Food Safety Research Information Office
Title:Molecular Biology of Human Pathogens Associated with Food
Objective:

Objective 1: Comparative genomic analyses of Campylobacter, Arcobacter, E. coli and S. enterica to identify novel genetic elements or polymorphisms that are associated with virulence, niche specialization or other adaptive traits.

Objective 2: Develop sequence-based typing methods to detect and analyze multiple critical food-borne pathogens from multiple sources.

Objective 3: Generate gene expression profiles for E. coli, S. enterica, and Campylobacter from varying sources and in response to various environmental stresses to identify factors contributing to virulence and survival in diverse habitats.

Objective 4: Develop rapid, simple and inexpensive multiplex assays for pathogen detection and virulence characterization using novel technology for use in surveillance and outbreak epidemiology.

Objective 5: Establish proteomic approaches for detecting and typing foodborne pathogens and toxins, and measure pathogen response to environmental stresses by mass spectrometry methods.

Objective 6: Investigate mechanisms of bacterial toxicity and evaluate novel methods for inactivating Shiga toxins by developing cell-based assays for assessing toxicity and comparing the relative toxicity of Shiga toxin 1 and 2 variants.

More Info:
Approach: Our objectives address fundamental research for comparative genomic analyses of Campylobacter and Arcobacter species, and pathogenic Escherichia coli and Salmonella enterica serovars to identify novel genetic elements or polymorphisms associated within virulence, niche specialization or other adaptive traits. We will analyze the genomic data to develop sequence-based typing methods to detect and analyze multiple critical food-borne pathogens from multiple sources for purposes of improved source tracking to identify reservoirs in food production environments. The genomic data will allow us to develop methods for gene expression profiling of pathogens from different sources and their responses to various environmental stresses to identify factors contributing to virulence and survival in diverse habitats; and develop rapid, simple and inexpensive multiplex assays for pathogen detection and virulence characterization using novel technology for use in surveillance and outbreak epidemiology. The genomic data facilitate developing "top-down" and "bottom-up" mass spectrometry approaches for proteomic analysis for detecting and typing foodborne pathogens and toxins, and measuring pathogen response to environmental stresses. Non-O157 Shiga toxin-producing E. coli (STEC) strains have emerged as a source of more human illness than appreciated previously. Data for isolating and detecting them are a critical need and will be provided through this research. We also will be researching mechanisms of bacterial toxicity to develop and evaluate novel methods for inactivating Shiga toxins by developing cell-based assays for assessing toxicity and comparing the relative toxicity of Shiga toxin 1 and 2 variants. In summary, we will use the latest analytical tools to obtain data for identifying foodborne pathogens, differences in strains related to fitness and virulence, novel interventions related to toxins and, ultimately, approaches for minimizing illness associated with food.
Funding Source:United States Department of Agriculture (USDA), Agricultural Research Service (ARS)
Type:Appropriated
Start Date:2011
End Date:2016
Project Number:5325-42000-047-00
Accession Number:421039
Institutions:USDA/ARS - Pacific West Area
Investigators:Fagerquist, Clifton (Keith)
Friedman, Mendel
Lazo, Gerard
Mandrell, Robert
Miller, William
Parker, Craig
Quinones, Beatriz
Project Reports:2013 Annual Report
2012 Annual Report
2011 Annual Report
Published Journal
Articles USDA
ARS (NP 108):
Effect of structure on the interactions between five natural antimicrobial compounds and phospholipids of bacterial cell membrane on model monolayers
Nowotarska SW, Nowotarski KJ, Friedman M, Situ C.
Molecules. 2014 Jun 6;19(6):7497-515.
Description of Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles
Fitzgerald C, Tu ZC, Patrick M, Stiles T, Lawson AJ, Santovenia M, Gilbert MJ, van Bergen M, Joyce K, Pruckler J, Stroika S, Duim B, Miller WG, Loparev VL, Sinnige JC, Fields PI, Tauxe RV, Blaser MJ, Wagenaar JA.
Int J Syst Evol Microbiol. 2014 Jun 4. [Epub ahead of print]
Top-down proteomic identification of Shiga toxin 2 subtypes from Shiga toxin-producing Escherichia coli by matrix-assisted laser desorption ionization-tandem time of flight mass spectrometry
Fagerquist CK, Zaragoza WJ, Sultan O, Woo N, Quinones B, Cooley MB, Mandrell RE.
Appl Environ Microbiol. 2014 May;80(9):2928-40.
A polysaccharide isolated from the liquid culture of Lentinus edodes (shiitake) mushroom mycelia containing black rice bran protects mice against Salmonellosis through upregulation of the Th1 immune reaction
Kim SP, Park SO, Lee SJ, Nam SH, Friedman M.
J Agric Food Chem. 2014 Mar 19;62(11):2384-91.
Top-down proteomic identification of Shiga toxin 2 subtypes from Shiga toxin-producing Escherichia coli (STEC) using Matrix-Assisted Laser Desorption Ionization-Tandem Time of Flight (MALDI-TOF-TOF) mass spectrometry
Fagerquist CK, Zaragoza WJ, Sultan O, Woo N, Quinones B, Cooley MB, Mandrell RE.
Appl Environ Microbiol. 2014 Feb 28. [Epub ahead of print]
Divergent distribution of the sensor kinase CosS in non-thermophilic Campylobacter species and its functional incompatibility with the Campylobacter jejuni CosR
Hwang S, Miller WG, Ryu S, Jeon B .
PLoS One. 2014 Feb 28. [Epub ahead of print]
Use of an improved atpA amplification and sequencing method to identify members of the Campylobacteraceae and Helicobacteraceae
Miller WG, Yee E, Jolley KA, Chapman MH.
Lett Appl Microbiol. 2014 Feb 12. [Epub ahead of print]
Biological roles of the O-methyl phosphoramidate capsule modification in Campylobacter jejuni
van Alphen LB, Wenzel CQ, Richards MR, Fodor C, Ashmus RA, Stahl M, Karlyshev AV, Wren BW, Stintzi A, Miller WG, Lowary TL, Szymanski CM.
PLoS One. 2014 Jan 30;9(1):e87051.
First closed genome sequence of Campylobacter fetus subsp. venerealis bv. intermedius
Van Der Graff L, Miller WG, Yee E, Bono JL, Rijnsburger M, Campero C, Wagenaar JA, Duim B.
Genome Announc. 2014 Jan;2(1):e01246-13.
Antibacterial, antiviral, and antifungal properties of wines and winery byproducts in relation to their flavonoid content
Friedman M.
J Agric Food Chem. 2014;62(26):6025-42.
Complete genome sequence of Campylobacter fetus subsp. testudinum type strain 03-427T
Gilbert MJ, Miller WG, Yee E, Blaser MJ, Wagenaar JA, Duim B .
Genome Announc. 2013 Dec 12;1(6):e01002-13.
The need for agriculture phenotyping: "Moving from genotype to phenotype"
Boggess MV, Lippolis JD, Hurkman WJ, Fagerquist CK, Briggs SP, Gomes AV, Righetti PG, Bala K.
J Proteomics. 2013 Nov 20;93:20-39.
A polysaccharide isolated from the liquid culture of Lentinus edodes (Shiitake) mushroom mycelia containing black rice bran protects mice against a Salmonella lipopolysaccharide-induced endotoxemia
Kim SP, Park SO, Lee SJ, Nam SH, Friedman M.
J Agric Food Chem. 2013 Nov 20;61(46):10987-94.
Multi-omics approaches to deciphering a hypervirulent strain of Campylobacter jejuni
Wu Z, Sahin O, Shen Z, Liu P, Miller WG, Zhang Q.
Genome Biol Evol. 2013 Nov 6;5(11):2217-30.
Quantification and characterization of mucosa-associated and intracellular Escherichia coli in inflammatory bowel disease
Elliott TR, Hudspith BN, Wu G, Cooley MB, Parkes G, Quinones B, Randall L, Mandrell RE, Fagerquist CK, Brostoff J, Rayment NB, Boussioutas A, Petrovska L, Sanderson JD .
Inflamm Bowel Dis. 2013 Oct;19(11):2326-38.
Concentration-dependent inhibition of Escherichia coli O157:H7 and heterocyclic amines in heated ground beef patties by apple and olive extracts, onion powder and clove bud oil
Rounds L, Havens CM, Feinstein Y, Friedman M, Ravishankar S.
Meat Sci. 2013 Aug;94(4):461-7.
Antimicrobial activity of plant compounds against Salmonella Typhimurium DT104 in ground pork and the influence of heat and storage on the activity
Chen CH, Sadhana R, Marchello J, Friedman M .
J Food Prot. 2013 Jul;76(7):1264–69.
The complete genome sequence of the Arcobacter butzleri cattle isolate 7h1h
Merga J, Winstanley C, Williams NJ, Yee E, Miller WG .
Genome Announc. 2013 Jul;1(4):e00655-13.
Hericium erinaceus(Lion’s Mane)mushroom extracts inhibit metastasis of cancer cells to the lung in CT-26 colon cancer-transplanted mice
Kim S, Nam S, Friedman M.
J Agric Food Chem. 2013 May 22;61(20):4898-904.
Review of the inhibition of biological activities of food-related selected toxins by natural compounds
Friedman M, Rasooly R.
Toxins. 2013 Apr 23;5(4):743-75.
Top-down proteomic identification of bacterial protein biomarkers and toxins using MALDI-TOF-TOF-MS/MS and post-source decay
Fagerquist CK.
Reviews in Analytical Chemistry. 2013 Apr;32(2):127-33.
Antitumor effects of dietary black and brown rice brans in tumor-bearing mice: relationship to composition
Kim S, Kang M, Nam S, Friedman M.
Mol Nutr Food Res. 2013 Mar;57(3):390-400.
Progressive genome-wide introgression in agricultural Campylobacter coli
Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Meric G, Kelly DJ, Cody A, Colles FM, Strachan NJ, Ogden ID, Forbes K, French NP, Carter P, Miller WG, McCarthy ND, Owen R, Litrup E, Egholm M, Affourtit JP, Bentley SD, Parkhill J, Maiden MC, Falush D.
Mol Ecol. 2013 Feb;22(4):1051-64.
Bactericidal activities of health-promoting, food-derived powders against the foodborne pathogens Escherichia coli, Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus
Friedman M, Henika PR, Levin CE.
J Food Sci. 2013 Feb;78(2):M270-5.
Using major outer membrane protein typing as an epidemiological tool to investigate outbreaks caused by milk-borne Campylobacter jejuni isolates in California
Jay-Russell MT, Mandrell RE, Yuan J, Bates A, Manalac R, Mohle-Boetani J, Kimura A, Lidgard J, Miller WG.
J Clin Microbiol. 2013 Jan;51(1):195-201.
Exploring the diversity of Arcobacter butzleri from cattle in the UK using MLST and whole genome sequencing
Merga JY, Williams NJ, Miller WG, Leatherbarrow AJ, Bennett M, Hall N, Ashelford KE, Winstanley C.
PLoS One. 2013;8(2):e55240.
Complete genome sequence of the clinical Campylobacter coli isolate 15-537360
Pearson BM, Rokney A, Crossman LC, Miller WG, Wain J, Van Vliet AH .
Genome Announc. 2013;1(6):e01056-13.
Composition of herba pogostemonis water extract and protection of infected mice against salmonella typhimurium-induced liver damage and mortality by stimulation of innate immune cells
Kim SP, Moon E, Nam SH, Friedman M.
J Agric Food Chem. 2012 Dec 12;60(49):12122-30.
Genotypic analyses of Shiga toxin-producing Escherichia coli O157 and non-O157 recovered from feces of domestic animals in rural farms in Mexico
Amezquita-Lopez BA, Quinones B, Cooley MB, Leon-Felix J, Castro-Del Campo N, Mandrell RE, Jimenez M, Chaidez C.
PLoS One. 2012 Dec;7(12):e51565.
Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm
Fagerquist CK, Sultan O, Carter MQ.
J Am Soc Mass Spectrom. 2012 Dec;23(12):2102-14.
Hyperosmotic stress response of Campylobacter jejuni
Cameron A, Frirdich E, Huynh S, Parker CT, Gaynor EC.
J Bacteriol. 2012 Nov;194(22):6116-30.
Diversity in the protein N-glycosylation pathways within the Campylobacter genus
Nothaft H, Scott NE, Vinogradov E, Liu X, Hu R, Beadle B, Fodor C, Miller WG, Li J, Cordwell SJ, Szymanski CM.
Mol Cell Proteomics. 2012 Nov;11(11):1203-19.
Changes in free amino acid, protein, and flavonoid content in jujube (Ziziphus jujube) fruit during eight stages of growth and antioxidative and cancer cell inhibitory effects by extracts
Choi SH, Ahn JB, Kim HJ, Im NK, Kozukue N, Levin CE, Friedman M.
J Agric Food Chem. 2012 Oct 17;60(41):10245-55.
Comprehensive detection and discrimination of Campylobacter species by use of confocal micro-Raman spectroscopy and multilocus sequence typing
Lu X, Huang Q, Miller WG, Aston DE, Xu J, Xue F, Zhang H, Rasco BA, Wang S, Konkel ME.
J Clin Microbiol. 2012 Sep;50(9):2932-46.
FdhTU-modulated formate dehydrogenase expression and electron donor availability enhance recovery of Campylobacter jejuni following host cell infection
Pryjma M, Apel D, Huynh S, Parker CT, Gaynor EC.
J Bacteriol. 2012 Aug;194(15):3803-13.
A functional mathematical index for predicting effects of food processing on eight sweet potato (Ipomoea batatas) cultivars
Bersani E, Friedman M, Finotti E, Prete ED.
J Food Comp Anal. 2012 Aug;27(1):81-6.
Isolation of Campylobacter from feral swine (Sus scrofa) on the ranch associated with the 2006 Escherichia coli O157:H7 spinach outbreak investigation in California
Jay-Russell MT, Bates A, Harden L, Miller WG, Mandrell RE.
Zoonoses Public Hlth. 2012 Aug;59(5):314-9.
Antidiabetic effects of rice hull smoke extract on glucose-regulating mechanism in type 2 diabetic mice
Yang JY, Moon E, Nam SH, Friedman M.
J Agric Food Chem. 2012 Jul 17;60(30):7442–9.
Hericium erinaceus mushroom extracts protect infected mice against Salmonella Typhimurium-Induced liver damage and mortality by stimulation of innate immune cells
Kim SP, Moon E, Nam SH, Friedman M.
J Agric Food Chem. 2012 Jun 6;60(22):5590-6.
Dietary rice bran component γ-oryzanol inhibits tumor growth in tumor-bearing mice
Kim SP, Kang MY, Nam SH, Friedman M.
Mol Nutr Food Res. 2012 Jun;56(6):935-44.
A new calibrant for matrix-assisted laser desorption/ionization time-of-flight-time-of-flight post-source decay tandem mass spectrometry of non-digested proteins for top-down proteomic analysis
Fagerquist CK, Sultan O.
Rapid Commun Mass Spectrom. 2012 May 30;26(10):1241-8.
O-antigen and virulence profiling of shiga toxin-producing Escherichia coli by a rapid and cost-effective DNA microarray colorimetric method
Quiñones B, Swimley MS, Narm KE, Patel RN, Cooley MB, Mandrell RE.
Front Cell Infect Microbiol. 2012 May 11;2:61.
Structure-activity relationships of α-, β(1)-, γ-, and δ-tomatine and tomatidine against human breast (MDA-MB-231), gastric (KATO-III), and prostate (PC3) cancer cells
Choi SH, Ahn JB, Kozukue N, Kim HJ, Nishitani Y, Zhang L, Mizuno M, Levin CE, Friedman M.
J Agric Food Chem. 2012 Apr 18;60(15):3891-9.
Plant extracts, spices, and essential oils inactivate Escherichia coli O157:H7 and reduce formation of potentially carcinogenic heterocyclic amines in cooked beef patties
Rounds L, Havens CM, Feinstein Y, Friedman M, Ravishankar S.
J Agric Food Chem. 2012 Apr 11;60(14):3792-9.
Multilocus sequence typing methods for the emerging Campylobacter Species C. hyointestinalis, C. lanienae, C. sputorum, C. concisus, and C. curvus
Miller WG, Chapman MH, Yee E, On SL, McNulty DK, Lastovica AJ, Carroll AM, McNamara EB, Duffy G, Mandrell RE.
Front Cell Infect Microbiol. 2012 Apr 2;2:45.
Escherichia coli serotype O55:H7 diversity supports parallel acquisition of bacteriophage at Shiga toxin phage insertion sites during evolution of the O157:H7 lineage
Kyle JL, Cummings CA, Parker CT, Quiñones B, Vatta P, Newton E, Huynh S, Swimley M, Degoricija L, Barker M, Fontanoz S, Nguyen K, Patel R, Fang R, Tebbs R, Petrauskene O, Furtado M, Mandrell RE.
J Bacteriol. 2012 Apr;194(8):1885-96.
Antidiabetic effects of rice hull smoke extract in alloxan-induced diabetic mice
Yang JY, Kang MY, Nam SH, Friedman M.
J Agric Food Chem. 2012 Jan 11;60(1):87-94.
Rice hull smoke extract inactivates Salmonella Typhimurium in laboratory media and protects infected mice against mortality
Kim SP, Kang MY, Park JC, Nam SH, Friedman M.
J Food Sci. 2012 Jan;77(1):M80-5.
Distinct transcriptional profiles and phenotypes exhibited by Escherichia coli O157:H7 isolates related to the 2006 spinach-associated outbreak
Parker CT, Kyle JL, Huynh S, Carter MQ, Brandl MT, Mandrell RE.
Appl Environ Microbiol. 2012 Jan;78(2):455-63.
Regulation of energy metabolism by the extracytoplasmic function (ECF) σ factors of Arcobacter butzleri
Martinez-Malaxetxebarria I, Muts R, van Dijk L, Parker CT, Miller WG, Huynh S, Gaastra W, van Putten JP, Fernandez-Astorga A, Wösten MM.
PLoS One. 2012;7(9):e44796.
Genome sequence of E. coli O104:H4 leads to rapid development of a targeted antimicrobial agent against this emerging pathogen
Scholl D, Gebhart D, Williams SR, Bates A, Mandrell R.
PLoS One. 2012;7(3):e33637.
Free amino acid and phenolic contents and antioxidative and cancer cell-inhibiting activities of extracts of 11 greenhouse-grown tomato varieties and 13 tomato-based foods
Choi SH, Kim HR, Kim HJ, Lee IS, Kozukue N, Levin CE, Friedman M.
J Agric Food Chem. 2011 Dec 28;59(24):12801-14.
Prevalence and molecular characterization of Escherichia coli O157:H7 by multiple-locus variable-number tandem repeat analysis and pulsed-field gel electrophoresis in three sheep farming operations in California
Kilonzo C, Atwill ER, Mandrell R, Garrick M, Villanueva V, Hoar BR.
J Food Prot. 2011 Sep;74(9):1413-21.
Distribution of free amino acids, flavonoids, total phenolics, and antioxidative activities of Jujube (Ziziphus jujuba) fruits and seeds harvested from plants grown in Korea
Choi SH, Ahn JB, Kozukue N, Levin CE, Friedman M.
J Agric Food Chem. 2011 Jun 22;59(12):6594-604.
Mechanism of Hericium erinaceus (Yamabushitake) mushroom-induced apoptosis of U937 human monocytic leukemia cells
Kim SP, Kang MY, Choi YH, Kim JH, Nam SH, Friedman M.
Food Funct. 2011 Jun;2(6):348-56.
Application of a functional mathematical index for antibacterial and anticarcinogenic effects of tea catechins
Finotti E, Bersani E, Friedman M.
J Agric Food Chem. 2011 Feb 9;59(3):864-9.
Application of a Functional Mathematical Quality Index to Asparagine, Free Sugar and Phenolic Acid Content of 20 Commercial Potato Varieties
Bersani E, Friedman M, Finotti E, Vivanti V.
J Food Qual. 2011 Feb;34(1):74-9.
Non-Journal Publications:
Two Shiga toxin 2 subtypes in a single Shiga toxin-producing Escherichia coli analyzed by RT-qPCR, MALDI-TOF-TOF-MS and top-down proteomic analysis - (Proceedings)
(06-Jun-14)
The microbiome structure and Campylobacter jejuni transcriptome in naturally-raised chickens - (Abstract Only)
(21-Feb-14)
Antimicrobial resistance in Escherichia coli O157 and non-O157 isolated from feces of domestic farm animals in Culiacan, Mexico- (Abstract Only)
(21-Feb-14)
Whole Genome Shotgun Analysis: the Resolving Power to Distinguish 2009 and 2010 Clinical Isolates of Salmonella Typhimurium Possessing the Same PFGE Type - (Abstract Only)
Accepted Publication (05-Aug-13)
Hypervariable purine biosynthesis genes contribute to stress response population heterogeneity in Campylobacter jejuni - (Abstract Only)
Accepted Publication (11-Jun-13)
The complete genome sequences of 65 Campylobacter jejuni and C. coli strains - (Abstract Only)
Accepted Publication (31-May-13)
Detection of Shiga toxin variants, virulence genes and the relationship to cytotoxicity in Shiga toxin-producing Escherichia coli (STEC) from domestic farm animals - (Abstract Only)
Accepted Publication (26-Mar-13)
Low-Density microarray technologies for rapid human norovirus genotyping - (Abstract Only)
Accepted Publication (06-Mar-13)
Whole-Genome Sequencing Reveals Laboratory Salmonella Typhimurium Strain 14028s as a Likely Source of Outbreak Isolates from 2009-2010 - (Abstract Only)
Accepted Publication (20-Feb-13)
Evidence of norovirus (NV)in a major produce production region watershed and a low density microarray strategy for detecting NV(Abstract) - (Abstract Only)
Accepted Publication (25-Oct-12)
Shiga toxin-producing Escherichia coli: importance, outbreaks, and characterization methods - (Proceedings)
Accepted Publication (06-Oct-12)
Microarrays for foodborne virus detection and typing(Abstract) - (Abstract Only)
Accepted Publication (25-Sep-12)
Distinct PFGE and MLVA Genotypes of Shiga Toxin-Producing Escherichia coli (STEC)Recovered from Feces of Farm Animals in the Culiacan Valley, Mexico(Abstract) - (Abstract Only)
Accepted Publication (23-Mar-12)
Selective recovery by different culture methods of Shiga toxin-producing Escherichia coli genotypes from a major produce production region in California(Abstract) - (Abstract Only)
Accepted Publication (22-Mar-12)
Genomics and isolation of emerging CHRO species - (Proceedings)
Accepted Publication (10-Aug-11)
Characterization of the extrachromosomal function (ECF) sigma factors of Arcobacter butzleri - (Abstract Only)
Accepted Publication (10-Aug-11)
Hybrid speciation in agricultural Campylobacter coli - (Abstract Only)
Accepted Publication (10-Aug-11)
O-Methyl Phosphoramidate Modifications on the Capsular Polysaccharide of Campylobacter Jejuni are Involved in Serum Resistance, Infection, and Insecticidal Activity - (Abstract Only)
Accepted Publication (10-Aug-11)
Mechanisms underlying zoonotic success of Campylobacter jejuni: the CprRS two-component regulatory system influences essential processes, biofilm formation, and pathogenesis - (Abstract Only)
Accepted Publication (01-Jun-11)
The civRT operon is important for Campylobacter jejuni strain 81-176 host cell interactions through regulation of the formate dehydrogenase operon - (Abstract Only)
Accepted Publication (01-Jun-11)
Mechanisms underlying zoonotic success of Campylobacter jejuni: the CprRS two-component regulatory system influences essential processes, biofilm formation, and pathogenesis - (Abstract Only)
Accepted Publication (21-Apr-11)
Insights into Evolution of Escherichia coli O157:H7 from Complete Genome Sequence of Closely Related O55:H7 Precursor - (Abstract Only)
Accepted Publication (24-Mar-11)
The atypical hyperosmotic stress response of Campylobacter jejuni - (Abstract Only)
Accepted Publication (11-Mar-11)
Genotypic Characterization of Shiga Toxin-Producing Escherichia coli (STEC) Strains Recovered from Farm Animal Feces in Mexico - (Abstract Only)
Accepted Publication (28-Feb-11)
Use of Photopolymerization for Genotyping Shiga Toxin-Producing Escherichia coli Recovered from Produce Production Regions in California - (Abstract Only)
Accepted Publication (28-Feb-11)
Food Safety Categories:Pathogen Biology
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