College of American Pathologists
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CAP Today




September 2012

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European partners create IT tool to fight antibiotic resistance

A new data-mining, clinical monitoring, and decision-support system provides a new weapon in the war on antibiotic resistance. The European Union-funded DebugIT project developed the system to collect data from multiple hospitals, identify trends showing which types of bacteria are becoming resistant to which types of antibiotics, and determine courses of treatment.

The data are often incomplete or stored in clinical information systems in formats and with structures that make sharing and analyzing them difficult.

The DebugIT project team, which consists of 14 partner organizations from 10 European countries, overcame that challenge by using a semantic interoperability framework to extract heterogeneous clinical data and antibiogram data from different hospital information systems.

The DebugIT system aggregates information from different sources and harmonizes it using a common ontology for microbes and infection control, to create a global but virtual clinical data repository. The data are then analyzed using statistical and data-mining techniques, and can be output via hospital information systems or even through a standalone Web application, and used to determine trends in antimicrobial resistance.

Dirk Colaert, MD, chief medical officer at Belgium’s Agfa HealthCare, coordinator of the project, said: “The system could be used to aggregate and analyze data from many hospitals to determine antimicrobial resistance in a region, country, or worldwide. However, in practice hospitals are reluctant to make their data available in this way. It’s not a privacy issue, but rather the fact that hospitals do not want to disclose information that can show how good or bad they are performing.” In DebugIT, he said, “we showed that this can be done, and we believe it should be done given the huge benefits to patients, society, and health care systems in being able to use antibiotics more smartly.”

Several hospitals involved in the project are carrying out validation trials, among them the University Hospital of Geneva, which plans to permanently incorporate the DebugIT platform into its HIS

Appeals court again upholds gene patents

In a 2-1 decision, the U.S. Court of Appeals for the Federal Circuit again reversed part of a lower court’s ruling in Association for Molecular Pathology, American College of Medical Genetics, et al. v. U.S. Patent and Trademark Office and Myriad Genetics.

The lawsuit, in which the CAP is a plaintiff, challenges gene patents on human DNA, specifically Myriad Genetics’ patent claims on BRCA1 and BRCA2 genes.

The appeals court on Aug. 16 reversed the district court’s decision that Myriad’s composition claims to “isolated” DNA molecules cover patent-ineligible products of nature. But it affirmed the court’s decision that Myriad’s method claims directed to “comparing” or “analyzing” DNA sequences are patent ineligible, saying that “such claims include no transformative steps and cover only patent-ineligible abstract, mental steps.”

This is the second time the Court of Appeals for the Federal Circuit considered this lawsuit. It had ruled in 2011 that the patents on the genes were valid but that the claims on methods to compare gene sequences were not. The U.S. Supreme Court ordered the case to be re-heard after ruling in March in Mayo Collaborative Services v. Prometheus Laboratories Inc. that Prometheus’ patents for its method of testing for metabolites of thiopurine in patients with GI disease were invalid because laws of nature are not patentable. The same three appeals court judges re-heard the case.

“The decision is disappointing, although not altogether surprising,” says Roger D. Klein, MD, JD, chair of the AMP Professional Relations Committee and pathologist in the Department of Molecular Pathology, Cleveland Clinic. “The majority opinion failed to acknowledge the reasoning underlying the Mayo decision. Further, it took an extremely narrow approach to the question of patent eligibility of the BRCA1 and BRCA2 genes, considering only whether there were physical changes to the genes’ organizational arrangements, not whether these changes altered their fundamental properties.” This was analogous, he says, to treating these genes as computer hardware, “when their essence is really that of software.

“In this case, of course,” he adds, “the software code was written by nature, not man.”

Idaho Technology now BioFire, new FilmArray panels in pipeline

Idaho Technology changed its name last month to BioFire Diagnostics and said its clinical trial for its FilmArray Blood Culture Identification panel is underway and it expects to launch the clinical evaluation for its GI panel in the first quarter of 2013.

“Pending regulatory clearance, we expect the BCID panel to be available commercially in the U.S. and Europe in the first half of 2013 and the GI panel to follow early in 2014,” said CEO Kirk Ririe in a statement.

Of the company’s new name, he said, “We have established strong momentum in the diagnostics marketplace and the new branding under BioFire Diagnostics better reflects the markets we serve.”

The BCID panel is designed to identify the organisms that can cause sepsis and to detect the presence of selected antibiotic resistance genes. It’s designed to detect about 90 percent of the pathogens isolated from positive aerobic blood cultures. Preliminary results when testing residual positive blood cultures at three external sites with a beta version of the panel showed “good concordance” between the FilmArray result and the gold standard of culture and biochemical identification, the company said.

The current version of FilmArray BCID tests simultaneously for eight gram-positive and 11 gram-negative bacteria, five yeast pathogens, and four antibiotic resistance genes.

The GI pathogen detection system aims to rapidly identify GI pathogens from minimally processed stool samples. The current development version of the panel simultaneously detects 25 different diarrheagenic pathogens, including bacteria, viruses, and protozoa.

Leica Biosystems to acquire Aperio

A Leica Biosystems affiliate has entered into a definitive agreement to acquire Aperio.

Aperio will be integrated into Leica, and the integrated business will continue to offer both the Aperio and the existing Leica portfolio of digital pathology solutions.

Aperio ePathology Solutions consist of whole-slide scanners, a Network solution that enables remote, real-time viewing and distribution of images, and a Precision solution for quantitative image analysis.

“This acquisition positions us to better address the growing demand for personalized medicine and the increasing challenge of staff shortage in the global pathology market,” Arnd Kaldowski, president of Leica Biosystems, said in a statement. Together, he said, the two companies offer the market an “end-to-end solution.”

Webinars on phlebotomy best practices

The Center for Phlebotomy Education continues its phlebotomy best practices webinar series with five new programs starting in November. They’re developed for those who teach, manage, and perform blood collection procedures.

The new schedule is as follows: Ending hemolysis in the ED and everywhere else, Nov. 15; Assessing phlebotomy competency, Dec. 11; Four pillars of world-class phlebotomy, Jan. 15, 2013; Industry update, Feb. 21, 2013; and Phlebotomy C.S.I. (challenging sticks investigation), March 7, 2013.

All content reflects the standards and guidelines of the Clinical and Laboratory Standards Institute. For more information or to register, visit or call 866-657-9857.