Whole Genome Sequencing Researchers
Sandra M. Tallent
Marc Allard, Ph.D.
Research Area Coordinator for Genomics
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.
Rebecca Bell, Ph.D.
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’s 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.
Eric Brown, Ph.D.
Director, Division of Microbiology
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.
Yi Chen, Ph.D.
Dr. Yi Chen is a research microbiologist and Listeria monocytogenes subject matter expert in CFSAN’s Division of Microbiology. He has developed, compared, and evaluated rapid methods for screening L. monocytogenes in food and environmental matrices, and both led and collaborated on efforts to validate qualitative and quantitative testing methods for the organism. Dr. Chen has studied the behavior of L. monocytogenes in various food matrices to elucidate the relative risk of L. monocytogenes contamination in these foods. He is also an expert on whole genome sequencing analysis of L. monocytogenes, having analyzed strains isolated during regular FDA surveillance and outbreak response. His work has improved understanding of the epidemiology and ecological persistence of this pathogen. He has provided scientific advice on various FDA assignments, outbreak investigations, and laboratory analyses. In addition, Dr. Chen has worked on the method validation and genetic characterization of Cronobacter spp. Dr. Chen received his Ph.D. in Food Science from the Department of Food Science at the Pennsylvania State University in 2007. He currently serves as a member of Microbial Method Validation Subcommittee of FDA, General Referee for AOAC International, Technical Committee member on MicroVal and Editorial Board member for Applied and Environmental Microbiology.
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.
Narjol Gonzalez-Escalona, Ph.D.
Dr. Gonzalez-Escalona is a Research Microbiologist in the Molecular Methods and Subtyping Branch, within the Division of Microbiology, at FDA’s Center for Food Safety and Applied Nutrition. 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 the identification of novel pathogenicity targets from foodborne pathogens such as E. coli, Clostridium botulinum, and Salmonella using whole genome sequencing approaches. He has developed new methods to detect Salmonella in produce, S. Enteritidis and S. Heidelberg in egg products, and alternative methods for Salmonella subtyping. He is a member of IAFP and ASM and is 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.
Maria Hoffmann, Ph.D.
Dr. Hoffmann'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.
Sara Lomonaco, Ph.D.
Andrea Ottesen, Ph.D.
Research Area Coordinator for Metagenomics
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).
Shashi Sharma, Ph.D.
Sandra Tallent serves as Chief of the Molecular Methods and Subtyping Branch, within the Division of Microbiology, at FDA’s Center for Food Safety and Applied Nutrition. Dr. Tallent began her career as a clinical microbiologist, but the continued challenges of antimicrobial resistance prompted her to alter her career focus to public health research. She earned her Ph.D. from the Medical College of Virginia in Richmond prior to selection as a CDC Emerging Infectious Disease Research Fellow with Virginia’s Division of Consolidated Laboratory Services. Dr. Tallent accepted an appointment with FDA in 2008, where her research continues to concentrate on virulence and pathogenicity of Staphylococcus aureus, but also includes numerous experiments on Bacillus cereus. As a research microbiologist, Dr. Tallent has validated new protocols in an effort to update the FDA’s Bacteriological Analytical Manual. She is currently developing new methods that are based on genomic sequence information.
Ruth Timme, Ph.D.
Ruth Timme is a Research Microbiologist at the FDA’s Office of Regulatory Science. She received her Ph.D. 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.
Jie Zheng, Ph.D.
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.
Phillip Curry, Ph.D.
Research Microbiologist, PulseNet Team
Research Microbiologist, PulseNet Team
Eric Stevens, Ph.D.
Statistics and Bioinformatics
James B. Pettengill, Ph.D.
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.
Hugh Rand, Ph.D.
Supervisory Mathematical Statistician
Hugh Rand is a Team Leader in the Biostatistics Branch at the FDA’s Center for Food Safety and Applied Nutrition. He received his Ph.D. 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.
Errol Strain, Ph.D.
Supervisory Mathematical Statistician
Maria Sanchez Leon
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.
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.
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.
Strain Curator for the Division of Microbiology