Food Safety Research Information Office
Title:Genomic and Proteomic Analysis of Foodborne Pathogens
Objective:

1. Conduct a functional and molecular characterization of Shiga-toxin producing Escherichia coli (STEC) with specific emphasis elucidating the responses to food-related stresses, and genomic and proteomic studies to assess changes in virulence and pathogenicity. 1A: Comparative phylogenomics and phenomics of non-O157 STEC. 1B: Examine and compare stress responses, including acid tolerance, in E. coli O157:H7 and non-O157 STEC. 1C: Role of SdiA in acid tolerance of STEC O157:H7 and non-O157 STEC. 1D: Molecular serotyping of E. coli. 1E: Methods for detection and identification of non-O157 STEC.

2: Conduct functional and molecular characterization of Campylobacter species with specific emphasis on responses to intrinsic and extrinsic stresses through genomic and proteomic studies, and examination of morphological and physiological changes. 2A: Determine the “mode of action” by which polyphosphates (extrinsic stress) enhance the survival of C. jejuni and C. coli strains. 2B: Use genomic and/or proteomic studies to molecularly characterize Campylobacter’s physiological response to food additives under poultry processing conditions. 2C: Determine if members of the microbial ecology of chicken exudates provide survival advantages/disadvantages to Campylobacter. 2D: Determine if common food additives change the composition of the microbial ecology of chicken exudate and if these changes are responsible for enhancing the survival of Campylobacter under food processing and storage conditions.

3: Conduct functional and molecular characterization of Listeria monocytogenes serotypes with specific emphasis on elucidating responses to food-related stresses through proteomics and genomics; and determining virulence differences among L. monocytogenes serotypes through sequencing and comparative genomics. 3A: Determine genes that are essential for the survival and growth of L. monocytogenes under weak organic acid conditions. 3B: Determine genetic responses of a pressure-resistant L. monocytogenes mutant exposed to the food preservative nisin. 3C: Determine genes responsible for the differences in virulence and stress responses among L. monocytogenes serotypes through sequencing, gene expression, and comparative genomics.

More Info:
Approach: The overall goal of this project is to apply comparative genomic/proteomic/phenomic technologies to understand how pathogens become resistant to food-related stresses and to uncover the genetic basis of their virulence. Three major food-borne pathogens will be investigated: Shiga toxin-producing Escherichia coli (STEC), Campylobacter species, and Listeria monocytogenes. A combination of “omics” techniques, including transcriptomics, comparative genomics, proteomics, and phenotypic arrays will be employed to analyze a large variety of strains of each of these pathogens to identify genes and proteins necessary for them to survive stresses encountered in food environments and to identify genes/mobile genetic elements necessary for them to cause human illness. Comparative genomic and gene expression techniques will be used to assess the virulence profiles of highly pathogenic non-O157 STEC strains and to determine genes responsible for the differences in virulence and stress responses among L. monocytogenes serotypes. STEC, Campylobacter spp., and L. monocytogenes will be exposed to food environments and food-processing related stresses, including acid, high pressure, exposure to antimicrobial compounds, and other stresses. In addition, we will investigate environmental stresses that affect the survival and persistence of Campylobacter spp. during poultry processing and the role that the microbial ecology of this environment plays in this process. The mechanism by which polyphosphates enhance the survival of C. jejuni and C. coli strains will be determined, and genomic and proteomic techniques will be used to molecularly characterize the physiological response of Campylobacter to food additives under poultry processing conditions. It will also be determined if members of the microbial ecology of chicken exudates provide survival advantages/disadvantages to Campylobacter. The microbiological and molecular data will aid in the development of practical preservation systems that minimize health risks and assist regulators in making science-based food safety decisions. The “omic” data will also reveal biomarkers useful for identification, molecular typing, and detection of the pathogens. Methods and platforms for molecular serotyping of E. coli and for detection and identification of non-O157 STEC will be developed. The research will expand our knowledge on the survival mechanisms of important food-borne pathogens, will provide insight into the evolution of pathogens, provide the tools to detect, identify, and type food-borne pathogens, and ultimately lead to better control strategies for STEC, Campylobacter, and L. monocytogenes in food.
Funding Source:United States Department of Agriculture (USDA), Agricultural Research Service (ARS)
Type:Appropriated
Start Date:2011
End Date:2016
Project Number:1935-42000-070-00
Accession Number:420999
Institutions:USDA/ARS - North Atlantic Area
Investigators:Fan, Xuetong
Fratamico, Pina
Gunther, Nereus (Jack)
Liu, Yanhong
Yan, Xianghe
Project Reports:2013 Annual Report
2012 Annual Report
2011 Annual Report
Pending USDA ARS Publications (NP 108):
Published Journal
Articles USDA
ARS (NP 108):
Detection of Shiga toxin-producing Escherichia coli (STEC) O157:H7, O26, O45, O103, O111, O121, and O145, and Salmonella in retail raw ground beef using the DuPont BAX system
Wasilenko JL, Fratamico PM, Sommers C, DeMarco DR, Varkey S, Phoden K, Tice G.
Front Cell Infect Microbiol. 2014 Jun 18;4:81.
Shiga toxin-producing Escherichia coli in swine: the public health perspective
Tseng M, Fratamico PM, Manning SD, Funk JA.
Anim Health Res Rev. 2014 Jun;15(1):63-75.
Shiga toxin-producing E. coli (STEC) in swine: prevalence over the finishing period and characteristics of the STEC isolates
Tseng M, Fratamico PM, Bagi L, Manzinger D, Funk JA.
Epidemiol Infect. 2014 May;8:1-10.
Detection and isolation of Shiga toxin-producing Escherichia coli (STEC) O104 from sprouts
Baranzoni GM, Fratamico PM, Rubio F, Glaze T, Bagi LK, Albonetti S.
Int J Food Microbiol. 2014 Mar 3;173:99-104.
Evaluation of a multiplex real-time PCR method for detecting Shiga toxin-producing Escherichia coli in beef and comparison to the FSIS microbiology laboratory guidebook method
Fratamico PM, Wasilenko JL, Garman B, Demarco D, Varkey S, Jensen M, Rhoden K, Tice G .
J Food Prot. 2014 Feb;77(2):180-8.
Nonlabeled quantitative proteomic comparison identifies differences in acid resistance between Escherichia coli O157:H7 curli production variants
Gunther NW 4th, Liu Y, Nunez A, Paul M, Uhlich GA.
Foodborne Pathog Dis. 2014 Jan;11(1):30-7.
Construction of Listeria monocytogenes mutants with in-frame deletions in the Phosphotransferase Transport System (PTS) and analysis of their growth under stress conditions
Liu Y, Ceruso M, Jiang Y, Datta AR, Carter L, Strain E, Pepe T, Anastasi A, Fratamico PM.
J Food Sci. 2013 Sep;78(9):M1392-8.
Gene expression profiling of a nisin-sensitive Listeria monocytogenes Scott A ctsR deletion mutant
Liu Y, Morgan S, Ream A, Huang L.
J Ind Microbiol Biotechnol. 2013 May;40(5):495-505.
Characterization and comparative analysis of a second thermonuclease from Staphylococcus aureus
Hu Y, Meng J, Shi C, Hervin K, Fratamico PM, Shi X.
Microbiol Res. 2013 Mar 30;168(3):174-82.
Fermentation optimization and antioxidant activities of mycelial polysaccharides from Morchella esculenta using soybean residues
Gang J, Fang Y, Wang Z, Liu Y.
African J Biotechnol. 2013 Mar 13;12(11):1239-49.
Full text available in the NAL Digital Collections.
How does Listeria monocytogenes combat acid conditions?
Smith JL, Liu Y, Paoli GC.
Can J Microbiol. 2013 Mar;59(3):141-52.
Detection of Shiga toxin-producing Escherichia coli in ground beef using the GeneDisc real-time PCR system
Fratamico PM, Bagi LK.
Front Cell Infect Microbiol. 2012 Dec 20;2:152.
Effect of stress on non-O157 Shiga toxin-producing Escherichia coli
Smith JL, Fratamico PM.
J Food Prot. 2012 Dec;75(12):2241-50.
Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food
Yan X, Gurtler JB, Fratamico PM, Hu J, Juneja VK.
BMC Cell Biosci. 2012 Nov 27;2(1):39.
Influence of primer sequences and DNA extraction method on detection of non-O157 Shiga toxin-producing Escherichia coli in ground beef by real-time PCR targeting the eae, stx, and serogroup-specific genes
Wasilenko JL, Fratamico PM, Narang N, Tillman GE, Ladely S, Simmons M, Cray WC Jr.
J Food Prot. 2012 Nov;75(11):1939-50.
Isolation of Shiga toxin-producing Escherichia coli serogroups O26, O45, O103, O111, O121, and O145 from ground beef using modified rainbow agar and post-immunomagnetic separation acid treatment
Tillman GE, Wasilenko JL, Simmons M, Lauze TA, Minicozzi J, Oakley BB, Narang N, Fratamico P, Cray AC Jr.
J Food Prot. 2012 Sep;75(9):1548-54.
Purification, characterization and decolorization of bilirubin oxidase from Myrothecium verrucaria 3.2190
Han X, Zhao M, Lu L, Liu Y.
Fungal Biol. 2012 Aug;116(8):863-71.
DNA sequence and analysis of a 90.1-kb plasmid in Shiga toxin-producing Escherichia coli (STEC) O145:NM 83-75
Yan X, Fratamico PM, Needleman DS, Bayles DO.
Plasmid. 2012 Jul;68(1):25-32.
pH fractionation and identification of proteins: comparing column chromatofocusing versus liquid isoelectric focusing techniques
Gunther NW IV, Paul M, Nuez A, Liu Y.
J Sep Sci. 2012 Jun;35(12):1399-405.
Application of ozonated dry ice (ALIGAL Blue Ice) for packaging and transport in the food industry
Fratamico PM, Juneja V, Annous BA, Rasanayagam V, Sundar M, Braithwaite D, Fisher S.
J Food Sci. 2012 May;77(5):M285-91.
Construction of Listeria monocytogenes mutants with in-frame deletions in putative ATP-binding cassette (ABC) transporters and analysis of their growth under stress conditions
Liu Y, Ceruso M, Pepe T, Cortesi ML, Gunther N, Fratamico P.
J Microbial Biochem Technol. 2012;4:141-6.
The expression of superoxide dismutase (SOD) and a putative ABC transporter permease is inversely correlated during biofilm formation in Listeria monocytogenes 4b G
Suo Y, Huang Y, Liu Y, Shi C, Shi X.
PLoS One. 2012;7(10):e48467.
Genes that are affected in high hydrostatic pressure treatments in a Listeria monocytogenes Scott A ctsR deletion mutant
Liu Y, Huang L, Rolf D, Joerger, Gunther NW IV.
J Microbial Biochem Technol. 2012;S2:003.
BS-KNN: An effective algorithm for predicting protein subchloroplast localization
Hu J, Yan X.
Evol Bioinform Online. 2012;8:79-87.
Prevalence, distribution, and molecular characterization of Salmonella recovered from swine finishing herds and a slaughter facility in Santa Catarina, Brazil
Kich JD, Coldebella A, Mors N, Nogueira MG, Cardoso M, Fratamico PM, Call JE, Fedorka-Cray P, Luchansky JB.
Int J Food Microbiol. 2011 Dec 15;151(3):307-13.
Detection of O antigens in Escherichia coli
DebRoy C, Roberts E, Fratamico PM.
Anim Health Res Rev. 2011 Dec;12(2):169-85.
Detection of Escherichia coli O157:H7 in food using real-time multiplex PCR assays targeting the stx1, stx2, wzyo157, and the fliCh7 or eae genes
Fratamico PM, DebRoy C.
Food Anal Methods. 2010 Dec;3(4):330-7.
Non-Journal Publications:
Detection and isolation of Shiga toxin-producing Escherichia coli (STEC) O104 and other STEC serogroups of public health concern - (Abstract Only)
(25-Mar-14)
Molecular serotyping of Escherichia coli: A verification and reclassification - (Abstract Only)
Yan, X., Fratamico, P.M., Tebbs, R., O'Connell, C., Baranzoni, G., Allred, A., Swimley, M., Debroy, C. 2014. Molecular serotyping of Escherichia coli: A verification and reclassification. Meeting Abstract. MA.
Non-O157 Shiga toxin-producing Escherichia coli - (Book / Chapter)
(24-Feb-14)
Complete genome sequence and comparison of two Shiga toxin-producing Escherichia coli O104 isolates - (Abstract Only)
Yan, X., Fratamico, P.M., Bono, J.L., Baranzoni, G., Tebbs, R., O'Connell, C. 2014. Complete genome sequence and comparison of two Shiga toxin-producing Escherichia coli O104 isolates. Meeting Abstract. MA.
DNA sequence and analysis of the O-antigen gene clusters of Escherichia coli serogroups O62, O68, O131, O140, O142, and O163 and serogroup-specific PCR assays - (Abstract Only)
Liu, Y., Fratamico, P.M., Debroy, C., Yan, X., Needleman, D.S., Li, R.W., Wang, W., Losada, L., Brinkac, L., Rodune, D., Toro, M., Meng, J. 2014. DNA sequence and analysis of the O-antigen gene clusters of Escherichia coli serogroups O62, O68, O131, O140, O142, and O163 and serogroup-specific PCR assays. Meeting Abstract. March 22-25, 2014.
Hafnia, the genus - (Book / Chapter)
Smith, J.L. 2014. Hafnia, the genus. In: Batt, C.A., Tortorello, M.L.(Eds.), Encyclopedia of Food Microbiology. Vol 2. Elsevier Ltd, Academic Press, p. 117-120.
Food safety concerns in the U.S. and research on Shiga Toxin-producing E. coli - (Proceedings)
Fratamico, P.M., Baranzoni, G. 2013. Food safety concerns in the U.S. and research on Shiga Toxin-producing E. coli. UJNR Food & Agricultural Panel Proceedings. P.
Vtec in the Usa - (Abstract Only)
Fratamico, P.M. 2013. VTEC in the USA. Meeting Abstract. MA.
Escherichia coli and other Enterobacteriaceae: Food poisoning and health effects - (Book / Chapter)
(02-Sep-13)
Shiga toxin-producing Escherichia coli - (Book / Chapter)
Smith, J.L., Fratamico, P.M., Gunther, N.W. 2014. Shiga toxin-producing Escherichia coli. Advances in Applied Microbiology. 86:145-197.
Construction of Listeria monocytogenes mutants with in-frame Deletions in the phosphotransferase transport system (PTS) and analysis of their growth under stress conditions - (Abstract Only)
Liu, Y. 2013. Construction of Listeria monocytogenes mutants with in-frame Deletions in the phosphotransferase transport system (PTS) and analysis of their growth under stress conditions. Meeting Abstract. pp.6-7.
A simulated metagenomic approach for bacterial serotyping using shotgun genome sequences coupled with O-Antigen gene cluster analysis - (Abstract Only)
Yan, X., Chen, C., Hu, J., Fratamico, P.M. 2013. A simulated metagenomic approach for bacterial serotyping using shotgun genome sequences coupled with O-Antigen gene cluster analysis. Meeting Abstract. MA.
Assessment of enhanced surveillance for non-O157 STEC in beef in the USA - (Popular Publication)
Fratamico, P.M. 2013. Assessment of enhanced surveillance for non-O157 STEC in beef in the USA. Safefood VTEC Knowledge Network E-Newsletter. safefood nig.com.
Detection of Shiga toxin-producing Escherichia coli (STEC) O157:H7, STEC serogroups O26, O45, O103, O111, O121, and O145, and Salmonella in naturally-contaminated ground beef using the BAX system-based PCR kits - (Abstract Only)
Wasilenko, J.L., Fratamico, P.M., Sommers, C.H., Demarco, D.R., Varkey, S., Rhoden, K., Tice, G. 2013. Detection of Shiga toxin-producing Escherichia coli (STEC) O157:H7, STEC serogroups O26, O45, O103, O111, O121, and O145, and Salmonella in naturally-contaminated ground beef using the BAX system-based PCR kits. Meeting Abstract. MA.
Cronobacter (Enterobacter) sakazakii - (Book / Chapter)
Accepted Publication (19-Nov-12)
Epidemiology of Shiga toxin-producing Escherichia coli (STEC) in finishing swine - (Abstract Only)
(12-Aug-12)
Detection of foodborne pathogens using microarray technology - (Abstract Only)
(11-Jun-12)
Escherichia coli O157 and other Shiga toxin producting E. coli: detection by immunomagnetic particle-based assays - (Book / Chapter)
Accepted Publication (01-Jun-12)
Advances in genomic- and proteomic-based methods to study food-borne pathogens - (Book / Chapter)
Accepted Publication (25-Apr-12)
Methods of detection and characterization of pathogenic Escherichia coli - (Book / Chapter)
Feng, P., Strockbine, N., Fratamico, P.M. 2012. Methods of detection and characterization of pathogenic Escherichia coli. In: Eds.UNESCO-EOLSS Joint Committee. Encyclopedia of Life Support Systems. Oxford,UK: Eolss Publishers. Available: http://www.eolss.net.
Pathogenic Escherichia coli - (Book / Chapter)
Accepted Publication (30-May-11)
Prevention, control, and treatment: food, animal, and human - (Abstract Only)
(07-May-12)
Pathogenic Escherichia coli - (Book / Chapter)
(30-May-11)
Food Safety Categories:Sanitation and Pathogen Control
Government Policy and Regulations
Pathogen Biology
Farm-to-Table Categories:Food processing
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