An official website of the United States government.
The overall goal of the Food Safety Research Consortium (FSRC) is to conduct and coordinate food safety research and to facilitate the development and use of research knowledge and new approaches and tools to help the food industry in their efforts to improve food safety. The specific goal of this new project is to expand the PathogenTracker database to include information on other foodborne pathogens (e.g., Salmonella, E. coli O157:H7, Campylobacter). The FSRC will thus serve as a central source of uniform information on foodborne pathogen DNA subtypes and associated characteristics. In addition, we propose to further expand the PathogenTracker database to allow users to perform statistical analyses and queries against this database, allowing them to quickly extract relevant subtype-associated information from our database.<P> The specific objectives of this project include: <OL> <LI> Expand the PathogenTracker database (i) to allow users to perform statistical analyses and queries against this database, enabling them to quickly extract relevant subtype-associated information from our database; (ii) to include ability to store and search data using new subtyping methods; and (iii) to allow more rapid data access by an increased number of users. <LI> Develop DNA sequencing-based subtyping methods for Salmonella serotypes and characterize Salmonella isolates from foods, animals, and humans by various DNA subtyping methods for inclusion in the PathogenTracker database. <LI> Use DNA sequencing-based subtyping methods and sequence data for L. monocytogenes and Salmonella to develop and evaluate new phylogenetic and statistical approaches for defining subtypes and clades and for determining the associations between bacterial subtypes and their ability to cause human foodborne disease. <LI> Initiate inclusion of Campylobacter and E. coli O157:H7 subtyping information in the PathogenTracker database. <LI> Develop and evaluate new automated and high throughput genomics-based subtyping methods for L. monocytogenes.
NON-TECHNICAL SUMMARY: Molecular subtyping methods for foodborne pathogens provide a unique opportunity to track and define specific bacterial human health hazards. Publicly accessible databases are required to allow the food industry to take advantage of these new techniques. The purpose of this project is to characterize a collection of bacterial foodborne isolates and to further develop an Internet database to allow broad access to DNA subtyping data for foodborne pathogens.
<P>
APPROACH: The FSRC program will be administered by faculty and staff in the Department of Food Science at Cornell. They will administer the funds and conduct research as specified and involve faculty at other universities and organizations as formal or informal collaborators. The program will interface with and draw on the existing "Cornell Food and Water SafetyProgram"(see http://www.foodscience.cornell.edu/fws/fws.htm) ,which includes more than 30 faculty members at different colleges with research, teaching, and extension efforts and interests in food and water safety. We will use the following specific approaches to accomplish the objectives described above: 1. Redesign the PathogenTracker database schema so that it can accommodate new features and boost database performance. Implement use of the new Microsoft ASP.NET system as an Internet interface. Develop interactive statistical modules that will allow users to correlate DNA fingerprint patterns and pathogenic phenotypes. 2. Use an animal Salmonella strain collection to initially develop DNA-sequencing-based subtyping methods for this organism and compare their discriminatory ability to other molecular subtyping methods such as ribotyping. 3. Use DNA sequencing data for human, animal, and food isolates of L. monocytogenes and Salmonella to define specific clusters or clades using various evolutionary and clustering methods and to evaluate their correlation with specific host ranges. 4. Expand and refine the PathogenTracker database to allow inclusion of relevant subtyping information on other foodborne pathogens such as Campylobacter. 5. Use quantitative RT-PCR methods for large scale gene expression analyses to define phenotypic differences between bacterial subtypes.
<P>
PROGRESS: 2002/07 TO 2005/06 <BR>
To track and control sources of foodborne pathogens, agricultural and food industries have a critical need for access to advanced molecular subtyping tools and data. To address this need we have developed a publicly accessibly WWW-based database (PathogenTracker; www.pathogentracker.net). In this project we have made various improvements to the userfriendliness of this database (e.g., we have included the ability of to develop and save customized search functions). We have also developed and implemented a number of advanced analysis tools, including a data analysis page, which can be used to analyze data trends and create data summary tables based on the data stored in PathogenTracker. While the PathogenTracker database initially focused on providing an extensive L. monocytogenes database and strain collection, we have also expanded the database and strain collection coverage to other foodborne pathogens with a focus on Salmonella, more than 300 Salmonella isolates are now included in this database. We have also developed molecular subtyping methods (specifically multilocus sequence typing [MLST] methods) for Salmonella. While serotyping and phage typing have been used widely to characterize Salmonella, sensitive subtyping methods that allow for evolutionary analyses (such as MLST) are essential for examining Salmonella transmission, ecology, and evolution. The MLST scheme developed as part of this project has been reported in a peer-reviewed publication (Sukhnanand et al. 2005. J. Clin. Microbiol. 43:3688-3698) and is used to continue to characterize Salmonella isolates representing a large number of serotypes. MLST types not only correlate well with serotypes, but also allow within serotype differentiation for most serotypes. Phylogenetic analyses showed that serotypes Kentucky and Newport could each be separated into two distinct evolutionary lineages, supporting that Salmonella serotypes represent both monophyletic and polyphyletic lineages. We have also further enhanced the functionality of our PathogenTracker database, e.g., by adding improved capabilities for adding and storing antibiotic resistance data, which is particularly relevant as we have added a number of multidrug-resistant Salmonella to our database. We have also developed a novel approach to use DNA sequence data to define phylogenetic clusters that overrepresent a given isolate source (e.g., human isolates); in initial studies this method has allowed to define specific L. monocytogenes clusters that are associated with human disease; this approach will allow further analyses of Salmonella MLST data to define Salmonella phylogenetic clusters that differ in their association with different ecological niches. Development of quantitative RT-PCR methods to characterize transcription of various L. monocytogenes genes have also been developed (see Sue et al. 2004. Microbiology 150: 3843-3855); these methods will facilitate more in-depth characterization of L. monocytogenes strains that differ in phenotypic characteristics that may affect their transmission to humans.
<BR><BR>
IMPACT: 2002/07 TO 2005/06<BR>
The development of an internet-based database will allow rapid exchange of molecular subtype data for bacteria causing foodborne diseases. The extended pathogen coverage and teh improved datbase tools developed through this project will provide a unique resource to help the food industry and public health officials to track sources of food contamination and to detect disease outbreaks. Our efforts on the development of Salmonella subtyping systems and data repositories will particularly enhance our ability to track the spread of new Salmonella subtypes, including multiple drug resistant subtypes. The Salmonella DNA sequence data generated (and deposited in the PathogenTracker database) will also be critical for the future development of DNA sequencing-based methods to replace traditional Salmonella serotyping strategies.