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Striving for a seamless workload
July 2013
by Ilene Schneider  |  Email the author


GAITHERSBURG, Md.—Fast, efficient identification of organisms in food-borne pathogen outbreaks and hospital-acquired infections using the latest technology for epidemiological surveillance can literally make the difference between life and death. A combination of analytical and data management tools is aiming at an integrated solution to enable researchers to strain type, identify responsible pathogens in a timely manner, limit disease outbreaks and appropriately treat patients all over the world.  
OpGen, a provider of genomic and DNA analysis systems and services, is collaborating with Applied Maths, a market leader in bioinformatics and analytical solutions for public health and research laboratories, to offer bioinformatics analysis software for microbial genomics and molecular strain typing. Under the terms of the agreement, Applied Maths has incorporated OpGen's Whole Genome Mapping Technology module into the Applied Maths BioNumerics 7 software suite, providing customers with seamless access to a new set of analytical tools for molecular typing and comparative genomics of microbial pathogens.  
According to Michael Farmer, director of marketing at OpGen, the collaboration represents a major launch into clinical and epidemiological testing of MRSA, the major cause of hospital-acquired infections, and foodborne pathogens that threaten public health, such as salmonella, listeria and E. coli, to confirm outbreaks and see whether strains are alike or different. As he says, "Microrganisms change and evolve in the face of antibiotics and other preventive measures. Whole Genome Mapping Technology quickly analyzes strains with highest level of discriminatory power and readily identifies changes in antibiotic resistant and virulence genes."  
David Hoekzema, senior director of business development at OpGen, adds, "Applied Maths software is tied closely to interpreting the data. It's a cornerstone of the bioanalytical framework. Combining the technologies, we can get maximum speed and efficacy in confirming outbreaks of disease."  
The objective "is to be able to provide any interested organization—hospitals, research labs, governments involved in food security or in clinical epidemiology—a combination of tools (hardware and software) that integrate seamlessly with existing epidemiological and typing databases and background information or enable the creation of a new environment for storing and analyzing this type of data," explains Bruno Pot, director of business development at Applied Maths.  
Applied Maths and OpGen got acquainted with each other through a Dutch research project dedicated to the study of the origins and distribution channels of LA-MRSA from the farm to the hospital, Pot says. The National Institute for Public Health and the Environment (RIVM) in the Netherlands provided the collection of the MRSA strains, OpGen (through the Dutch department Piext) provided the hardware for the analysis and Applied Maths developed software to integrate the Whole Genome Maps in an existing database for microbiological typing information. The researchers could then perform the necessary statistical analysis as well as the validation and comparison of the Whole Genome Mapping technology with the traditional methodologies used for MRSA. This research just recently led to a scientific paper in the journal PLOS ONE.  
The initial contacts quickly led to new collaborations, including a larger EU-funded research project, PathoNGenTrace, which will use whole-genome sequencing information in clinical microbiology and disease surveillance to provide clinically relevant parameters to doctors, directly extracted from the NGS sequence. The EU research project PathoNGenTrace, which was launched in January 2012, will run for 54 months and receive nearly $7.8 million in funding from the European Union's 7th Framework Programme. The project participants want to develop NGS combined with Whole Genome Mapping as next-generation DNA analysis tools into a highly efficient technology that can be used for the typing and diagnostics of pathogens which pose a serious medical threat and an important challenge when it comes to their treatment.   
Applied Maths has 20 years of experience in storage and analysis of typing information and delivers the driving software for large worldwide networks such as PulseNet International, according to Pot. New technologies such as the Whole Genome Mapping make these activities faster than other technologies like pulsed-field gel electrophoresis (PFGE), but also raise considerable challenges on data analysis. The BioNumerics application provides the software environment for typing and identification.   
"The collaboration with OpGen, therefore, allows us to keep up in a timely manner with the new technological developments in the world of surveillance and epidemiology," Pot says.  
Both products are in validation testing now in state laboratories and the Centers for Disease Control and Prevention. During the summer OpGen is planning to open a CLIA-certified laboratory to provide diagnostic tests and epidemiology analysis involving MRSA, Clostridium difficile and other healthcare-associated infections, Farmer says.  
Code: E071316



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