Striving for a seamless workload

OpGen and Applied Maths team up to do efficient strain typing for public health

Ilene Schneider
GAITHERSBURG, Md.—Fast, efficient identification oforganisms in food-borne pathogen outbreaks and hospital-acquired infectionsusing the latest technology for epidemiological surveillance can literally makethe difference between life and death. A combination of analytical and data managementtools is aiming at an integrated solution to enable researchers to strain type,identify responsible pathogens in a timely manner, limit disease outbreaks andappropriately treat patients all over the world.
OpGen, a provider of genomic and DNA analysis systems andservices, is collaborating with Applied Maths, a market leader inbioinformatics and analytical solutions for public health and researchlaboratories, to offer bioinformatics analysis software for microbial genomicsand molecular strain typing. Under the terms of the agreement, Applied Mathshas incorporated OpGen's Whole Genome Mapping Technology module into theApplied Maths BioNumerics 7 software suite, providing customers with seamlessaccess to a new set of analytical tools for molecular typing and comparativegenomics of microbial pathogens.
According to Michael Farmer, director of marketing at OpGen,the collaboration represents a major launch into clinical and epidemiologicaltesting of MRSA, the major cause of hospital-acquired infections, and foodbornepathogens that threaten public health, such as salmonella, listeria and E. coli, to confirm outbreaks and seewhether strains are alike or different. As he says, "Microrganisms change andevolve in the face of antibiotics and other preventive measures. Whole GenomeMapping Technology quickly analyzes strains with highest level ofdiscriminatory power and readily identifies changes in antibiotic resistant andvirulence genes."
David Hoekzema, senior director of business development atOpGen, 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 interestedorganization—hospitals, research labs, governments involved in food security orin clinical epidemiology—a combination of tools (hardware and software) thatintegrate seamlessly with existing epidemiological and typing databases andbackground information or enable the creation of a new environment for storingand analyzing this type of data," explains Bruno Pot, director of businessdevelopment at Applied Maths.
Applied Maths and OpGen got acquainted with each other througha Dutch research project dedicated to the study of the origins and distributionchannels of LA-MRSA from the farm to the hospital, Pot says. The NationalInstitute for Public Health and the Environment (RIVM) in the Netherlandsprovided the collection of the MRSA strains, OpGen (through the Dutchdepartment Piext) provided the hardware for the analysis and Applied Mathsdeveloped software to integrate the Whole Genome Maps in an existing databasefor microbiological typing information. The researchers could then perform thenecessary statistical analysis as well as the validation and comparison of theWhole Genome Mapping technology with the traditional methodologies used forMRSA. 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 usewhole-genome sequencing information in clinical microbiology and diseasesurveillance to provide clinically relevant parameters to doctors, directlyextracted from the NGS sequence. The EU research project PathoNGenTrace, whichwas launched in January 2012, will run for 54 months and receive nearly $7.8million in funding from the European Union's 7th Framework Programme. Theproject participants want to develop NGS combined with Whole Genome Mapping asnext-generation DNA analysis tools into a highly efficient technology that canbe used for the typing and diagnostics of pathogens which pose a seriousmedical threat and an important challenge when it comes to theirtreatment. 
Applied Maths has 20 years of experience in storage andanalysis of typing information and delivers the driving software for largeworldwide networks such as PulseNet International, according to Pot. Newtechnologies such as the Whole Genome Mapping make these activities faster thanother technologies like pulsed-field gel electrophoresis (PFGE), but also raiseconsiderable challenges on data analysis. The BioNumerics application providesthe software environment for typing and identification. 
"The collaboration with OpGen, therefore, allows us to keepup in a timely manner with the new technological developments in the world ofsurveillance and epidemiology," Pot says.
Both products are in validation testing now in statelaboratories and the Centers for Disease Control and Prevention. During the summer OpGen isplanning to open a CLIA-certified laboratory to provide diagnostic tests andepidemiology analysis involving MRSA, Clostridiumdifficile and other healthcare-associated infections, Farmer says.

Ilene Schneider

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