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U.S. Department of Health and Human Services

Food

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Research

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

Statistics/bioinformatics
Errol Strain
James Pettengill
Yan Yan

Staff scientists
Christine Keys
David Melka
Charles Wang
Dwayne Roberson

ORISE fellows or other contractors
Maria Hoffman
Cary Pirone
Justin Payne
George Kastanis
Tim Muruvanda
 


Principal investigators

Eric Brown, Ph.D.

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

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

Marc Allard, Ph.D.

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

Yuansha Chen, Sampa Mukherjee, Maria Hoffmann, Michael Kotewicz, Shenia Young, Jason Abbott, Yan Luo, Maureen Davidson, Marc Allard, Patrick McDermott, and Shaohua Zhao. Whole Genome Sequencing of Gentamicin-Resistant Campylobacter coli isolated from U. S. Retail Meats Reveals Novel Plasmid Mediated Aminoglycoside Resistance Genes. Submitted to Antimicrobial Agents and Chemotherapy section Mechanisms of Resistance. In Press Antimicrobial Agents and Chemotherapy.

Hoffmann M, Luo Y, Lafon PC, Timme R, Allard MW, McDermott PF, Brown EW, Zhao S. 2013. Genome sequences of Salmonella enterica serovar Heidelberg isolates isolated in the United States from a multistate outbreak of human Salmonella infections. Genome Announcement. 1(1):e00004-12. doi:10.1128/genomeA.00004-12.

Andrea R Ottesen, Antonio Gonzalez, James R White, James B Pettengill, Cong Li, Sarah Allard, Steven Rideout, Marc Allard, Thomas Hill, Peter Evans, Errol Strain, Steven Musser, Rob Knight and Eric Brown.  Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiology 2013, 13:114 doi:10.1186/1471-2180-13-114

Jinling Shen, Jianghong Meng, Feng Li, Robert Housley, Heather Carolan, Irene Yasuda, Erik Burrows, Rachel Binet, Rebecca Bell, Fei Wang, Shaohua Zhao, Rangarajan Sampath, and Marc Allard.  Identification and Subtyping of Non-O157 Shiga Toxin-Producing Escherichia coli using PCR-Mass Spectrometry. 2012, Foodborne Pathogens and Disease. doi:10.1089/fpd.2012.1469.

Guojie Cao, Wenting Ju, Lydia Rump, Shaohua Zhao, Likou Zou, Charles Wang, Errol Strain, Yan Luo, Ruth Timme, Marc Allard, Eric Brown, and Jianghong Meng. 2013. Genome Sequences of two Emerging Non-O157 Shiga Toxin-producing Escherichia coli Strains. Genome Announcement. 1(3):e00200-13. doi:10.1128/genome Announcement A.00200-13.

Jianmin Zhang, Guojie Cao, Xuebin Xu, Huimin Jin, Qiong Zhang, Jianwei Chen, Xiaowei Yang, Haijian Pan, Xiuli Zhang, Marc Allard, Eric Brown, and Jianghong Meng.  2013.  Whole Genome Sequences of Four Salmonella Newport Strains from Humans" press Genome Announcement. 1(3):e00213-13. doi:10.1128/genomeA.00213-13.

Marc W. Allard, Tim Muruvanda, Errol Strain, Ruth Timme, Yan Luo, Charles Wang, Christine E. Keys, Justin Payne, Tony Cooper, Khai Luong, Yi Song, Chen-Shan Chin, Jonas Korlach, Rich J. Roberts, Peter Evans, Steven M. Musser, and Eric W. Brown.  2013.  Fully assembled genome sequence for Salmonella enterica subsp. Enterica serovar Javiana CFSAN001992. Genome Announcement 1(2):e00081-13. Doi:10.1128/genomeA.00081-13.

Zhang J, Cao G, Xu X, Jin H, Yang X, Allard M, Brown E, Meng J. 2013. Draft genome sequences of three Salmonella enterica serovar Agona strains from China. Genome Announc. 1(1):e00203-12. doi:10.1128/genomeA.00203-12.

Cao G, Meng J, Strain E, Stones R, Pettengill J, et al. (2013) Phylogenetics and Differentiation of Salmonella Newport Lineages by Whole Genome Sequencing. PLoS ONE 8(2): e55687. doi:10.1371/journal.pone.0055687

Marc W. Allard, Yan Luo, Errol Strain, James Pettengill, Ruth Timme, Charles Wang, Cong Li, Christine E. Keys, Jie Zheng Robert Stones, Mark R. Wilson, Steven M. Musser, and Eric W. Brown. On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004. PLoS ONE 8(1): e55254. doi:10.1371/journal.pone.0055254

Mark R. Wilson, Marc W. Allard, Eric W. Brown. The Forensic Analysis of Foodborne Bacterial Pathogens in the Age of Whole Genome Sequencing. In press Cladistics 2013. DOI: 10.1111/cla.12012

Tina S Lusk, Andrea R Ottesen, James R White, Marc W Allard, Eric W Brown and Julie A Kase. Characterization of Microflora In Latin-Style Cheeses by Next-Generation Sequencing Technology. 2012 BMC Micro. 12(1):254.

James B Pettengill, Eugene McAvoy, James R White, Marc Allard, Eric Brown, Andrea Ottesen. Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection. BMC Research Notes 2012, 5:378

Sarah E. Pierce, Rebecca L. Bell, Rosalee S. Hellberg, Chorng-Ming Cheng, Kai-Shun Chen, Donna M. Williams-Hill, William B. Martin, Marc W. Allard. Detection and identification of Salmonella enterica, Escherichia coli, and Shigella spp. via PCR-ESI-MS: isolate testing and analysis of food samples. 2012, Applied and Environmental Microbiology 78(23):8403-11.

Wenting Ju, Guojie Cao,  Lydia Rump, Errol Strain, Yan Luo, Ruth Timme 3, Marc Allard, Shaohua Zhao, Eric Brown and Jianghong Meng. Phylogenetic analysis of non-O157 Shiga toxin-producing Escherichia coli by whole genome sequencing. 2012, J. Clinical Micro. 50(12):4123-7

Ruth Timme, Marc Allard, Yan Luo, Errol Strain, James Pettengill, Charles Wang, Cong Li, Christine Keys, Jie Zheng, Robert Stones, Mark Wilson, Steven Musser, and Eric Brown. Draft Genome Sequence of 21 Salmonella Enteritidis strains. 2012. J. Bacteriol. 194(21):5994-5. JB01289-12R1),

Guojie Cao, Shaohua Zhao, Errol Strain, Yan Luo, Ruth Timme, Charles Wang, Eric Brown, Jianghong Meng and Marc Allard.  Draft Genome Sequence of Eight Salmonella Newport Strains from Diverse Hosts and Locations. 2012, J. Bacteriol. 194:5146; doi:10.1128/JB.01171-12

D. Imes, E. J. Wictum, M. W. Allard, and B. N. Sacks. Identification of Single Nucleotide Polymorphisms within the mtDNA Genome of the Domestic Dog to Discriminate Individuals with Common HVI Haplotypes. In Press Forensic Sciences International: Genetics 2012.6(5):630-9 http://dx.doi.org/10.1016/j.fsigen.2012.02.004 disclaimer icon ,

L. V. Rump, J. Meng,  E. A. Strain, G. Cao, M. W. Allard and N. Gonzalez-Escalona. Complete DNA Sequence Analysis of Enterohemoragic Escheria coli Plasmid pO157_2 in B-Glucuronidase-Positive Escherichia coli O157:H7 Reveals a Novel Evolutionary Path. 2012, J. Bact. 194(13):3457-3463.

Maria Hoffmann, Shaohua Zhao, Yan Luo, Cong Li, Jason Folster, Jean Whichard, Marc Allard, Eric Brown, and Patrick McDermott. Genome sequences of Five Salmonella enterica Serovar Heidelberg Isolates Associated with a 2011 Multistate Outbreak in the United States. 2012, J. Bact. 194(12):3274-3275.

Marc W. Allard, Yan Luo, Errol Strain, Cong Li, Christine E. Keys, Insook Son, Robert Stones, Steven M. Musser, and Eric W. Brown. High Resolution Clustering of Salmonella enterica serovar Montevideo Strains Using a Next-Generation Sequencing Approach. 2012, BMC Genomics 13:32  doi:10.1186/1471-2164-13-32

Rebecca L. Bell, Guojie Cao, J. Meng, Marc W. Allard, Christine Keys, Thomas Hill, Andrea Ottesen and Eric W. Brown. Salmonella Newport Contamination of Produce: Ecological, Genetic and Epidemiological Aspects. in "Salmonella: Classification, Genetics and Disease Outbreaks" (Jodi Schlapa ed.). 2012 Nova Science Publishers, Inc., Hauppauge, NY.

Eric W. Brown*,  Rebecca L. Bell, Marc W. Allard, Narjol Gonzalez-Escalona, Andrei Perlloni, Joseph E. LeClerc, and Thomas A. Cebula.  Reticulate Evolution Among the Group I Salmonellae: An Ongoing Role for Horizontal Gene Transfer.  In Salmonella - A Diversified Superbug (Yashwant Kumar, ed.). 2012 InTech - Open Access Publisher. ISBN 978-953-307-781-9. http://www.intechweb.org/ disclaimer icon

Maria Hoffmann1, 2*, Steven R. Monday1, Marc W. Allard, Errol A. Strain1, Paul Whittaker1, Marianna Naun1, Peter J. McCarthy3, Jose V. Lopez4, Markus Fischer2 and Eric W. Brown1 Vibrio caribbeanicus sp. nov., isolated from marine sponge Scleritoderma cyanea. 2012 IJSEM 62(8):1736-43.

Yi Chen, Errol Strain, Marc Allard, and Eric Brown. 2011. Genome sequences of Cronobacter sakazakii E899, a Strain Associated with Human Illness J. Bacteriology 193(20):5861

Chen Y., Strain E.A. Allard M. and Brown E.W.  Genome sequences of Listeria monocytogenes strains J1816 and J1-220 associated with human outbreaks. J. Bacteriol.. 2011 Jul;193(13):3424-5; electronic doi:10.1128/JB.05048-11.

Rump L. V.1,2, Strain E. A.2, Cao G. 2, Allard M. W. 2, Fischer M.2, and Gonzalez-Escalona N.1* Draft genome sequences of six Escherichia coli isolates from the stepwise model of emergence of Escherichia coli O157:H7  J Bacteriol. 2011 193(8):2058.

E. Kurt Lienau, Ph.D., Errol Strain Ph.D., Charles Wang, B.S., Guojie Cao, M.S., Jie Zheng, D.V.M., Ph.D., Jianghong Meng, D.V.M., M.P.V.M., Ph.D., Andrea Ottesen, Ph.D., Christine Keys, M.S., Robert Stones, M.S., Thomas Hammack, M.S., Steven Musser, Ph.D., Eric W. Brown, Ph.D., and Marc W. Allard, Ph.D. Next-Generation Sequencing Provides High Resolution Clustering of Food and Clinical Sources during a Foodborne Outbreak of Salmonellosis. This letter (10.1056/NEJMc1100443) was published on February 23, 2011, at NEJM.org.

Walters-Conte, Kathryn B., Johnson, Diana L.E., Allard, Marc and Pecon-Slattery, Jill. Carnivore specific SINEs (Can-SINEs): Distribution, Function, Evolution and Genomic Advances. Journal of Heredity 102(Suppl 1):S2-S10.

Sufian F. Al-Khaldi, Magdi M. Mossoba, Marc Allard, E. Kurt Lienau, and Eric D. Brown. 2011. in "Microbial Systems Biology: Methods and Protocols" a Methods in Molecular biology series,  (ed. Navid), Who Said We Can't Reinvent the Wheel: A Closer Look at Bacterial Identification and Subtyping in Food Using DNA Microarray and DNA Sequencing in Press Humana press.

Jeffrey M. Blazar,1,2 E. Kurt Lienau,1 and Marc W. Allard1*  2011.  Insects as Vectors of Foodborne Pathogenic Bacteria. vol. 4 (1) in Terrestrial Arthropod Reviews 2011, 4(1):5–16, http://brill.publisher.ingentaconnect.com/content/brill/tar disclaimer icon

E. Kurt Lienau, Rob DeSalle, Marc Allard, Eric W. Brown David Swofford, Jeffery A. Rosenfeld, Indra N. Sarkar, Paul J. Planet (2011).  The Mega-Matrix tree of life: Using horizontal gene transfer and sequence evolution data as information about the vertical history of life. Cladistics 27(4):417-427.

Webb, K.M. and Allard, M.W. (2010).  Assessment of minimum sample sizes required to adequatelyrepresent diversity reveals inadequacies in datasets of domestic dog mitochondrial DNA.Mitochondrial DNA. 2010 Feb; 21(1):19-31.

Briana B. Smalling,1 M.S.; Jessica A. Satkoski,2 Ph.D.; Bradley K. Tom,1 M.S.; Wing Yi Szeto,2 B.A.S.; Bethany Joy-Alise Erickson,2 B.S.; Theresa F. Spear,1 M.A.; David Glenn Smith,1,2,3 Ph.D.; Bruce Budowle,4 Ph.D.; Kristen M. Webb,5 Ph.D.; Marc Allard,6 Ph.D. and Sreetharan Kanthaswamy,1,2,3 Ph.D. 2009.  Geographic differences in mitochondrial DNA (mtDNA) distribution among United States (US) domestic dog populations. 2009 Open Forensic Science Journal

Webb, K.M. and Allard, M.W. (2009).  Mitochondrial genome DNA analysis of the domestic dog: identifying informative SNPs outside of the control region. J Forensic Sci. 2009 Mar;54(2):275-88

Webb, K.M. and Allard, M.W. (2009).  Identification of forensically informative SNPs in the domestic dog mitochondrial control region. J Forensic Sci. 2009 Mar;54(2):289-304.

Arjun B. Prasad, Marc W. Allard, NISC comparative sequencing program and Eric D. Green. 2008. Confirming the phylogeny of mammals by use of large comparative sequence data sets.. 2008 Mol Biol Evol. 2008 Sep;25(9):1795-808. Epub 2008 May 2.

Andrea L. Himmelberger; Theresa F. Spear; Jessica A. Satkoski, Debra A. George, Wendy T. Garnica, Venkat S. Malladi,  David G. Smith; Joy L. Halverson, Kristen Webb, Marc W. Allard, Sreetharan Kanthaswamy.  2008. Forensic utility of the mitochondrial hypervariable 1 region of domestic dogs, in conjunction with breed and geographic information, the Journal of Forensic Sciences, 53:81-89.

Andrea Ottesen, Ph.D.

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

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).

Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere Plos One (2013) Ottesen, A.R., Gonzalez, A., Bell R., Arce, C., Rideout, S., Allard, M., Evans, P., Musser, S., Knight, R., Brown, E.W.,and  Pettengill, J.B.

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato) BMC Microbiology (2013) Ottesen, A.R., Gonzalez, A., White, J.R., Pettengill, J.B., Li, C., Allard, S., Rideout, S.,Allard, M., Hill, T., Evans, P., Strain, E., Musser, S., Knight, R., Brown, E.W.

Comparing Source of Agricultural Contact Water and the Presence of Fecal Indicator Organisms on the Surface of 'Juliet' Grape Tomatoes Journal of Food Protection (2013) Pahl, D., Telias, A., Newell, M., Ottesen, A.R., Walsh, C.S.

Characterization of microflora in Latin-style cheese via next-generation sequencing technology BMC Microbiology (2012) Lusk, T., Ottesen, A.R., White,J.R., Kase, J.A.

Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection BMC Microbiology (2012) Pettengill, J.B., McAvoy, E., White, J.R., Allard, M.W., Brown, E.W., Ottesen, A.R.

Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: Diversity and seasonal variability  Plos One (2012) 7(6):e38204 White, J.R., Patel, J., Ottesen, A.R., Arce, C., Lopez, J.V.

In. Salmonella: Classification, Genetics and Disease; Salmonella Newport Contamination of Produce: Ecological, Genetic, and Epidemiological Aspects Nova Biomedical Press (2012) Bell, R. L., Cao, G., Allard, M.W., Keys, C., Hill, T., Ottesen, A.R., and Brown, E.W.

Next-Generation Sequencing Provides High Resolution Clustering of Food and Clinical Sources during a Foodborne Outbreak of Salmonellosis New England Journal of Medicine (2011) 364:981-982  Lienau, K., Strain, E.A., Wang, C., Cao, G., Zheng, J., Ottesen, A.R., Keys, C., Stones, R., Hammack, T., Musser, S., Brown, E.W., Allard, M.W.

Bacterial Community Diversity and Variation in Spray Water Sources and the Tomato Fruit Phyllosphere BMC Microbiology (2011) 11:81: 1471-2180 Telias, A., White, J.R., Pahl, D., Ottesen, A.R., Walsh, C.S.

Unique dynamics of Vibrio speciation in deep-water Porifera sponge microcosms  International Society for Microbial Ecology (2010) 1-5:1751-7362 Hoffmann, M., Fischer, M., Ottesen A.R., McCarthy, P.J., Lopez, J.V., Brown, E.W., Monday, S.

In: Pathogens and toxins in foods: Challenges and interventions; Natural toxins in food plants  American Society of Microbiology Press  (2010) 19: 301-313 Ottesen, A.R., Magnuson, B. (Book Chapter)

Duke’s handbook of medicinal plants of Latin America CRC Press (2009) Duke, J.A., Bogenschutz-Godwin, M.J., Ottesen, A.R. (Reference Book)

The impact of organic and conventional management on the microbial ecology of an apple crop (2009) 72(11):2321-2325 Journal of Food Protection Ottesen, A.R., White, J.R., Skaltsas, D.N., Newell, M.J., Walsh, C.S.

The effect of organic and conventional management programs on apple and Asian Pear tree growth, productivity, expenses and revenues in a hot, humid climate Acta Horticulturae (2009) Walsh, C.S., Ottesen, A.R., Hanson, J.C., Newell, M.J., and Leone, E.H.

Ruth Timme, Ph.D.

Research Microbiologist
Ruth.Timme@fda.hhs.gov

Dr. 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.

Allard, M. W., Luo, Y., Strain, E., Pettengill, J., Timme, R., Wang, C., et al. (2013a). On the Evolutionary History, Population Genetics and Diversity among Isolates of Salmonella Enteritidis PFGE Pattern JEGX01.0004. PloS one, 8(1), e55254.

Allard, M. W., Muruvanda, T., Strain, E., Timme, R., Luo, Y., Wang, C., et al. (2013b). Fully assembled genome sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992. Genome announcements, 1(2), e0008113.

Basavanna, U., Gonzalez-Escalona, N., Timme, R., Datta, S., Schoen, B., Brown, E. W., et al. (2013). Draft Genome Sequence of a Clostridium botulinum Isolate from Water Used for Cooling at a Plant Producing Low-Acid Canned Foods. Genome announcements, 1(1).

Handy, S. M., Timme, R. E., Jacob, S. M., & Deeds, J. R. (2013). Development of a locked nucleic acid real-time polymerase chain reaction assay for the detection of Pinus armandii in mixed species pine nut samples associated with dysgeusia. Journal of agricultural and food chemistry, 61(5), 1060–1066.

Hoffmann, M., Luo, Y., Lafon, P. C., Timme, R., Allard, M. W., McDermott, P. F., et al. (2013). Genome Sequences of Salmonella enterica Serovar Heidelberg Isolates Isolated in the United States from a Multistate Outbreak of Human Salmonella Infections. Genome announcements, 1(1).

Ju, W, G Cao, L Rump, E Strain, Y Luo, R Timme, M Allard, S Zhao, E Brown, J Meng. (2012). Phylogenetic Analysis of Non-O157 Shiga Toxin-Producing Escherichia coli Strains by Whole-Genome Sequencing. Journal of Clinical Microbiology 50(12): 4123-4127.

Timme, RE, Allard, M. W., Luo, Y., Strain, E., Pettengill, J., Wang, C., et al. (2012). Draft Genome Sequences of 21 Salmonella enterica Serovar Enteritidis Strains. Journal of Bacteriology, 194(21), 5994–5995.

Cao, G., Zhao, S., Strain, E., Luo, Y., Timme, R., Wang, C., Brown, E., et al. (2012). Draft Genome Sequences of Eight Salmonella enterica serotype Newport Strains from Diverse Hosts and Locations. Journal of Bacteriology, 194(18), 5146.

Delaux, P.-M., Xie, X., Timme, R. E., Puech-Pages, V., Dunand, C., Lecompte, E., Delwiche, C. F., et al. (2012). Origin of strigolactones in the green lineage. The New phytologist, 195(4), 857–871.

Timme, R. E., Bachvaroff, T. R., & Delwiche, C. F. (2012). Broad phylogenomic sampling and the sister lineage of land plants. PloS one, 7(1), e29696.

Delwiche, CF and RE Timme. 2011. Plants. Current Biology 21(11):R417-R422.

De Smet, I, U Voss, S Lau, M Wilson, N Shao, RE Timme, R Swarup, I Kerr, C Hodgman, R Bock, M Bennett, G Jurgens, and T Beeckman. 2011. Unraveling the Evolution of Auxin Signaling. Plant Physiology 155(1):209-21.

Finet, C, RE Timme, CF Delwiche and F Marlétaz. 2010. Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants. Current Biology 20:1-6.

Timme, RE and CF Delwiche. 2010. Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes. BMC Plant Biology 10:96.

Handy, SM, TR Bachvaroff, RE Timme, DW Coats, S Kim, CF Delwiche. 2009. Phylogeny of four Dinophyciacean genera (Dinophyceae, Dinophysiales) based on rDNA sequences from single cells and environmental samples. Journal of Phycology 45(5): 1163-1174.

Narjol Gonzalez-Escalona, Ph.D.

Research Microbiologist
Narjol.Gonzalez-Escalona@fda.hhs.gov

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.

Walters S. P., Gonzalez-Escalona N., Son I., Melka D. C., Sassoubre L. M., Boehm A. B. (2013). Salmonella enterica diversity in central Californian coastal waterways. Appl. Environ. Microbiol., 79 (14): 4199–4209.

Basavanna U., Gonzalez-Escalona N., Timme R., Datta S., Schoen B., Brown E. W., Zink D., and Sharma S. K. (2013). Draft Genome Sequence of a Clostridium botulinum Isolate from Water Used for Cooling at a Plant Producing Low-Acid Canned Foods. Genome Announc., 1 (1): e00200-12.

Turner J. W., Paranjpye R. N., Landis E. D., Biryukov S. V., González-Escalona N., Nilsson W. B., and Strom M. S. (2013). Population Structure of Clinical and Environmental Vibrio parahaemolyticus from the Pacific Northwest Coast of the United States. PLoS One, 8 (2):e55726.

L. V. Rump, J. Meng, E. A. Strain, G. Cao, M. W. Allard and N. Gonzalez-Escalona, (2012), Complete DNA sequence analysis of EHEC pO157_2 in GUD+ Escherichia coli O157:H7 reveals a novel evolutionary pathway. J. Bacteriol., 194 (13): 3457-63.

Gonzalez-Escalona N., Brown E. W., and Zhang G. (2012).  Development of a multiplex TaqMan real-time PCR (qPCR) assay targeting invA and ttrRSBCA locus for accurately detection of Salmonella in produce and eggs. Food Research International, 48: 202-8.

Williams-Woods J., González-Escalona N., Burkhardt W. 3rd (2011). Direct sequencing of hepatitis A virus and norovirus RT-PCR products from environmentally contaminated oyster using M13-tailed primers. J. Virol, Methods., 178 (1-2): 253-7.
Zhang G., Brown E. W., and Gonzalez-Escalona N. (2011) Comparison of quantitative real-time PCR, quantitative reverse transcriptase real-time PCR, loop-mediated isothermal amplification and conventional microbiological method by the U.S. Food and Drug Administration for the detection of Salmonella spp. in produce. Appl. Environ. Microbiol., 77 (18): 6495–6501.

Margarita Gomila, Ludmila Tvrzová, Andrea Teshim, Ivo Sedláček, Narjol González-Escalona, Zbyněk Zdráhal, Ondrej Šedo, Jorge Froilán González, Antonio Bennasar, Edward R. B. Moore, Jorge Lalucat and Silvia E. Murialdo (2011) Achromobacter marplatensis sp. nov., isolated from a pentachlorophenol contaminated soil. Int. J. Syst. Evol. Microbiol., 61: 2231-7.

Gonzalez-Escalona N., Strain E. A., De Jesus A. J., Jones J. L., and DePaola A (2011) Draft genome sequence of a clinical O4:K12 serotype Vibrio parahaemolyticus strain 10329. J. Bacteriol., 193 (13): 3405–6.

Rump L.V., Fischer M. and Gonzalez-Escalona N. (2011) Strains of Escherichia coli O157:H7 stepwise evolutionary model exhibit different IS629 transposition frequencies. Appl. Environ. Microbiol., 77 (14): 5030-3.

Rump L.V., Fischer M. and González-Escalona N. (2011) Prevalence, distribution and evolutionary significance of the IS629 insertion element in the stepwise emergence of Escherichia coli O157:H7. BMC Microbiol., 11:133.

Rump L. V., Strain E. A., Cao G., Allard M. W., Fischer M., Brown E. W. and González-Escalona N. (2011) Draft genome sequences of six Escherichia coli isolates from the stepwise model emergence of Escherichia coli O157:H7. J. Bacteriol., 193 (8): 2058-9.

Rebecca L. Bell, González-Escalona N., and Eric W. Brown (2011) Phylogenetic evaluation of the Typhimurium complex of Salmonella strains using a seven gene multi-locus sequence typing analysis. Infect. Gen. Evol., 11(1):83-91.

Rump L.V., Asamoah B. and Gonzalez -Escalona N. (2010) Comparison of commercial RNA extraction kits for preparation of DNA-free total RNA from Salmonella cells. BMC Res. Notes, 3 (1): 211.

Deer D., Lampel K.A. and González -Escalona N. (2010). A Versatile Internal Control for Use as DNA in Real-Time PCR and as RNA in Real-Time Reverse Transcription PCR Assays. Lett. Appl. Microbiol., 50 (4):366-72.

González-Escalona N., Hammack TS, Russell M, Jacobson AP, De Jesús AJ, Brown EW, Lampel KA (2009). Detection of live cells of Salmonella spp. in produce by a TaqMan® based quantitative RT-qPCR targeting invA mRNA. Appl. Environ. Microbiol., 75 (11): 3714-20.

C. N. Johnson, A. R. Flowers, V. C. Young, N. Gonzalez-Escalona, A. DePaola, N. F. Noriea, III, and D. J. Grimes (2009). Genetic relatedness among tdh+ and trh+ Vibrio parahaemolyticus cultured from Gulf of Mexico oysters (Crassostrea virginica) and surrounding water and sediment. Microb. Ecol., 57 (3): 437-43.

Erika Harth, Luis Matsuda, Cristina Hernández, M. Luisa Rioseco, Jaime Romero, González-Escalona N., and Romilio T. Espejo (2009). Epidemiology of Vibrio parahaemolyticus outbreaks, southern Chile. Emerg. Infect. Dis., 15 (2): 163-8.

Jie Zheng, Ph.D.

Staff Fellow
Jie.Zheng@fda.hhs.gov

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.

J. Zheng, J. Meng, S. Zhao, R. Singh and W. Song. 2008. Campylobacter-induced interleukin-8 secretion in polarized human intestinal epithelial cells requires Campylobacter-secreted cytolethal distending toxin- and Toll-like receptor-mediated activation of NF-κB. Infect. Immun. (76):4498-4508

J. Zheng, S. Cui, L. Teel, S. Zhao, R. Singh, A. O’Brien and J. Meng. 2008 Identification and characterization of shiga toxin 2 variants in Escherichia coli isolated from animals, food, and humans. Appl. Environ. Microbil. (74): 5645-5652

M. Xi, J. Zheng, S. Zhao, E.W. Brown and J. Meng. 2008 An enhanced discriminatory pulsed-field gel electrophoresis scheme for subtyping Salmonella serotypes Heidelberg, Kentucky, SaintPaul, and Hadar. J. Food Prot. (71): 2067-2072

B. Yang, J. Zheng, E.W. Brown, S. Zhao and J. Meng. 2009 Characterization of antimicrobial resistance associated integrons and mismatch-repair mutation in Salmonella serovars Int J Antimicrob Agents. (33): 120-124

J. Zheng, S. Cui and J. Meng. 2009 Effect of transcriptional Activators RamA and SoxS on expression of multidrug efflux pumps AcrAB and AcrF in fluoroquinolone-resistant Salmonella Typhimurium. J. Antimicrob Chemother (63): 95-102

X. Xia, J. Meng, P.F. McDermott, S. Ayers, . Blickenstaff, T.-T. Tran, J. Abbott, J. Zheng and S. Zhao. 2010 Presence and Characterization of Shiga Toxin-Producing Escherichia coli and Other Potentially Diarrheagenic E. coli Strains in Retail Meats. Appl. Environ. Microbil. (76): 1709-1717

J. Zheng, C.E. Keys, S. Zhao, R. Ahmed, J. Meng and E.W. Brown. 2011 Simultaneous Analysis of Multiple Enzymes Increases Accuracy of PFGE in Assigning Genetic Relationships among Homogeneous Salmonella Strains. J Clin. Microbiol. (49): 85-94

E. K. Lienau, E. Strain, C. Wang, J. Zheng, G. Cao, A. R. Ottesen, R. Stones, J. Meng, C. E. Keys, T. S. Hammack, S. M. Musser, E. W. Brown, M. W. Allard 2011 Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing New Eng. J. of Med., (364), 981-982

J. Zheng, F. Tian, S. Cui, J. Song, E. W. Brown and J. Meng. 2011 Differential gene expression by RamA in ciprofloxacin-resistant Salmonella Typhimurium. PLoS One, 6 (7): e22161. doi:10.1371/journal.pone.0022161

Ruth E. Timme, Marc W. Allard, Yan Luo, Errol Strain, James Pettengill, Charles Wang, Cong Li, Christine E. Keys, Jie Zheng, Robert Stones, Mark R. Wilson, Steven M. Musser and Eric W. Brown. Draft Genome Sequences of 21 Salmonella enterica Serovar Enteritidis Strains. J. Bacteriol. 2012, 194(21):5994

Wang, Hua; Gill, Vikas S.; Irvin, Kari A.; Byrd, Mindi; Bolger, Cathryn M.; Zheng, Jie; Dickey, Erin E.; Duvall, Robert E.; Jacobson, Andrew P.; Hammack, Thomas S. Recovery of Salmonella from Internally and Externally Contaminated Whole Tomatoes Using Several Different Sample Preparation Procedures. J. AOAC Int. 2012, 95(5): 1452-1456.

Marc W. Allard, Yan Luo, Errol Strain, James Pettengill, Ruth Timme, Charles Wang, Cong Li, Christine E. Keys, Jie Zheng, Robert Stones, Mark R. Wilson, Steven M. Musser, Eric W. Brown. 2013 On the Evolutionary History, Population Genetics and Diversity among Isolates of Salmonella Enteritidis PFGE Pattern JEGX01.0004. PLoS One, 8(1): e55254. doi:10.1371/journal.pone.0055254

Insook Son, Jie Zheng, Christine E. Keys, Shaohua Zhao, Jianghong Meng, Eric W. Brown 2013 Analysis of pulsed field gel electrophoresis profiles using multiple enzymes for predicting potential source reservoirs for strains of Salmonella Enteritidis and Salmonella Typhimurium isolated from humans. Infection, Genetics and Evolution. (16) 226-233

Jie Zheng, Sarah Allard, Sara Reynolds, Patricia Millner, Gabriela Arce, Robert J. Blogett, Eric W. Brown 2013 Colonization and Internalization of Salmonella enterica in Tomato Plants. Appl. Environ. Microbil. (79): 2494-2502.

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.

Shen, J., Rump, L., Zhang, Y., Chen, Y., Wang, X., Meng, J. 2013. Molecular subtyping and virulence gene analysis of Listeria monocytogenes isolates from food. Food Microbiology. Aug 35 (1): 58-64

Lomonaco, S., Verghese, B., Gerner-Smidt, P., Tarr, C., Gladney, L., Joseph, L., Katz, L., Turnsek, M., Frace, M., Chen, Y., Brown, E., Meinersmann, R., Berrang, M., and Knabel, S.J. 2013. Novel epidemic clones of Listeria monocytogenes, United States, 2011. , Emerging infectious diseases. Jan; 19 (1): 147

Chen, Y. Noe, K., Thompson, S., Elems, C., Brown, E.W., Lampel, K.A. and Hammack, T.S. 2012. Evaluation of a revised FDA method for the detection of Cronobacter in powdered infant formula: Collaborative Study. J. Food Prot. Jun; 75(6): 1144-7
Chen, Y., Strain, E.A., Allard, M. and Brown, E.W. 2011. Genome Sequence of Cronobacter sakazakii E899, a Strain Associated with Human Illness. J. Bacteriol. Oct; 193(20): 5861.

Verghese, B., Lok, M., Wen, J., Alessandria, V., Chen Y.,  Kathariou, S. and Knabel, S.J. 2011. comK Prophage Junction Fragments as Markers for Listeria monocytogenes Genotypes Unique to Individual Meat and Poultry Processing Plants and a Model for Rapid Niche-specific Adaptation, Biofilm Formation, and Persistence. Appl Environ Microbiol. May;77(10):3279-3292.

Chen Y., Kumar, N. and Siddique, N. 2011. Development and Evaluation of a Real-Time Polymerase Chain Reaction Assay Targeting iap for the Detection of Listeria monocytogenes in Select Food Matrices. Foodborne Pathog Dis. Oct; 8(10): 1063-1069

Chen Y., Strain, E.A., Allard, M., Brown, E.W. 2011. Genome Sequences of Listeria monocytogenes Strains J1816 and J1-220, Associated with Human Outbreaks. J Bacteriol. Jul;193(13):3424-3425.

Chen Y., Kumar, N. and Siddique, N. 2011. Incorporation of an Internal Control into the PCR Assay Published in "Development of an Improved Protocol for the Isolation and Detection of Enterobacter sakazakii (Cronobacter) from Powdered Infant Formula, J. Food Prot. 73(6):1016-1022 (2010)”. J Food Prot. Jun;74(6):872-873.

Chen, Y., Song, K.Y., Brown, E.W. and Lampel, K.A. 2010. Development of an Improved Protocol for the Isolation and Detection of Enterobacter sakazakii (Cronobacter) from Powdered Infant Formula. J. Food Prot. 73(6): 1016-1022
Hammack, T.S. and Chen, Y. 2010. General Referee Reports: Food Microbiology, Nondairy. J. AOAC Intl. 93 (1), 11B-22B

Chen, Y., Hammack, T.S. and Lampel, K.A. 2009. Evaluation of a Revised Bacteriological Analytical Manual Method for the Detection of Enterobacter sakazakii in Powdered Infant Formula: Pre-Collaborative Study. J. AOAC Intl. 92(3): 862-872.

Lomonaco, S., Chen, Y. and Knabel, S.J.. 2008. Analysis of additional virulence genes and virulence gene regions in Listeria monocytogenes confirms the epidemiologic relevance of multi-virulence-locus sequence typing. J. Food Prot. 71(12): 2559-2566

Chen, Y. and Knabel, S.J. 2008. Prophages in Listeria monocytogenes contain SNPs that differentiate outbreak clones within epidemic clones. J. Clin. Microbiol. 46(4) 1478-1484

Rebecca Bell, Ph.D.

Research Microbiologist
Rebecca.Bell@fda.hhs.gov

 

Shashi Sharma, Ph.D.

Research Microbiologist
Shashi.Sharma@fda.hhs.gov

 


 

Statistics and Bioinformatics

Errol Strain, Ph.D.

Supervisory Mathematical Statistician

James B. Pettengill, Ph.D.

Statistician

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.

Pettengill J.B., González Peña A, Bell R, Arce C, Rideout S, Allard M, Evans P, Strain E, Musser S, Knight R, Brown E, Ottesen AR. Taxonomic profiles of the co-enriching microflora associated with culture methods to detect Salmonella from tomato phyllosphere. PLoS One.

Ottesen A.R., González Peña A, White JR, Pettengill JB, Li C, Allard S, Rideout S, Allard M, Hill T, Evans P, Strain E, Musser S, Knight R, Brown E. 2013. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol. 13:114. doi: 10.1186/1471-2180-13-114.

Cao GJ, Meng JH, Strain E, Stones R, Pettengill J, Zhao SH, McDermott P, Brown E, Allard M (2013). Phylogenetics and Differentiation of Salmonella Newport Lineages by Whole Genome Sequencing. PloS One 8.

Allard M.W., Luo Y, Strain E, Pettengill JB, Timme R, Wang C, Li C, Keys CE, Zheng J, Stones R, Wilson MR, Musser SM, Brown EW. On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis. PLoS One.

Timme R.E., Allard MW, Luo Y, Strain E, Pettengill J, Wang C, Li C, Keys CE, Zheng J, Stones R, Wilson MR, Musser SM, Brown EW (2012). Draft Genome Sequences of 21 Salmonella enterica Serovar Enteritidis Strains. Journal of bacteriology 194: 5994-5995.

Pettengill J.B., McAvoy E, White JR, Allard M, Brown E, Ottesen A. 2012. Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection. BMC Research Notes 5:378.

Pettengill J.B., Moeller DA. 2012. Phylogeography of speciation: Allopatric speciation and secondary contact of sister Clarkia species. Molecular Ecology 21: 4578–4592.

Pettengill J.B., Moeller DA. 2012. Tempo and mode of mating system evolution between incipient Clarkia species.  Evolution 66: 1210–1225.

Pettengill J.B., Neel MC. 2011. A sequential approach using genetic and morphological analyses to test species status: The case of United States federally endangered Agalinis acuta (Orobanchaceae). American Journal of Botany 98: 859–871.

Pettengill, J.B., Neel MC. 2010. An evaluation of candidate plant DNA barcodes and assignment methods for diagnosing species in the genus Agalinis (Orobanchaceae). American Journal of Botany 97:1391–1406.

Pettengill J.B., Burnett RK, Neel MC. 2009. Characterization of 21 microsatellites within Agalinis acuta (Orobanchaceae) and cross–species amplification among closely related taxa. Molecular Ecology Resources 9:1375–1379.

Yan Luo

Staff Fellow
Yan.Luo@fda.hhs.gov


Staff scientists

Christine Keys

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

David Melka

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

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.

E. Kurt Lienau,. Errol Strain,. Charles Wang, B.S. Jie Zheng,., Andrea R. Ottesen, Christine E. Keys,., Thomas S. Hammack, M.S., Steven M. Musser, Eric W. Brown. Marc W. Allard, Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing New Engl. J. Med. 364, 981–982, 2011

Dwayne Roberson

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

________________________________


ORISE fellows / contractors

Maria Hoffman, Ph.D.

Postdoctoral Fellow
Maria.Hoffman@fda.hhs.gov

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.

Comparative genomic analysis of closely related Salmonella enterica Serotype Heidelberg isolated from human, retail meats and animals.
Hoffmann,, M., Zhao, S., Pettengill, J., Luo, Y., Abbott, J., Ayers, S. L., Hediye, C. N., Li, C., Monday, S. R., Allard, M. W., Whichard, J., Brown, E. W. & McDermott, P. F. (2013). Submitted.

Presence of disinfectant resistance genes in Escherichia coli isolated from retail meats in the United States.
Zou, L., Zhao, S., McDermott, P.F., Wang, F., Yang, Q., Cao, G., Hoffmann, M. & Meng, J. (2013). Submitted.

Whole genome sequencing of gentamicin-resistant Campylobacter coli isolated from U. S. retail meats reveals novel plasmid mediated aminoglycoside resistance genes.
Chen, Y., Mukherjee, S., Hoffmann, M., Kotewicz, M. L., Young, S., Abbott, J., Luo, Y., Davidson, M. K., Allard, M. W., McDermott, P. F., and Zhao, S. (2013). Accepted for publishing in Antimicrob Agents Chemother.

Genome sequences of Salmonella enterica Serovar Heidelberg isolates isolated in the United States from a multistate outbreak of human Salmonella infections.
Hoffmann, M., Luo, Y., Lafon, P. C., Timme, R., Allard, M. W., McDermott, P. F., Brown, E. W. & Zhao, S. (2012). Genome Announc 1(1):doi:10.1128/genomeA.00004-12.

Genetic and phylo-genetic evidence for horizontal gene transfer among ecologically groups of marine Vibrio. Hoffmann, M., Monday, S. R., McCarthy, P. J., Lopez, J. V., Fischer, M. & Brown, E. W. (2013). Cladistics 29(1), 46-64.

Genome sequences of five Salmonella enterica Serovar Heidelberg isolates associated with a 2011 multistate outbreak in the United States.
Hoffmann, M., Zhao, S., Luo, Y., Li, C., Folster, J. P., Whichard, J., Allard, M. W., Brown, E. W. & McDermott, P. F. (2012). J Bacteriol 194, 3274-3275.

Genetic and phylogenetic evidence for misidentification of Vibrio species within the Harveyi clade.
Hoffmann, M., Monday, S. R., Fischer, M. & Brown, E. W. (2012). Lett Appl Microbiol 54, 160-165.

Vibrio caribbeanicus sp. nov., isolated from marine sponge Scleritoderma cyanea.
Hoffmann, M., Monday, S. R., McCarthy, P. J., Lopez, J. V., Whittaker P., Naum M., Fischer, M. and Brown, E. W., (2012). Int J Syst Evol Micr 62, 1736-1743.

Population dynamics of Vibrio spp. associated with marine sponge microcosms.
Hoffmann, M., Fischer, M., Ottesen, A., McCarthy, P. J., Lopez, J. V., Brown, E. W. and Monday, S. R. (2010). ISME J 4, 1608-1612.

Evaluating the use of fatty acid profiles identify deep-sea Vibrio isolates.
Hoffmann, M., Fischer, M. and Whittaker, P. (2010). Food Chem 122, 943-950.
PCR-based method for targeting 16S-23S rRNA intergenic spacer regions among Vibrio species.
Hoffmann, M., Brown, E. W., Feng, P. C. H., Keys, C. E., Fischer, M. and Monday, S. R. (2010). BMC Microbiol 10:90.

Evaluation of multiple strains of Enterobacter sakazakii using fatty acid profiles.
Hoffmann, M., Keys, C.E., Song, K. Y., Brown, E. W., Fry, F. S. and Whittaker, P. (2008). Food Chem 107, 1623-1628.

Salmonellen in Vormarsch / Salmonella on the Rise.
Hoffman, M. 2013. In: Neue und Alte Infektionskrankheiten (Fischer, M. ed.) Springer Spektrum Research, Springer Verlag, Heidelberg Germany. In press.

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. 

Prior, N.A., Little, S.A., Pirone, C., Gill, J.E., Smith, D, Han, J., Hardie, D., O’Leary, S.J., Wagner, R.E., Cross, T., Coulter, A., Borchers, C., Olafson, R.W., and P. von Aderkas. Application of proteomics to the study of pollination drops. Applications in Plant Sciences (in press).

Cron, G., Pirone, C. Bartlett, M., Specht, C., and J. Kress. Evolution and relationships in the Strelitziaceae (Zingiberales). Systematic Botany 37(3): pp. 606–619.
*First 2 authors contributed equally

Pirone C., Quirke J.M., Johnson, J.V., Priestap H.A., and D.W. Lee. 2010. Bilirubin Present in Diverse Angiosperms. AoB plants 2010: plq 020, doi:10.1093/aobpla/plq020.

Pirone C.L., Quirke J.M., Johnson, J.V., Priestap H.A., and D.W. Lee. 2010. The
Animal Pigment Bilirubin identified in Strelitzia reginae, the Bird of Paradise Flower. Horticultural Science 45: 1411 - 1415.

Pirone C.L, Quirke J.M., Priestap H.A., and D.W. Lee. 2009. Animal Pigment Bilirubin Discovered in Plants. Journal of the American Chemical Society. 131: 2830.

Pirone, C.L., Alexander, L.C., and W.O. Lamp. 2005. Patterns of Starch Accumulation in Alfalfa Subsequent to Potato Leafhopper (Homoptera: Cicadellidae) Injury. Environmental Entomology 34 (1): 199-204.

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.

Tim Muruvanda

Bioinformatics contractor
Tim.Muruvanda@fda.hhs.gov