**-  North Atlantic  
-  Eastern Regional Rsch. Ctr. 
-  Microbial Food Safety Research Unit 
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**Location: Microbial Food Safety Research Unit**
**2006 Annual Report**
**1.What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)?  How serious is the problem?  Why does it matter?**													Escherichia coli, Salmonella spp., Campylobacter spp., Clostridium perfringens and other pathogens can become resistant to food-preservation techniques and antibiotics.  Since pathogen survival processes are not well understood, an elucidation of the physiological and genetic factors that induce increased tolerance to stressful environments is necessary.  Moreover, bacteria modulate a number of cellular functions, including sporulation, biofilm formation, toxin production, competence, and virulence through cell-to-cell signaling processes known as quorum sensing.  Little is known, however, on the role of quorum sensing in the growth and survival, toxin production, and virulence expression of bacterial pathogens in food environments.  Control strategies that modulate production or that inactivate signaling molecules produced through bacterial quorum sensing systems may offer a means to control the growth of undesirable bacteria in food.  Finally, improved methods for accurate identification of food-borne pathogens are needed.  Novel approaches and tools to type and characterize emerging pathogens, including new serogroups of E. coli associated with diarrheal illness, non-jejuni/coli species of Campylobacter, and antibiotic resistant organisms are also essential for identification and control of new threats, including agents that may be employed for bioterrorism.  
The primary goal of this project is to understand the mechanisms of bacterial stress responses and cell-to-cell signaling processes that play a role in bacterial growth, survival, virulence, and biofilm formation in food and in the environment.  The specific objectives of the project are the following:1)	Investigate the mechanisms for pathogen adaptation in foods to determine what 	conditions affect survival, resistance, and pathogenicity; 2)	Investigate bacterial cell-to-cell signaling mechanisms (quorum sensing) and their role in 	growth, survival, biofilm formation, and pathogenicity in foods; 3)	Develop/utilize sensitive/specific genetic-based methods for identification, typing, and 	characterization of food-borne pathogens and food safety threats.
This project responds to the goals of National Program 108, Food Safety.  Specifically it addresses:  (1) Problem statement 1.2.1, “Detection and Validation”, to develop diagnostic tools that allow the highest detection capability, innovative approaches for sample collection and processing, rapid systems for target amplification to maximize detection potential, multiple platform systems that will be combined with multiple target assays, and systems that function in real or near real-time or have the potential to be automated for high throughput; (2) Problem statement 1.2.3, “Production and Processing Ecology”, research aimed at utilizing and validating new, improved, and innovative methods to detect, differentiate, and quantify pathogens in foods and within processing environments. Develop methods for recovery of injured, stressed, and viable but non-culturable microorganisms;  (3) Problem statement 1.2.5, “Omics”, research aimed at sequencing and annotating of genomes, construction of microarrays, gene expression analyses, identification of genes that contribute to pathogenicity and viability, and construction of databases of critically important bacterial food-borne pathogens; (4) Problem statement 1.2.8, “Pathogenicity”, to determine whether quorum sensing occurs in foods or on surfaces (biofilm formation), and if so, whether it is a factor involved in regulating pathogen virulence, to determine through analysis of gene/protein expression profiles the responses to intrinsic and extrinsic sensors imposed during production, processing, and storage, and to develop improved detection and identification methods that enable differentiation of virulent from non-virulent strains. Identify conditions in which pathogen growth is restricted. Determine if intervention strategies induce adaptive responses, for example, increased resistance to antimicrobials and/or increased virulence.  Identify and characterize the genes and determine their regulation and expression; (5) Problem statement 1.2.9, “Food Security”, to develop sample collection and analysis systems for foods of concern and validate methods and diagnostics developed for the detection of select agents in foods; and  (6) Agency Performance Measure 3.1.2, Develop and transfer to Federal agencies and the private sector systems that rapidly and accurately detect, identify, and differentiate the most critical and economically important food-borne pathogens are addressed.
Customers of the research include: (1) the USDA Food Safety and Inspection Service (FSIS), for whom methods and tools for pathogen identification will be evaluated/developed; (2) scientists in the food industry and academia, who will benefit from research on techniques for pathogen identification and from knowledge of bacterial stress responses and quorum sensing; and (3) consumers who demand safe and wholesome food free of microbial pathogens. 

**2.List by year the currently approved milestones (indicators of research progress)**													FY2006	Complete investigations on the effect of temperature and competitive flora on Campylobacter	Initiate research the understand the role of “curli” in biofilm formation and the regulation of curli production	Complete investigations on development of PCR and PCR-RFLP based assay for speciating Campylobacter using Campylobacter spp. genes as targets
FY2007	Expand the investigations on the effect of oxygen and other stresses on Campylobacter	Expand research on the role of curli in biofilm formation	Complete research on typing and identification of virulence factors in Salmonella spp. isolated from swine
FY2008	Expand research using genomics and proteomics tools to examine stress responses in E. coli and Campylobacter	Complete research on construction of GFP-labeled E. coli O157:H7, Salmonella spp., and L. monocytogenes	Expand research on identification of novel quorum sensing mechanisms in Campylobacter	Complete research on characterization of E. coli and Salmonella strains from different sources, including food, animals, humans, and the environment (virulence genes, antibiotic resistance, stress tolerance)
FY2009	Complete investigations on regulation of curli in E. coli	Expand investigations on stress responses in Campylobacter	Expand research on the role of quorum sensing in survival of Campylobacter	Complete investigations on biofilm formation using GFP-labeled strains	Complete research on development of genetic-based PCR and microarray-based systems for speciating Campylobacter
FY2010	Expand research on the effect of stress adaptation on cross protection in food-borne pathogens 	Complete investigations on role of LuxS in Campylobacter, E. coli, and Salmonella quorum sensing  	Complete research on the development of genetic-systems for typing E. coli, and on     development of microarrays for identification of food safety threat agents 	Complete research on sequencing and analysis of Salmonella antibiotic resistance plasmids						
**4a.List the single most significant research accomplishment during FY 2006.**													This Project recently completed the NP 108 OSQR Review Process and was certified.  See the report for 1935-42000-051-00D.						
**4b.List other significant research accomplishment(s), if any.**													This Project recently completed the NP 108 OSQR Review Process and was certified.  See the report for 1935-420000-050-00D.						
**4c.List significant activities that support special target populations.**													This Project recently completed the NP 108 OSQR Review Process and was certified.  See the report for 1935-42000-051-00D.						
**4d.Progress report.**													Research Project:  1935-42000-060-01S  This report serves to document research conducted under Specific Cooperative Agreement No. 58-1935-5-542 between ARS and PPG Industries.  Additional details of research can be found in the report for the parent project, 1935-42000-060-00D.  The objective of this research is to evaluate anti-microbial coating materials using a variety of surfaces, including glass, ceramic, and stainless steel under a variety of test conditions for their ability to inactivate food-borne pathogens and prevent biofilm formation.  PPG Industries has provided coated materials to ARS and also provided technical assistance and support of ARS activities related to pilot test programs.  ARS has conducted pilot studies using glass coated with titanium dioxide nanoparticles and with silver under a variety of test conditions.  E. coli O157:H7 and Salmonella Newport were used as the test pathogens.  The research supports the CRIS project plan and will lead to the development of coated materials that can be used by the food industry and the consumer to inactivate pathogens and to prevent biofilm formation on food and non-food contact surfaces.  
Research Project:  1935-42000-060-02M  This report serves to document research conducted under Memorandum of Understanding No. 58-1935-6-602M between ARS and the Department of Defense, U.S. Army Medical Research and Materiel Command, Biotechnology High Performance Computing Software Applications Institute (BHSAI).  Additional details of the research can be found in the report for the parent CRIS, 1935-42000-060-00D.  Both ARS and the Department of Defense are involved in research designed to increase knowledge of agents of food-borne disease and to develop methods for detection and diagnosis and for genome analysis.  The goal of this research is to develop science and technology to aid in the development of DNA biomarkers in food-borne pathogens and for genome analysis.  BHSAI will provide existing software for DNA fingerprinting for ARS to utilize for the research, making modifications to software as needed.  ARS will provide DNA genomic information on food-borne pathogens of mutual interest and use software provided by BHSAI.  Results of experimental validation of software will be provided to BHSAI.  A computational biologist was recently hired in this CRIS project who is assisting in this research.  This research supports the CRIS project plan and will provide information on biomarkers in food-borne pathogens, as well as information on software that will be useful for the scientific community.						
**5.Describe the major accomplishments to date and their predicted or actual impact.**													This Project recently completed the NP 108 OSQR Review Process and was certified.  See the report for 1935-42000-051-00D.						
**6.What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end-user (industry, farmer, other scientists)?  What are the constraints, if known, to the adoption and durability of the technology products?**													This Project recently completed the NP 108 OSQR Review Process and was certified.  See the report for 1935-42000-051-00D.						
**7.List your most important publications in the popular press and presentations to organizations and articles written about your work.  (NOTE:  List your peer reviewed publications below).**													This Project recently completed the NP 108 OSQR Review Process and was certified.  See the report for 1935-42000-051-00D.						
    Project TeamFratamico, Pina Yan, Xianghe Chen, Chin-Yi Uhlich, Gaylen Gunther, Nereus  - *Jack* 
Project Annual Reports FY 2009 FY 2008 FY 2007 FY 2006 Publications  Publications 
Related National Programs Food Safety, (animal and plant products)(108) Patents Method To Quickly Genetically Identify Strains Of Most Common Cause Of Bacterial Gastrointestinal Infection: Campylobacter  							Last Modified: 03/24/2010 		ARS Home |USDA.gov |Site Map |Policies and Links FOIA |Accessibility Statement |Privacy Policy |Nondiscrimination Statement |Information Quality |USA.gov |White House

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