Food

Researchers

Below you will find biographies for the researchers who are part of FDA’s foods whole genome sequencing program.

Principal Investigators
Eric Brown
Peter Evans
Marc Allard
Andrea Ottesen
Ruth Timme
Narjol Gonzalez-Escalona
Jie Zheng
Yi Chen
Rebecca Bell
Shashi Sharma

Genomics Coordinators
Christine Keys
David Melka

Statistics/Bioinformatics
Errol Strain
Hugh Rand
James Pettengill
Yan Luo

Staff Scientists
Charles Wang
Dwayne Roberson
Tim Muruvanda

ORISE Fellows or Other Contractors
Maria Hoffman
Cary Pirone
Justin Payne
George Kastanis
Shasha Gorham 
Christina Ferreira


Principal Investigators

Eric Brown, Ph.D.
Director, Division of Microbiology
Eric.Brown@fda.hhs.gov

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Dr. Eric W. Brown currently serves as Director of the Division of Microbiology in the Office of Regulatory Science. He oversees a group of 50 researchers and support scientists engaged in a multi-parameter research program to develop and apply microbiological and molecular genetic strategies for detecting, identifying, and differentiating bacterial foodborne pathogens such as Salmonella and shiga-toxin producing E. coli.  His early work on horizontal gene transfer among foodborne pathogens has aided in elucidating the etiologies of several emerging pathogens including many of the group I salmonellae as well as enterohemorrhagic and enteropathogenic E. coli.  More recently, his laboratory has been instrumental in adapting next-generation sequencing technologies to augment foodborne outbreak investigations at the FDA. Dr. Brown received his Ph.D. in Microbial genetics from The Genetics Program in the Department of Biological Sciences at The George Washington University.  He has conducted research in microbial evolution and microbial ecology as a research fellow in the National Cancer Institute, the U.S. Department of Agriculture, and as a tenure-track Professor of Microbiology at Loyola University of Chicago.  Dr. Brown came to the Food and Drug Administration in 1999 and has since carried out numerous experiments relating to the detection, identification, and discrimination of foodborne pathogens. He has been a member of the American Society for Microbiology since 1994 and has co-authored more than 70 publications and book chapters on the molecular differentiation and molecular evolution of bacterial pathogens. His primary research interests are currently to investigate the role of next-generation genome sequencing in the resolution of foodborne outbreaks and to continue to employ a variety of methods that allow for rapid and sensitive identification of enteric pathogens from the food supply.

Peter Evans, Ph.D.
Chief, Molecular methods and subtyping branch
Peter.Evans@fda.hhs.gov

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Peter Evans serves as Chief of the Molecular Methods and Subtyping Branch (MMSB) in CFSAN, which is responsible for developing methods for rapidly detecting and differentiating microbial foodborne pathogens of importance to FDA. This group has been a proponent of using whole genome sequencing (WGS) to track the sources of outbreaks, and using networks of sequencers to build databases such as the 100K pathogen Genome Project. Prior to coming to FDA in October 2012, Dr. Evans was a senior microbiologist with USDA-Food Safety and Inspection Service. He received his doctoral degree in cellular and molecular biology from the University of Wisconsin, and a masters of public health degree from the Johns Hopkins Bloomberg School of Public Health.

Marc Allard, Ph.D.
Research area coordinator for Genomics
Marc.Allard@fda.hhs.gov

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Marc W. Allard received his Ph.D. in biology in 1990 from Harvard University, Cambridge, MA.  Dr. Allard was the Louis Weintraub Associate Professor of Biology (and Genetics) at George Washington University (Washington, DC) for 14 years from 1994 to 2008.  He has had appointments to the Visiting Scientists Program both at the Federal Bureau of Investigation’s Counterterrorism and Forensic Science Research Unit (CTFSRU) and in the Chem Bio Sciences Unit (CBSU) for 8 years, where he assisted in the anthrax investigations and human genetics data-basing.  Dr. Allard joined FDA's Office of Regulatory Science and the Division of Microbiology in November 2008 and he is using DNA sequence information from the genomes of food borne pathogens to identify unique single nucleotide polymorphisms (SNPs), SAAPs and whole proteins to rapidly identify the various strains of bacteria, particularly Salmonella, E. coli, Shigella and Listeria.  Dr. Allard specializes in both phylogenetic analysis and bioinformatics methods, as well as the wet laboratory methods which generate this genetic information.

Andrea Ottesen, Ph.D.
Research Area Coordinator for Metagenomics
Andrea.Ottesen@fda.hhs.gov

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Dr. Andrea Ottesen is the Research Area Coordinator (RAC) for Metagenomics at FDA's Center for Food Safety and Applied Nutrition (CFSAN) in the Molecular Methods and Subtyping Branch (MMSB) of the Division of Microbiology. She received her Ph.D. in 2000 from the University of Maryland.  Ottesen works to provide target and non target metagenomic data to describe ecologies associated with high risk crops. Her ecological data are used to complement and improve Salmonella detection methods and provide data to improve recommendations for Good Agricultural Practices (GAPs).

Ruth Timme, Ph.D.
Research Microbiologist
Ruth.Timme@fda.hhs.gov

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Ruth Timme is a Research Microbiologist at the FDA’s Office of Regulatory Science. She received her PhD in 2006 in Plant Biology at The University of Texas at Austin. Her research background is focused mainly on utilizing comparative genomics and phylogenetics methods to answer evolutionary questions. Although her training is in botany, her published research spans a diversity of organisms, including sunflowers (Helianthus), Dinoflagellates, Charophyte green algae, and Salmonella. At the FDA she is implementing phylogenomic methods for tracking foodborne pathogens through the US food supply.

Narjol Gonzalez-Escalona, Ph.D.
Research Microbiologist
Narjol.Gonzalez-Escalona@fda.hhs.gov

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Dr. Gonzalez-Escalona is a Research Microbiologist in the Office of Regulatory Science (ORS), division of Microbiology, branch of molecular methods and subtyping, in the Center for Food Safety and Applied Nutrition, FDA, at College Park, MD. He is been working in ORS developing new methods to detect Salmonella in produce, S. Enteritidis and Heidelberg in eggs products, and alternative methods for Salmonella subtyping. He is the lead scientist in charge of testing and applying Ion Torrent technology for fast foodborne pathogens sequencing in ORS. His research interests include the ecology and evolution of marine bacteria, especially those of the genus Vibrio. Other research interests include tracking, subtyping, evolution, comparative genomics and identification of novel pathogenicity targets from foodborne pathogens such as E. coli, Clostridium botulinum, and Salmonella using whole genome sequencing approaches. He is also the curator of the MLST website for V. parahaemolyticus. Dr. Gonzalez-Escalona received his Ph.D. from the University of Chile in 2004 and completed further postdoctoral training at the Gulf Coast Seafood Laboratory (GCSL), FDA, Dauphin Island, AL.

Jie Zheng, Ph.D.
Staff Fellow
Jie.Zheng@fda.hhs.gov

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Dr. Jie Zheng currently serves as a staff microbiologist of the Molecular Methods and Subtyping Branch within the Division of Microbiology. Dr. Zheng finished her Ph.D. in Food Science from University of Maryland at College Park, MD in 2006 and her dissertation is on "Campylobacter jejni/coli – Host Intestinal Epithelial Cell Interaction". Dr. Zheng joined the laboratories at the Center for Food Safety and Applied Nutrition (CFSAN) in July of 2008 after her two-year post-doctoral training at UM. She is interested in development of SNP-based detection, identification and subtyping methods for various phyletic and pathovar divisions of pathogenic Salmonella. She is also engaged in reducing carriage of Salmonella Newport on tomato plants with bio-control intervention method.

Yi Chen, Ph.D.
Visiting Scientist
Yi.Chen@fda.hhs.gov

Dr. Yi Chen obtained his Ph.D. degree in Food Science from Pennsylvania State University in 2007. His Ph.D. thesis work focused on the development of rapid detection and molecular subtyping schemes for L. monocytogenes. He joined FDA in 2008 and has been working on the rapid detection, molecular subtyping and whole genome sequencing analysis of Cronobacter and L. monocytogenes.  He is the subject matter expert for L. monocytogenes in Office of Regulatory Science and has been involved in various FDA assignments, outbreak investigations, analytical worksheet reviews and corrective action plan reviews for L. monocytogenes.

Rebecca Bell, Ph.D.
Research Microbiologist
Rebecca.Bell@fda.hhs.gov

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Dr. Rebecca Bell is a Research Microbiologist in the Molecular Methods and Subtyping Branch within the Division of Microbiology at the Food and Drug Administration Center for Food Safety and Applied Nutrition. Dr. Bell received her Ph.D. in microbiology from The Ohio State University in 2005. Afterwards, she joined CFSAN in 2006 as a postdoctoral fellow in the Division of Analytical Chemistry where she worked on bacterial protein profiling using liquid chromatography/mass spectrometry. In 2008, Dr. Bell moved to MMSB. She continues to collaborate with the DAC on LC/MS work as well as working on molecular subtyping of Salmonella enterica, the development of rapid screening methods for Salmonella contamination of foods and ecological surveillance of the tomato growing environment for Salmonella.

Shashi Sharma, Ph.D.
Research Microbiologist
Shashi.Sharma@fda.hhs.gov

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Genomics Coordinators

Christine Keys
Research Microbiologist, PulseNet Coordinator
Christine.Keys@fda.hhs.gov

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David Melka
Research Microbiologist, PulseNet Team
David.Melka@fda.hhs.gov

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Statistics and Bioinformatics

Errol Strain, Ph.D.
Supervisory Mathematical Statistician
Errol.Strain@fda.hhs.gov

Hugh Rand, Ph.D.
Supervisory Mathematical Statistician
Hugh.Rand@fda.hhs.gov

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Hugh Rand is a Team Leader in the Biostatistics Branch at the FDA’s Center for Food Safety and Applied Nutrition. He received his PhD in 1995 in Applied Mathematics at The University of Washington. His research interests focus on the application of mathematical and statistical tools to the analysis of biological problems, primarily in the area of human health. Much of his early work involved the applications of bioinformatics in drug discovery within inflamation and oncology. Currently, a major focus of his efforts at the FDA are in the use of genomic sequencing for aiding in tracking foodborne pathogens through the US food supply.

James B. Pettengill, Ph.D.
Staff Fellow
James.Pettengill@fda.hhs.gov

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Dr. Pettengill uses metagenomic approaches (i.e., the sequencing of DNA contained in an environmental sample) to investigate important agricultural and food safety questions.  Specifically, he and other scientists at the FDA have employed metagenomics to describe the effects of different bacterial enrichment procedures and how they might impact our ability to detect specific pathogens.  They are also evaluating how different pesticides alter microbial diversity and the prevalence of certain pathogens within the ecosystem.

Yan Luo
Staff Fellow
Yan.Luo@fda.hhs.gov


Staff Scientists

Charles Wang
Research Microbiologist
Charles.Wang@fda.hhs.gov

Charles Wang runs the various sequencing platforms in the lab, including the Pac Bio RS, Roche 454, Illumina Miseq, and ancillary equipment.

Dwayne Roberson
Strain curator for the Division of Microbiology
Dwayne.Roberson@fda.hhs.gov

Tim Muruvanda
Research Microbiologist
Tim.Muruvanda@fda.hhs.gov

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Tim Muruvanda collects and analyzes NGS data from the Pacific Biosciences RS II sequencers. He is primarily focused on generating closed microbial reference genomes to support the applicability of WGS in public health.


ORISE Fellows / Contractors

Maria Hoffman, Ph.D.
Postdoctoral Fellow
Maria.Hoffman@fda.hhs.gov

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Dr. Hoffman's thesis research was, performed at the U.S. Food and Drug Administration in College Park, Maryland, under Dr. Eric Brown, focused on the molecular evolution and speciation of the genus Vibrio. She completed her Ph.D. work in July 2012 at the University of Hamburg. Currently she is performing analyses to acquire data for differentiation and characterization of pathogens, particularly outbreak isolates from non-outbreak isolates and closely-related antibiotic-resistant Salmonella species using whole genome sequencing (WGS) and comparative genomic analyses. Further using the Pacific Biosciences (PacBio) RS sequencer and their hierarchical genome assembly process (HGAP) we are sequencing different pathogens to completly close reference genomes which will support the pilot studies of testing the applicability of WGS in public health surveillance activities.

Cary Pirone, Ph.D.
ORISE Postdoc fellow
Cary.Pirone@fda.hhs.gov

Dr. Pirone earned her Ph.D. in 2010 in Biology at the Florida International University. As a postdoc in the Office of Regulatory Science, she uses the PacBio sequencer to collect and analyze whole genome sequence data from various pathogenic bacteria, with an emphasis on Salmonella.  Dr. Piron also plans on using SNP identification, phylogenetics, and methylation patterns to type isolates and to explore the basis of epigenetic modifications. 

Justin Payne
ORISE fellow
Justin.Payne@fda.hhs.gov

Justin Payne is an integration and bioinformatics developer and the author of "Bootsie", a statistical tool for RFLP analysis. He graduated in 2011 from the University of Nebraska, Lincoln with a Bachelor of Science degree in biochemistry. At FDA-CFSAN, his work is primarily focused on database development, high-throughput assembly of NGS data, and transparent integration with NCBI data stores.

George Kastanis
ORISE fellow
George.Kastanis@fda.hhs.gov

George Kastanis is part of genomics team working under the supervision of Dr. Marc Allard. His primary function is to run the MiSeq personal sequencing of various isolates that come through the pipeline.

Sasha Gorham
ORISE fellow
Sasha.Gorham@fda.hhs.gov

Sasha Gorham performs research in metagenomics under the supervision of Dr. Andrea Ottesen. Her primary responsibilities surround the operation and management of metagenomic sequencing using the MiSeq platform. She graduated from Smith College in 2010 with two Bachelor degrees in Biological Sciences and Biochemistry. The primary focus of her research is to evaluate microbial communities in different agricultural environments and identify the effect, if any, agricultural practices have on the composition of microbial populations.

Christina Ferreira
ORISE fellow
Christina.Ferreira@fda.hhs.gov

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Christina Ferreira is Molecular Microbiologist in the Division of Microbiology-Molecular Methods and Subtyping Branch. She graduated in 2008 from Clarion University of Pennsylvania, with a Bachelor of Science degree in Molecular Biology and Biotechnology. At FDA-CFSAN, her work is primarily focused on development of a mass spectrometry based assay for rapid identification of Salmonella species in food. She is also working on the validation of assembled genomes through comparisons with whole genome (optical) maps, analysis of the evolution of S.enterica Typhimurium over the last 70 years, and an investigation of SNP variations in clinical STEC strains.

Page Last Updated: 11/07/2014
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