Author: Tom Ulrich

Mapping antibiotic resistance near you: ResistanceOpen

antibiotic resistance mapping ResistanceOpen

At the moment, it would appear the bacteria are winning. Antibiotic resistance is on the rise globally (in part because much of the public may not really understand how antibiotics work), threatening doctors’ ability to treat bacterial infections and potentially making surgery, chemotherapy and other medical procedures whose safety depends on antibiotic prophylaxis more risky.

Mapping antibiotic resistance — which bacteria are resistant to which drugs, and where — can help clinicians and public health officials decide how best to focus their control efforts. The challenge to date has been compiling resistance data in geographically useful ways.

“The data about antibiotic resistance are fragmented across laboratories and hospitals globally,” says Derek MacFadden, MD, a doctoral student at the Harvard T.H. Chan School of Public Health who is working with the HealthMap team in Boston Children’s Computational Health Informatics Program. “Most of the data that are available are very high level, so you can’t get an understanding of regional-level antibiotic resistance.”

This is where ResistanceOpen could come in handy. This new tool, launched by HealthMap team this week during the World Health Organization’s World Antibiotic Awareness Week, provides a window into regional and local antibiotic resistance patterns across the globe.

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Siddhartha Mukherjee: Have we lost the fire to tackle childhood cancers?

Siddhartha Mukherjee, MD, PhD, takes his audience on a tour of 60 years’ worth of successes in cancer. What does the future hold?

We’ve all heard the George Santayana quote, “Those who cannot remember the past are condemned to repeat it.” But there’s another way of thinking about the lessons that the past holds for the future: Those who do remember the past can recapture and harness earlier feelings of energy, urgency and possibility to overcome new problems, now and in the future.

That line of thinking threaded its way throughout the keynote address oncologist Siddhartha Mukherjee, MD, PhD, author of The Emperor of All Maladies, delivered today at Boston Children’s Hospital’s Global Pediatric Innovation Summit + Awards 2015.

In taking the audience on a tour through the last 60 years of advances in cancer biology, genomics and treatment, Mukherjee highlighted the central role pediatrics played as the starting point for the cancer successes we see today. How, he asked, did children come to play such a central role? What can we learn from the successes in the 1950s and ’60s, when pediatric cancer started to evolve from a death sentence to a treatable, even curable disease?

And how, he asked, can we recapture and harness the energy and urgency of that time today?

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Improved cell cloning technique makes the jump from mice to humans

cells somatic cell nuclear transfer cloning

Roughly a year ago we told you about Yi Zhang, PhD — a stem cell biologist in Boston Children’s Hospital’s Program in Cellular and Molecular Medicine — and his efforts to make a cloning technique called somatic cell nuclear transfer (SCNT) more efficient.

With SCNT, researchers take an egg cell and replace its nucleus with that of an adult cell (such as a skin cell) from another individual. The donated nucleus basically reboots an embryonic state, creating a clone of the original cell.

It’s a hot topic in both agriculture and regenerative medicine. SCNT-generated cells can be used to clone an animal (remember Dolly the sheep?) or produce embryonic stem (ES) cell lines for research. But it’s an inefficient process, producing very few animal clones or ES lines for the effort and material it takes.

Zhang’s team reported last year that they could boost SCNT’s efficiency significantly by removing an epigenetic roadblock that kept embryonic genes in the donated nucleus from activating in cloned cells. Now, in a new paper in Cell Stem Cell, Zhang and his collaborators report that they’ve extended their work to improve the efficiency of SCNT in human cells.

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Gene sifting for gene snipping: GWAS as a source of gene editing targets

Magnifying glass people GWAS gene editing
(Digital Storm/Shutterstock)

When genome-wide association studies (GWAS) first started appearing 10 years ago, they were heralded as the answer to connecting human genetic variation to human disease. These kinds of studies—which sift population-level genetic data—have revealed thousands of genetic variations associated with diseases, from age-related macular degeneration to obesity to diabetes.

However, thus far GWAS have largely come up short when it comes to finding new therapies. Few significant drug targets have come to light based on GWAS data (though some studies suggest that these studies could help drug makers find new uses for existing molecules).

Part of the problem may be that, until now, the right tools haven’t been available to exploit GWAS data. But a few recent studies—including two out of Dana-Farber/Boston Children’s Cancer and Blood Disorders Center—have used GWAS data to identify therapeutically promising targets, and then manipulated those targets using the growing arsenal of gene editing methods.

Does this mean that GWAS’ day has finally come?

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Are tweets a good measure of patient experience and health care quality?

Twitter speech bubblesWhen it comes to gauging quality, we often turn to Twitter, Yelp, Angie’s List and other networks for instant feedback on pretty much any company, contractor or store we do business with.

In contrast, hospitals often rely on tools like the Hospital Consumer Assessment of Healthcare Providers and System (HCAHPS) survey, which gives voice to patients and their concerns about the care they receive. But a new study published in the journal BMJ Quality & Safety suggests social media have something to add to that.

Notes_title_for_overlay“The main problems with measuring patient experience by survey are the small numbers of people who respond to surveys and the lag time,” says Jared Hawkins, MMSc, PhD, of Boston Children’s Hospital’s Computational Health Informatics Program (CHIP). “It can take up to two years before survey data are released to the public. Given that social media data are close to real time, we wanted to see if we could capture this discussion and if the content is useful.”

Hawkins, with Boston Children’s chief innovation officer, John Brownstein, PhD, and their colleagues collected more than 400,000 public tweets directed at the Twitter handles of nearly 2,400 U.S. hospitals between 2012 and 2013. Using machine learning, natural language processing and manual curation, they tagged 34,735 patient experience tweets directed at 1,726 hospital-owned Twitter accounts.

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My work, my life, my innovations: Katherine Janeway, MD

“It’s all about the patients,” says Katherine Janeway, MD, when asked about the motivations behind her efforts to bring precision medicine to pediatric oncology. But it’s more than that; the drive to combine science and care is in her blood. A solid tumor specialist and cancer genomics researcher at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Janeway is the sixth generation of her family to choose a scientific or medical path—not just as a career, but also as a form of service.

Janeway will bring her patient-centered perspective to the Cancer Genomics + Care panel at Boston Children’s Global Pediatric Innovation Summit + Awards 2015. Read more about her life, work and innovations—and inspirations—by hovering over the objects that surround her everyday.

Learn more about the Boston Children’s summit and register to attend.

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The MERS death rate in Saudi Arabia is double that in South Korea. Why?

map South Korea Saudi Arabia MERS
(Wikimedia Commons)

The Middle East respiratory syndrome (MERS) virus outbreak in South Korea is essentially over. (Not so in Saudi Arabia, where the virus first emerged, though—authorities there have reported a major uptick in new MERS cases in recent days.) And while the country gets back on its feet, some interesting data are starting to come out, especially about the outbreak’s case fatality rate (CFR; the percent of patients infected with the virus who died from it).

John Brownstein, PhD, and Maimuna Majumder, MPH, from Boston Children’s HealthMap team just reported in the journal Emerging Infectious Diseases that MERS’ CFR in South Korea (22 percent) is fully half that seen in Saudi Arabia (44 percent).

This infographic about Brownstein and Majumder’s MERS paper gives a snapshot of the data the analyzed, and what they think those data mean:

MERS virus South Korea Saudi Arabia infographic

Read Brownstein and Majumder’s analysis and check out Boston Children’s Hospital’s news release about the MERS paper.

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Progress in the treatment of childhood leukemia

Although treatments for childhood cancer patients are improving, cancer remains the leading cause of death by disease in children. Doctors and researchers are also focused on decreasing the toxicity of these treatments, which can have side effects years after a child finishes treatment.

“The war against childhood cancer is hardly over,” says Kimberly Stegmaier, MD, a pediatric oncologist at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center. “We need to do better.”

Stegmaier, who focuses her research on identifying new drug targets and new drugs for childhood leukemiaEwing sarcoma, and neuroblastoma, recently discussed advances in childhood cancer treatment in a Science, Innovation, and Discovery Talk (SID Talk) at Dana-Farber. During the TED Talk-style presentation, Stegmaier explained some of her research in the treatment of sub-microscopic acute lymphoblastic leukemia (ALL) as well as genetic targets in childhood cancers.

“What you can do in an environment where you have chemists, biologists, and clinicians adjacent and working collaboratively is very powerful,” says Stegmaier. “That’s why I’m here today—we need to cure 100 percent of kids, and we can’t do this alone.”

This story originally ran on Dana-Farber Cancer Institute’s Insight blog.

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So far, so good for gene therapy patient Emir Seyrek

Emir Seyrek gene therapy Wiskott-Aldrich ThrivingRemember Emir Seyrek, the Turkish boy who last year was the first patient in gene therapy trial for a genetic immunodeficiency called Wiskott-Aldrich Syndrome? Emir traveled back to the U.S. earlier this month for an annual follow-up visit with his care team at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center. The news was quite good.

“Emir is the star of the trial,” Sung-Yun Pai, MD—a Dana-Farber/Boston Children’s gene therapy and immunodeficiency transplant specialist and lead (along with David Williams, MD, and Luigi Notarangelo, MD) of the U.S. arm of the trial—tells our sister blog, Thriving. “He has the highest platelet count of all of the children who have gone through gene therapy with this vector so far. His immune function is excellent, and we have no worries whatsoever from a bleeding standpoint. He’s perfectly safe to play like a normal child.”

Learn more about Emir’s progress on Thriving.


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My work, my life: John Brownstein, PhD

Boston Children’s Hospital’s new chief innovation officer, John Brownstein, PhD, is an epidemiologist by training and a founding father of the growing field of digital epidemiology—the use of digital (especially social and mobile) data from a variety of sources to detect and track disease and promote health. As co-founder of HealthMap and director of the Computational Epidemiology Group in the hospital’s Computational Health Informatics Program, he infuses his work into many aspects of his life—along with a healthy helping of hot sauce.

Hover over the icons in the photo below to learn about the things in Brownstein’s phone, office and life that keep him going.

Brownstein will be one of four panelists discussing Patient Engagement in a Big Data World at Boston Children’s Global Pediatric Innovation Summit + Awards 2015. Learn more about the summit and register to attend.

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