Supplementary Materials for Manuscripts

Supplementary Materials are organized by year below.

  • Beno et al., 2017, J. Dairy Sci. (Submitted) 
    Beno, S. M., H. A. Brooks, R. H. Orsi, D. J. Kent, L. M. Carroll, S. J. Reichler, J. Kovac, S. Tang, N. H. Martin, K. J. Boor, and M. Wiedmann. 2017. Characterization of Paenibacillus odorifer isolates reveals psychrotolerance is not associated with phylogeny.
    • Supplemental Table 1: List of 101 isolates tested in the initial screen and associated growth data for all isolates in Skim Milk Broth (SMB) at 6°C
    • Supplemental Table 2: Twelve protein domains previously associated with growth at low temperatures used for Hidden Markov Model (HMM) analyses
    • Supplemental Table 3: Detailed information on the 58 Paenibacillus isolates and 3 Viridibacillus isolates characterized by whole genome sequencing.
    • Supplemental Table 4: Growth data for 28 Paenibacillus isolates (25 P. odorifer and 3 closely related) in four media/temperature combinations.
    • Supplemental Table 5: Hidden Markov Model (HMM) results for 25 P. odorifer and 3 closely related isolates
    • Supplemental Table 6: OrthoMCL results: List of genes enriched in phylogenetic A
    • Supplemental Table 7: OrthoMCL results: List of genes enriched in phylogenetic clade B
    • Supplemental Table 8: OrthoMCL results: List of GO terms enriched in phylogenetic clade A
    • Supplemental Table 9: OrthoMCL results: List of GO terms enriched in phylogenetic clade B
  • Beno et al., 2017, J. Dairy Sci. (Submitted) 
    Beno, S. M.,  R. H. Orsi, D. J. Kent, J. Kovac, R. A. Miller, N. H. Martin, and M. Wiedmann. 2017. A number of genes are associated with psychrotolerant Bacillus cereus group isolates.
  • Weller, et al., 2017.  J. of Food Prot. (submitted)
    Daniel L. Weller, Jasna Kovač, Sherry Roof, David J. Kent, Jeff I. Tokman, Barbara Kowalcyk, David Oryang, Renata Ivanek, Anna Aceituno, Christopher Sroka, and Martin Wiedmann. 2016. Survival of Escherichia coli on lettuce under field conditions encountered in the Northeastern United States.  
    • Supplemental Materials S1: This field study was conducted in a romaine lettuce (Lactuca sativa L. var. longifolia cv. Green Towers; Harris Seeds, Rochester NY) field at the Homer C. Thompson Vegetable Research Farm in Freeville, New York. The field consisted of an 8.5 m x 59.5 m planted area (1A) with 5 longitudinal beds separated by 0.6 m furrows (1B). Each bed consisted of 4 rows of seed planted 0.4 m apart (20 rows in total; 1C). The field was surrounded by a bare ground buffer of at least 3.1 m on each side (1A).
    • Supplemental Materials S2: The R script used to implement the method outlined by Cochran to calculate the most probable number of E. coli cells per sample.
    • Supplemental Materials S3: Weather conditions for the day of lettuce head inoculation, and 1-9 d after lettuce head inoculation.
  • Beno, et al., 2016.  J. of Food Prot. (submitted)
    Beno, S. M., M. J. Stasiewicz, A. D. Andrus, R. D. Ralyea, D. J. Kent, N. H. Martin, M. Wiedmann, and K. J. Boor. 2016. Development and validation of pathogen environmental monitoring programs for small cheese processing facilities. 
    • sjl38 [at] cornell.edu (subject: Beno%202016%20Supplementary%20Table%20S1) (Supplemental Material Table S1 pdf):  Routine monthly sample sites tested for Listeria spp. and L. monocytogenes, organized by facility. 
    • Ho, et al., 2016.  J. of Pub. Health Mgmt. (submitted)
      Ho, Alphina DVM; Pennell-Huth, Paula MPH; Newman, Alexandra DVM, MPH; Zansky, Shelley PhD; Wiedmann, Martin Dr med vet, PhD. 2016. Foodborne illness outbreak investigation training needs: a survey among state public health staff in the Northeast and Mid-Atlantic United States.
      • sjl38 [at] cornell.edu (subject: Ho%202016%20Supplemental%20Table%20S1) (Supplemental Table S1 pdf: ) Raw data and analysis for "General Planning and Preparedness" topics. 
      • sjl38 [at] cornell.edu (subject: Ho%202016%20Supplemental%20Table%20S2) (Supplemental Table S2 pdf:) Raw data and analysis for "Challenges in Foodborne Outbreak Investigations" topics.
      • sjl38 [at] cornell.edu (subject: Ho%202016%20Supplemental%20Table%20S3) (Supplemental Table S3 pdf:) Raw data and analysis for "Needs in Food Safety Core Competency Training" topics.
      • sjl38 [at] cornell.edu (subject: Ho%202016%20Supplemental%20Table%20S4) (Supplemental Table S4 pdf:) Raw data and analysis for "Training Formats".

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    • Ryan et al. 2015. J. Food Prot. (submitted)
      Ryan, G.T., S. Roof, L. Post, M. Wiedmann. 2015. Evaluation of rapid molecular detection assays for Salmonella in challenging food matrices at low inoculation levels and using difficult to detect strains. J. Food Prot.
      • sjl38 [at] cornell.edu (subject: Ryan%202015%20Supplementary%20Tables) (Supplementary Tables pdf):  Description of strain information (Table S1); Detailed analysis of unpaired samples (Table S2) and paired samples (Table S3) for Salmonella in dry pet food and dark chocolate.

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    • Weller et al.  2014. J. Food Sci. Edu.
      Weller, D., Robbins, J., Elmore, A., and Wiedmann, M.  2014. Master of Professional Studies in Agriculture and Life Science offered through the Field of Food Science and Technology at Cornell University:  A Model for the Development of a Course-Based Graduate Degree in Food Science and Technology.  J. Food Sci. Edu.
      • sjl38 [at] cornell.edu (subject: Weller%202014%20Alumni%20Questionnaire%20Supplementary%20Materials) (Alumni Questionnaire pdf)
    • Chapin et al.  2014. J. Food Prot.
      Chapin, T.C., K.K. Nightingale, R.W. Worobo, M. Wiedmann, L.K. Strawn.  2014.  Prevalence and Remotely-sensed Predictors of Listeria species Detected in Produce Preharvest and Natural Environments.  J Food Prot.
      • sjl38 [at] cornell.edu (subject: Chapin%202014%20Supplemental%20Table%20S1) (Supplemental Table S1 pdf):  Names, Descriptions, and Units of Measurement (where applicable) of the Variables Used in the RandomForest Models (Produce Preharvest and Natural Environments)
    • Weller et al.  2015. J. Food Prot. (submitted 2014)
      Daniel Weller, Martin Wiedmann, Laura K. Strawn.  2015.  Irrigation is Significantly Associated with an Increased Prevalence of Listeria monocytogenes in Produce Production Environments in New York State.  J Food Prot.
      • sjl38 [at] cornell.edu (subject: Weller%202014%20Supplemental%20Table%20S1) (Supplementary Table S1 pdf):  Description of the environmental factors used for univariate analysis and model development.

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    • Fortes et al. 2013. J. Food Prot. (in press)
      Fortes, E.D., J. David, R. Koeritzer and M. Wiedmann. 2013. Validation of the 3M Molecular Detection System for the Detection of Listeria in Meat, Seafood, Dairy, and Retail Environments. J Food Prot (in press; #: JFP-12-552).
      • Supplemental Table S1: Detailed results for (i) eight samples where cultural methods and 3M Molecular Detection System results did not coincide and (ii) four samples that were positive by the 3M Molecular Detection System only, but these results were deemed to represent cross-contamination events.
    • Stasiewicz et al. 2014. J. Food Prot (submitted 2013)
      Stasiewicz, M.J., N. Martin, S. Laue, Y.T. Grohn, K.J. Boor, and M. Wiedmann. 2014. Responding to bioterror concerns by increasing milk pasteurization temperature would increase estimated annual deaths from listeriosis.  J. Food Prot.
      • sjl38 [at] cornell.edu (subject: Stasiewicz%202013%20Supplementary%20Materials) (Supplementary Materials pdf) includes Supplemental Figure Legends, Supplemental Figures S1-S4, and Supplemental Tables S1-S3.
    • Soyer et al. 2013. J. Food Prot.
      Soyer, Y., Richards, J., Hoelzer, K., Warnick, L. D., Fortes, E., McDonough, P., Dumas, N.B., Grohn, Y.T. and M. Wiedmann. 2013. Antimicrobial drug resistance patterns among cattle and human associated Salmonella. Journal of Food Protection.
      • sjl38 [at] cornell.edu (subject: Soyer%202013%20Supplemental%20Table%20%28ST1%29%201) (Supplemental Table 1 pdf). All isolates included in this study.
      • sjl38 [at] cornell.edu (subject: Soyer%202013%20Supplemental%20Table%20%28ST2%29%202) (Supplemental Table 2 pdf)Salmonella isolates tested for antimicrobial resistance genes.
      • sjl38 [at] cornell.edu (subject: Soyer%202013%20Supplemental%20Table%20%28ST3%29%203) (Supplemental Table 3 pdf). Primers.
      • sjl38 [at] cornell.edu (subject: Soyer%202013%20Supplemental%20Table%20%28ST4%29%204) (Supplemental Table 4 pdf). parC and gyrA mutations found among three nalidixic acid resistant and six nalidixic acid sensitive isolates.
    • sjl38 [at] cornell.edu (subject: 2013%20Supplemental%20Material%20Vangay%20Quest%201) (Vangay, P. - Risk Analysis - Questionnaire 1 pdf)
    • sjl38 [at] cornell.edu (subject: 2013%20Supplemental%20Material%20Vangay%20Quest%202) (Vangay, P. - Risk Analysis - Questionnaire 2 pdf)

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    • Ivy, et al. 2013. J. Food Prot. (submitted 2012)
      Ivy RA, Farber JM, Pagotto F, Wiedmann M. 2013. International Life Science Institute North America Cronobacter (Formerly Enterobacter sakazakii) isolate set. Journal of Food Protection.
      • sjl38 [at] cornell.edu (subject: Ivy%202012%20Supplemental%20Table%20S1) (Supplemental Table S1 pdf:) Allelic assignments using 7-gene multilocus sequence typing.
      • sjl38 [at] cornell.edu (subject: Ivy%202012%20Supplemental%20Figure%20S1) (Supplemental Figure S1 pdf:) Maximum parsimony phylogenic tree of partial 16S rDNA sequences of isolates in the ILSI NA Cronobacter collection and relevant type strains.
    • Malley, et al. 2013. J. Food Prot. (submitted 2012)
      Thomas J. V. Malley, Matthew Stasiewicz, Yrjö T. Gröhn, Sherry Roof, Steven Warchocki, Kendra Nightingale and Martin Wiedmann. 2013. Implementation of statistical tools to support identification and management of persistent Listeria monocytogenes contamination in smoked fish processing plants. J Food Prot.
      • sjl38 [at] cornell.edu (subject: Malley%202012%20Supplemental%20Figure%201) (Supplemental Figure 1 pdf:)  This file contains results of L. monocytogenes  isolation and ribotyping results for 6- and 12-month baseline samples for plant D.
      • sjl38 [at] cornell.edu (subject: Malley%202012%20Supplemental%20Figure%202) (Supplemental Figure 2 pdf:)  This file contains results of L. monocytogenes  isolation and ribotyping results for 6- and 12-month baseline samples for plant N.

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    • Ivy et al. 2010.  Foodborne Pathogens and Disease. 7(11): 1337-1349
      • Table S1.  Primers used for the construction of response regulator null mutants
      • sjl38 [at] cornell.edu (subject: Ivy%202010%20Supplemental%20Table%20S2) (Table S2 pdf.)  Summary of gene deletion effects on transcription levels of various Listeria monocytogenes stress and virulence genes
    • Bergholz, et al 2010. Salt Stress Phenotypes in Listeria Monocytogenes/Vary by Genetic Lineage and Temperature
      • Table S1: This file contains initial cell density, lag phase duration, maximum growth rate, and final cell density values for each of the 40 /L. monocytogenes/ strains grown in BHI and BHI + 6% NaCl, at 7 and 37C.
    • sjl38 [at] cornell.edu (subject: Hoelzer%202010%20Supplemental%20Quest%201) (Hoelzer, Karin - Risk Analysis, Questionnaire 1 pdf)
    • sjl38 [at] cornell.edu (subject: Hoelzer%202010%20Supplemental%20Quest%202) (Hoelzer, Karin - Risk Analysis, Questionnaire 2 pdf)

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    • Soyer et al, 2009, BMC Evolutionary Biology 9:264
      Soyer, Y., R.H. Orsi, L. Rodriguez, Q. Sun, and M. Wiedmann. 2009. Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes. BMC Evolutionary Biology BMC Evol Biol. 2009 Nov 14:9:264.
      • sjl38 [at] cornell.edu (subject: Soyer%202009%20Supplemental%20Additional%20File%201) (Additional File 1 pdf:)  Salmonella Isolates (n=42) Used
      • sjl38 [at] cornell.edu (subject: Soyer%202009%20Supplemental%20Additional%20File%202) (Additional File 2 pdf:)  PCR Conditions and Primers for the Four Genes
      • sjl38 [at] cornell.edu (subject: Soyer%202009%20Supplemental%20Additional%20File%203) (Additional File 3 pdf:)   Detailed Information for 81 Genes Which Showed Evidence for Positive Selection from Initial Analysis
      • sjl38 [at] cornell.edu (subject: Soyer%202009%20Supplemental%20Additional%20File%204) (Additional File 4 pdf:)  Detailed Information for 41 Genes Which Showed Evidence for Positive Selection from Initial Analysis
      • Additional File 5:  Alignments for Genes under Positive Selection
    • Sauders et al, 2009, J. Food Prot (submitted)
      Sauders, B. D., D. Sanchez, D. H. Rice, J. Corby, S. Stich, E. D. Fortes, S. E. Roof, and M. Wiedmann, 2009.   Prevalence and Molecular Diversity of Listeria monocytogenes in Retail Establishments.  J. Food Prot. (submitted).
      • sjl38 [at] cornell.edu (subject: Sauders%202009%20Supplemental%20Figure%201) (Supplemental Figure 1 pdf:)  PFGE patterns for L. monocytogenes isolates from five establishments where L monocytogenes was isolated on two separate samplings.
      • sjl38 [at] cornell.edu (subject: Sauders%202009%20Supplemental%20Figure%202) (Supplemental Figure 2 pdf:)  Correlation between establishment size (in sq ft; panel A) and employee numbers (panel B) and L. monocytogenes prevalence found in our study.
      • sjl38 [at] cornell.edu (subject: Sauders%202009%20Supplemental%20Table%201) (Supplemental Table 1 pdf:)  Basic characteristics of the 121 retail establishments included in this study.
      • sjl38 [at] cornell.edu (subject: Sauders%202009%20Supplemental%20Table%202) (Supplemental Table 2 pdf:)  List of all 121 establishments with L. monocytogenes isolates and ribotypes isolated.
    • Soyer et al. 2009.  Foodborne Pathogens and Disease 2010 Jun;7(6):707-17
      • Supplemental Table 1. Salmonella isolates (n=335) used in this study  
      • Supplemental Table 2. Detailed information for clinical bovine Salmonella isolates collected from farms at multiple visits  
      • sjl38 [at] cornell.edu (subject: Soyer%202009%20Supplemental%20Figure%201) (Supplemental Figure 1 pdf). PFGE patterns, for isolates from farms 524, 490, 259, 584, and 510, which show closely related PFGE patterns and identical STs
      • sjl38 [at] cornell.edu (subject: Soyer%202009%20Supplemental%20Figure%202) (Supplemental Figure 2 pdf.) Geographical  associations of human and bovine isolates with PFGE types that were found among both humans and cattle
    • Stasiewicz et al. 2009: Journal of Food Protection. 73(4):631-40
      Matthew J. Stasiewicz, Teresa Bergholz, and Martin Wiedmann, The Combination of Lactate and Diacetate Synergisticallly Reduces Cold Growth in BHI Broth Across Listeria monocytogenes Lineages.  J Food Prot. 2010 Apr; 73(4):631-40
      • sjl38 [at] cornell.edu (subject: Stasiewicz%202009%20Supplemental%20Table%20S1) (Supplemental Table S1 pdf:)  This file contains initial cell density, lag phase duration, maximum growth rate, and final cell density values for each of the thirteen L. monocytogenes strains grown in the presence or absence of sodium diacetate and/or sodium lactate.
      • sjl38 [at] cornell.edu (subject: Stasiewicz%202009%20Supplemental%20Table%20S2) (Supplemental Table S2 pdf:)  This file contains correlation coefficients for all pairs of growth parameters for the overall data set, as well as for each individual growth inhibitor treatment

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    • Ollinger et al. 2008. Foodborne Path and Dis 5: 281-293
      • sjl38 [at] cornell.edu (subject: Ollinger%202008%20Supplemental%20Table%20S1) (Supplemental Material Table S1 pdf.) Statistical analyses determining the effects of strain, condition, and interactions between strain and conditions on transcript levels for different group I, II, and III genes  
      • sjl38 [at] cornell.edu (subject: Ollinger%202008%20Supplemental%20Figure%20S1) (Supplemental Figure S1 pdf.) Transcript levels for the group II genes (a) lmo0178 and (b) lmo0278 in the L. monocytogenes parent strain 10403S and isogenic ΔsigB, ΔprfA, and ΔsigBΔprfA strains.  
      • sjl38 [at] cornell.edu (subject: Ollinger%202008%20Supplemental%20Figure%20S2) (Supplemental Figure S2 pdf.) Transcript levels for the group I gene plcA in the L. monocytogenes parent strain 10403S and isogenic ΔsigB, ΔprfA, and ΔsigBΔprfA strains .  
      • sjl38 [at] cornell.edu (subject: Ollinger%202008%20Supplemental%20Figure%20S3) (Supplemental Figure S3 pdf.) Transcript levels for the group III genes (a) opuCA, (b) bsh, (c) lmo0596, and (d) lmo0654 in the L. monocytogenes parent strain 10403S and isogenic ΔsigB, ΔprfA, and ΔsigBΔprfA strains
    • McGann et al. 2008 Foodborne Path and Dis 5:417-35
      • sjl38 [at] cornell.edu (subject: McGann%202008%20Supplemental%20Table%20S1) (Supplemental Table S1 pdf.) Sequencing primers used in this study  
      • sjl38 [at] cornell.edu (subject: McGann%202008%20Supplemental%20Table%20S2) (Supplemental Table S2 pdf.) 70-mer oligonucleotides used for microarray expression analysis  
      • sjl38 [at] cornell.edu (subject: McGann%202008%20Supplemental%20Table%20S3) (Supplemental Table S3 pdf.) TaqMan primers and probes used in this study  
      • sjl38 [at] cornell.edu (subject: McGann%202008%20Supplemental%20Table%20S4) (Supplemental Table S4 pdf.) Summary of data from the internalin and internalin-like genes that did not show consistent, significant changes in transcript levels between both probes and/or between both array blocks
    • Orsi et al. 2008 BMC Genomics 9:539
      • Supplemental Material. Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.
    • Orsi et al. 2008 Infection, Genetics and Evolution 8: 566-576
      • sjl38 [at] cornell.edu (subject: Orsi%202008%20Supplemental%20Table%201) (Supplementary Table 1 pdf.) L. monocytogenes isolates used and their characteristics.  
      • sjl38 [at] cornell.edu (subject: Orsi%202008%20Supplemental%20Table%202) (Supplementary Table 2 pdf.) PCR primers used for L. monocytogenes prfA cluster sequencing  
      • sjl38 [at] cornell.edu (subject: Orsi%202008%20Supplemental%20Table%203) (Supplementary Table 3 pdf.) Recombination events identified by GENECONV
    • Pradhan et al. 2008 Food Prot 72: 978-989
      Abani Pradhan, Renata Ivanek, Yrjö T. Gröhn, Ifigenia Geornaras, John Sofos, and Martin Wiedmann. 2008. Quantitative Risk Assessment for Listeria monocytogenes in Selected Categories of Deli Meats: Impact of Lactate-Diacetate on Listeriosis Cases. J. Food Prot. 72: 978-989
      • Risk assessment models: This links to a ZIP file which contains all the programs and files needed to run the risk assessment described in this manuscript.
      • sjl38 [at] cornell.edu (subject: Pradhan%202008%20Read-me%20file) (Read-me file pdf:) This read me file provides the instructions for how to install and run the programs and files contained in the ZIP file.
      • Data file: This file contains kinetic parameters (exponential growth rate and  lag time) data for selected categories of deli meats formulated with or without growth inhibitors, used in this risk assessment.

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    • sjl38 [at] cornell.edu (subject: Jia%202007%20Supplemental%20Table%201) (Jia et al., 2007 Foodborne Pathogens and Disease 4:222-232 pdf)
    • Nightingale et al., 2007; J. Food Prot. 70:482-488
      ​K. K. Nightingale*, S. R. Milillo, R. A. Ivy, A. J. Ho, H. F. Oliver, and M. Wiedmann 2006. Appl. Enviro.Microbiol Listeria monocytogenes F2365 is characterized by an elevated frequency of truncated genes, including inlB, and by unique phenotypic characteristics that limit its appeal to represent human outbreak associated strains.
    • Nightingale et al., 2007, J. Microbiol. Meth. 68:52-59
      Kendra Nightingale, Liselle Bovell, Ashley Grajczyk, and Martin Wiedmann. 2006. Combined DNA sequencing and multiplex PCR provides a good alternative to conventional serotyping of Listeria monocytogenes isolates and differentiates serotype 4b isolates belonging to lineages I and III. J. Microbiol. Meth.
      • sjl38 [at] cornell.edu (subject: Nightingale%202007%20Supplemental%20Table%201) (Supplemental Table 1 pdf.)
    • Fugett et al., 2007. J. Clin. Microbiol. 45:865-873
      Fugett, E. B., D. Schoonmaker-Bopp, N. B. Dumas, J. Corby, and M. Wiedmann. 2006. Pulsed-field gel electrophoresis analysis of temporally matched Listeria monocytogenes isolates from human clinical cases, foods, ruminant farms, and urban and natural environments reveals source associated as well as widely distributed PFGE types. J. Clin. Micro. (in preparation)
      • sjl38 [at] cornell.edu (subject: Fugett%202007%20Supplemental%20Table%20ST1) (Supplemental Table ST1 pdf)  Listeria monocytogenes isolates.
      • sjl38 [at] cornell.edu (subject: Fugett%202007%20Supplemental%20Figure%20S1) (Supplemental Figure S1 pdf)   Geospatial and source distributions of PFGE types occurring at least 5 times. Source abbreviations are as follows: H, human; Fd, food; Fm, farm; E, environmental. All foods except those denoted with an asterisk (*) are ready-to-eat. Dates of isolation are given as month/year.
    • Chan et al. 2007. J. Food Prot. 71:420-5 Y. C. Chan, Y. Hu, S. Chaturongakul, K. D. Files, B. M. Bowen, K. J. Boor, and M. Wiedmann.  2007.  Contributions of Two Component Regulatory Systems, Alternative σ Factors, and Negative Regulators to L. monocytogenes Growth at Low Temperature.  J. Food Prot. (submitted)
      • sjl38 [at] cornell.edu (subject: Chan%202007%20Supplemental%20Table%20S1) (Supplemental Table S1 pdf.)  Primers used for generation of null mutants not reported in published manuscripts.
      • Supplemental Figure S1.  Growth of L. monocytogenes strain 10403S and null mutants between 0 and 12 days at 4°C using a starting inoculum of 10^8 CFU/mL. 
      • Supplemental Figure S2. Growth in BHI over 12 days at 4°C of L. monocytogenes strain 10403S and selected null mutant strains, using a starting inoculum of 10^8 CFU/ml. 
      • Supplemental Figure S3.  Growth in BHI over 84 days at 4°C of L. monocytogenes strain 10403S and selected null mutant strains using a starting inoculum of 10^2 CFU/mL. 
      • Supplemental Figure S4.  Growth in BHI over 12 days at 4°C of cold-adapted L. monocytogenes strain 10403S and selected null mutants, using a starting inoculum of 10^8 CFU/ml.

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    • Pohl et al 2006. Am. J. Vet. Res. 67: 616-626
      Pohl, M. A., K. K. Nightingale, M. Wiedmann. 2006. Listeria monocytogenes genotypes are associated with distinct clinical manifestations of listeriosis in cattle. American Journal of Veterinary Research 67(4): 616-626.
      • sjl38 [at] cornell.edu (subject: Pohl%202006%20Supplemental%20Table%20S1) (Supplemental Table S1 pdf). Summary of analysis for variable dN/dS ratios among sites
      • sjl38 [at] cornell.edu (subject: Pohl%202006%20Supplemental%20Table%20S2) (Supplemental Table S2 pdf). Summary of actA sites deemed to have undergone positive selection
      • sjl38 [at] cornell.edu (subject: Pohl%202006%20Supplemental%20Table%20S3) (Supplemental Table S3 pdf).   Summary of inlA sites deemed to have undergone positive selection
    • Tsai et al. 2006. Infection, Genetics and Evolution 6:378-389.
      Tsai, Y-H. L., R. H. Orsi, K. K. Nightingale and M. Wiedmann. 2005. Listeria monocytogenes internalins are highly diverse and evolved by intragenic recombination and positive selection. Infection, Genetics and Evolution (e-pub)
      • sjl38 [at] cornell.edu (subject: Tsai%202006%20Supplemental%20Table%20S1) (Supplementary Table S1 pdf).  Genetic characteristics of the 40 Listeria monocytogenes isolates included in this study.
      • sjl38 [at] cornell.edu (subject: Tsai%202006%20Supplemental%20Table%20S2) (Supplementary Table S2 pdf).  Primers used for PCR amplification and sequencing.
    • Garner et al., 2006. Appl. Environ. Micro. 72:5384-5395
      M. R. Garner, K. E. James, M.C. Callahan, M. Wiedmann, and K. J. Boor. 2006. Exposure to salt and organic acids increases the ability of Listeria monocytogenes to invade Caco-2 cells but decreases L. monocytogenes’ ability to survive gastric stress Appl. Env. Micro. Submitted
      • sjl38 [at] cornell.edu (subject: Garner%202006%20Supplemental%20Table%20St1) (Supplementary Table ST1 pdf). Doubling times of L. monocytogenes cultured in the presence of food additives.
      • sjl38 [at] cornell.edu (subject: Garner%202006%20Supplemental%20Figure%20S1) (Supplemental Fig.S1 pdf). Evaluation of L. monocytogenes growth in the presence of salt and organic acids using OD600 measurements.
      • sjl38 [at] cornell.edu (subject: Garner%202006%20Supplemental%20Figure%20S2) (Supplemental Fig.S2 pdf). Evaluation of L. monocytogenes growth in the presence of salt and organic acids using OD600 measurements.
      • sjl38 [at] cornell.edu (subject: Garner%202006%20Supplemental%20Figure%20S3) (Supplemental Fig.S3 pdf). Viability of L. monocytogenes 10403S∆sigB inoculated into BHI broth containing food additives.
      • sjl38 [at] cornell.edu (subject: Garner%202006%20Supplemental%20Figure%20S4) (Supplemental Fig.S4 pdf). Evaluation of L. monocytogenes growth in the presence of salt and organic acids using OD600 measurements using a low starting concentration (~5x101 CFU/ml) of L. monocytogenes
      • sjl38 [at] cornell.edu (subject: Garner%202006%20Supplemental%20Figure%20S5) (Supplemental Fig. S5 pdf). Box plot of L. monocytogenes 10403S invasion efficiency into Caco-2 tissue culture cells inoculated with varying L. monocytogenes concentrations.
      • sjl38 [at] cornell.edu (subject: Garner%202006%20Supplemental%20Figure%20S6) (Supplemental Fig. S6 pdf). Box plot of L. monocytogenes invasion efficiency into Caco-2 tissue culture cells for (i) L. monocytogenes strains grown to stationary phase in the presence of no additives, NaCl, or SL, and (ii) L. monocytogenes grown to stationary phase in BHI alone but added to Caco-2 cells with filter sterilized supernatant from L. monocytogenes grown in the presence of no additives, NaCl or SL (thus adding SL or NaCl in BHI as well as bacterial supernatant molecules).
      • sjl38 [at] cornell.edu (subject: Garner%202006%20Supplemental%20Figure%20S7) (Supplemental Fig. S7 pdf). Box plot of L. monocytogenes invasion efficiency into Caco-2 tissue culture cells with (i) L. monocytogenes grown to stationary phase in the presence of no additives, NaCl, or SL, and (ii) L. monocytogenes strains grown to stationary phase in the presence of no additives, NaCl, or SL with infections performed by adding L. monocytogenes cells as well 100µl synthetic gastric fluid pH 4.5 to Caco-2 cells.
    • Alcaine et al., 2006 Appl. Environ. Micro. 72:7575-7585
      S. D. Alcaine, Y. Soyer, L. D. Warnick, W.-L. Su, S. S. Sukhnanand, J. Richards, E. Fortes, P. McDonough, T. Root, N. B. Dumas, Y. Groehn, and M. Wiedmann. 2006. Multilocus sequence typing supports that bovine and human associated Salmonella represent distinct and overlapping populations, including clonal groups with duplication and deletion events in genes encoding cell surface molecule associated proteins. J. Clin. Micro. (in preparation)
      • sjl38 [at] cornell.edu (subject: Alcaine%202006%20Supplemental%20Table%20S1) (Supplemental Material Table S1 pdf)  Salmonella isolates included in study
    • Ho et al., 2006. J. Dairy Sci. 90:2517-2524
      A. J. Ho, V. R. Lappi, and M. Wiedmann. 2006. Longitudinal monitoring of Listeria monocytogenes contamination patterns in a farmstead dairy processing facility. J. Dairy Sci. 90(5): 2517-2524.
      • sjl38 [at] cornell.edu (subject: Ho%202006%20Supplemental%20Table%20S1) (Supplemental Manuscript Table S1 pdf.)  Sampling sites used in study
    • Huck et al. 2006. J. Food Prot. 70:2354-64
      J.R. Huck, N.H. Woodcock, R.D. Ralyea, and K.J. Boor.  2006. Molecular subtyping and characterization of psychrotolerant endospore-forming bacteria in two New York State fluid milk processing systems.  J. Food Prot. (submitted)
      • sjl38 [at] cornell.edu (subject: Huck%202006%20Supplemental%20Table%201) (Supplemental Table ST1 pdf.) 16S rDNA, rpoB and combined sequence type data for isolates subtyped in this study.
      • sjl38 [at] cornell.edu (subject: Huck%202006%20Supplemental%20Table%202) (Supplemental Table ST2 pdf.)  Contamination patterns by endospore-forming bacteria in NYS dairy plant U over three consecutive weeks of sampling.
      • sjl38 [at] cornell.edu (subject: Huck%202006%20Supplemental%20Table%203) (Supplemental Table ST3 pdf.)  Contamination patterns by endospore-forming bacteria in NYS dairy plant M over three consecutive weeks of sampling.

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    • Nightingale et al., 2005 J. Bacteriol. 187:5537-5551.
      K. K. Nightingale, K. Windham and M. Wiedmann. 2005. Evolution and molecular phylogeny of Listeria monocytogenes isolated from human and animal listeriosis cases and foods. J. Bacteriol. 197:5537-5551.
      • sjl38 [at] cornell.edu (subject: Nightingale%202005%20Supplemental%20Table%20S1%20JB) (Supplemental Table S1 pdf).  L. monocytogenes isolates and allelic types
      • sjl38 [at] cornell.edu (subject: Nightingale%202005%20Supplemental%20Table%20S2%20JB) (Supplemental Table S2 pdf). PCR Primers for L. monocytogenes multilocus sequence
      • sjl38 [at] cornell.edu (subject: Nightingale%202005%20Supplemental%20Table%20S3%20JB) (Supplemental Table S3 pdf). PCR Conditions for L. monocytogenes multilocus sequence typing
      • sjl38 [at] cornell.edu (subject: Nightingale%202005%20Supplemental%20Figure%201%20) (Supplemental Figure 1 pdf). Phylogram inferred by neighbor joining from a concatenated sequence containing gapprs, and sigB for unique L. monocytogenes sequence types and L. innocua.
      • sjl38 [at] cornell.edu (subject: Nightingale%202005%20Supplemental%20Figure%202) (Supplemental Figure 2 pdf).  Neighbor joining phylogram inferred from a single sequence selected to represent unique sigB allelic types for 120 L. monocytogenes, 48 L. innocua, 48 L. seeligeri, and 48 L. welshimeri isolates
    • Nightingale et al., 2005 Appl. Environ. Micro 71:8764-8772.
      Nightingale, K. K., K. Windham, K. E. Martin, M. Yeung, and M. Wiedmann. 2005. Selected Listeria monocytogenes subtypes commonly found in foods show reduced invasion in human intestinal cells due to distinct nonsense mutations in inlA leading to expression of truncated and secreted internalin A. Applied and Environmental Microbiology 71:8764-8772.
      • sjl38 [at] cornell.edu (subject: Nightingale%202005%20AEM%20Supplemental%20Table%20S1) (Supplemental Table ST1 pdf).  Description of L. monocytogenes isolates
      • sjl38 [at] cornell.edu (subject: Nightingale%202005%20AEM%20Supplemental%20Table%20S2) (Supplemental Table ST2 pdf).  Primers for partial inlA sequencing and primers for PCR-RFLP assay
      • sjl38 [at] cornell.du (subject: Nightingale%202005%20AEM%20Supplemental%20Table%20S3) (Supplemental Table ST3 pdf).  PCR Amplification conditions for partial inlA sequencing and PCR-RFLP
    • sjl38 [at] cornell.edu (subject: Alcaine%202005%20Supplemental%20table) (Alcaine et al., 2005 J. Antimicro Agents Chemo. 49:4061-5067 pdf)
    • Sukhnanand et al., 2005 J. Clin. Micro. 43:1177-1186
      Sukhnanand, S., S. Alcaine, W.-L. Su, J. Hof, M. P. J. Craver, L. D. Warnick, P. McDonough, K. J. Boor, and M. Wiedmann. 2004. DNA sequence-based subtyping and evolutionary analysis of selected Salmonella enterica serotypes. J. Clin. Microbiol. 43:1177-1186.
      • Supplemental Table S1. Allelic profiles and MLST types for the initial set of 25 Salmonella isolates characterized by seven-gene MLST
      • sjl38 [at] cornell.edu (subject: Sukhnanand%202005%20Supplementary%20Table%20ST2) (Supplementary Table S2 pdf). Allelic profiles and MLST types for the 66 isolate serotype diversity collection

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    2004

    2003

    • sjl38 [at] cornell.edu (subject: Kazmierczak%202003%20supplemental%20table) (Kazmierczak et al., 2003 J. Bacteriol. 185:5722-5734 pdf)

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