a few minutes a day. It can help you relax. Slow, deep breathing may also help lower blood pressure.
9. Wash your hands often. Scrubbing up with soap and water often during the day is a great way to protect your heart and health. The flu, pneumonia, and other infections can be very hard on the heart.
10. Count your blessings. Taking a moment each day to acknowledge the blessings in your life is one way to start tapping into other positive emotions. These have been linked with better health, longer life, and greater well-being, just as their opposites — chronic anger, worry, and hostility — contribute to high blood pressure and heart disease.
Read more from Harvard Medical School………..
Switching from heels to flats
Q. I know high heels are bad for the feet, but when I switched to flats, my feet started to hurt. Why?
A. Wearing heels for long periods can result in a shortening and tightening of the Achilles’ tendon. When you walk in a relatively flat shoe, your foot flexes up (dorsiflexes) when your heel hits the ground and then flexes down (plantarflexes) as you toe off. If the Achilles’ tendon is short and tight because of high heels, the foot loses its ability to flex up and down, so switching to a flat can cause heel and calf pain. Flats can also aggravate conditions like plantar fasciitis if they lack good arch and heel support.
If you’re moving away from high heels to flats, do so gradually, wearing lower heels at first. That will give your Achilles’ tendon time to relax and stretch out. You might also try doing some of the standard exercises for stretching the Achilles’ tendon.
The basic maneuver involves keeping your heel on the ground and your leg straight as you lean forward.
— James P. Ioli, D.P.M.
Brigham and Women’s Hospital