Progress 12/22/15 to 09/30/20
Outputs
(N/A)
Impacts
What was accomplished under these goals?
One long-term goal of this Hatch project was setting up an applied food safety laboratory. This involved setting up all the major equipment necessary for basic microbiology in a new laboratory space, developing the safety and quality SOPs for graduate students to conduct the research, and then optimizing space and maintaining equipment for the duration of the project. Subsequent research conducted in that lab, by individual objective, is described below: Obj 1. To facilitate persistent pathogen identification and control, the overall project has pushed forward on practical genomics and data collection approaches to manage persistent pathogens. Specifically, one line of research evaluated if CRISPR spacer patterns could be used as a subtyping tool for Listeria monocytogenes (LM) short term evolution within a facility. The basic answer to that question was no, but we did get that negative result published given the strong study designed to test it. The project also evaluated if persistent versus sporadic LM exhibited differences in central carbon metabolism or food associated stress responses. While we found significant diversity of phenotypes among genotypes, the specific variable of persistence status was not associated consistently with any given stress response. Work of other researchers has since shown a likely effect of selection for sanitizer resistance among strains that are able to persist in a facility. We did not see evidence for such selection in our study, likely because all strains tested were originally isolated from food facilities, and therefore had some demonstrated ability to survive there, even if for a shorter time. Obj 2. To facilitate improved mycotoxin sorting, this project develop a custom UV-visible-NIR spectrometer that can measure reflectance (350-1150 nm) and UV-fluorescence (same range) of single kernels dropped through the tube. This was then used to identify aflatoxin contaminated single kernels from corn from an inoculated field trial. This found that features consistent with discoloration were most informative. The project also contributed to a review of single kernel spectral analysis, classification, and sorting methods. Future work for the project is ongoing. That work will seek to identify classification features for kernels in motion collected from naturally contaminated corn from Texas. Obj 3. To value reductions in pathogens, our work has taken two distinct projects, meat waste and share table safety. In the meat waste project we collected records of meat and poultry recalls over 22 years. We found that recall count and size were not increasing over that time, while U.S. production did increase. This relates to value by providing a commodity specific baseline for quantifying how further improvements in safety, therefore reductions in recalls, may prevent food loss. In the other projects, we have begun work to develop models of foodborne pathogen transmission in K-12 school cafeteria settings. The goal is to model the potential transmission of hazards due to share tables. The goal here is to estimate how much increase risk sharing food poses, and science-driven methods to manage that risk. The ultimate goal is to remove this food safety as a barrier to share tables, and therefore promote increased food security among school children.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2019
Citation:
Cheng, X., A. Vella and M.J. Stasiewicz. 2019. Classification of aflatoxin contaminated single corn kernels by ultraviolet to near infrared spectroscopy. Food Control. 98:253-261.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2019
Citation:
Taylor, A.J. and M.J. Stasiewicz. 2019. Persistent and sporadic Listeria monocytogenes strains do not differ when growing at 37 degrees C, in planktonic state, under different food associated stresses or energy sources. BMC Microbiol. 19:257.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2020
Citation:
Chavez, R.A., X. Cheng and M.J. Stasiewicz. 2020. A review of the methodology of analyzing aflatoxin and fumonisin in single corn kernels and the potential impacts of these methods on food security. Foods. 9.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2020
Citation:
Cheng, X., R.A. Chavez and M.J. Stasiewicz. 2020. When to use one-dimensional, two-dimensional, and Shifted Transversal Design pooling in mycotoxin screening. Plos One. 15.
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:This project has provided research training to the students working on the project, including twoMS students (Obj. 1 and 2) and one undergraduate student (Obj 2). The PI and students also presented this work at a conference. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This period the project has provided projects for twoMS students and onemulti-semester undergraduate student. Students have learned to perform Biosafety Level 2 microbiology work, keep digital laboratory notebooks, and perform code-based statistical analysis. The undergraduate has since graduated and gone to graduate school in food science at Minnesota, mentioning this experience was important to that successful application. How have the results been disseminated to communities of interest?In this reporting period the PI and students presented at one academic conference, the 2019 Annual Meeting of the International Association for Food Protection. What do you plan to do during the next reporting period to accomplish the goals?For the next reporting period, Obj 1 work will include finishing both the antimicrobial in ham paper, including some additional data collection related to confirming results with a more sensitive experimental design. Obj 2 work will includepre-enriching commercial corn samples to identify more positive kernels for wet lab testing. Obj 3 work will include building the basic value-chain simulation for leafy greens pathogen sampling.
Impacts
What was accomplished under these goals?
Obj 1. To facilitate persistent pathogen identification and control, the MS student working on phenotyping persistent strains hasresponded to peer-review of a manuscript on this work and is nearly finished a second revision. We have also published a manuscript detailing work to determine if CRISPR spacers may be used for further subtyping persistent strains. Another MS student finished her experimental work to identify synergistic combinations of antimicrobials in miniaturized hams and we are drafting a manuscript ofthis screen tool work. Finally, the PI spent some time working on genomics of Salmonella isolated from the meat supply chain. Obj 2. To facilitate improved mycotoxin sorting, the MS student on the project analyzed samples of over 600 kernels from 2018 harvest of commercial corn from Texas. We have presented these data at conferences detailing the great skewness in both aflatoxin and fumonisin contamination. Work to develop sorting algorithms has been delayed as we identify opportunities to enrich for more positive samples. Obj 3. We have begun work to develop models of foodborne pathogen sampling throughout the leafy green supply chain to determine at which points sampling for pathogens would be most valuable. These simulations will incorporate realistic challenges such as low prevalence of pathogens, very large fields, and relatively limited sample collection abilities.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Acar, S., E. Bulut, M.J. Stasiewicz, and Y. Soyer. 2019. Genome analysis of antimicrobial resistance, virulence, and plasmid presence in Turkish Salmonella serovar Infantis isolates. Int. J. Food Microbiol. https://doi.org/10.1016/j.ijfoodmicro.2019.108275.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Taylor, A.J. and M.J. Stasiewicz. 2019. CRISPR-based subtyping using whole genome sequence data does not improve differentiation of persistent and sporadic Listeria monocytogenes strains. J. Food Sci. 84:319-326. https://doi.org/10.1111/1750-3841.14426.
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:This project has provided research training to the students working on the project, including: 3 MS students (Obj. 1 and 2) and one undergraduate student (Obj 2). The PI also presentedwork related to this project at two conferences, one industry focused and one academic. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?In this reporting period the PI was invited to present project results to two professional meetings, one industry focused and the other an academic conference. These provided important contacts and collaborative opportunities, such as planning and ultimately submitting an collaborative NIFA grant with Dr. Haibo Yao (for Obj. 2). In addition, this period the project has provided projects for 3 MS students and 1 short-term undergraduate student. Students have learned to perform Biosafety Level 2 microbiology work, keep digital laboratory notebooks, and perform code-based statistical analysis. How have the results been disseminated to communities of interest?Two invited presentations. An industry conference, the Corn Utilization and Technology Conference, focused on Obj 2 work in mycotoxin sorting. An academic conference, the American Dairy Science Association Annual Meetings, focused on Obj 1 work in persistent pathogen genomics and phenotyping. What do you plan to do during the next reporting period to accomplish the goals?For the next reporting period, Obj 1 work will include: Finishing both the phenotyping and CRISPR manuscripts, which are both in various levels of revision after first round of peer-review and potentially screening for additional phenotypes of persistent strains. Obj 2 work will include: Continuing to developing robust calibrations for Texas corn kernels, particularly by attempting to pre-enrich for positive kernels to increase the number of positive kernels in our data set.Obj 3 work will include: Attempting to finish the manuscript for the CUPHD data analysis project which requires sourcing raw data from the student who has since graduated.
Impacts
What was accomplished under these goals?
The long-term goal of setting up an applied food safety laboratory was completed the year prior, and work on this sub-task involves simply optimizing space and maintaining facilities. Progress on each individual objective is described below: Obj 1. To facilitate persistent pathogen identification and control, the MS student working on phenotyping persistent strains has completed his experimental work. Results suggest persistent strains are not more resistant food associated stresses, compared to closely related but sporadic isolates (the control group is an innovation of this work). During the time range of this reporting period, the manuscript was submitted for peer-review. To determine if CRISPR spacers may be used for further subtyping persistent strains, we have also analyzed whole genome sequences of a panel of 175 Listeria monocytogenes from previous retail deli work for CRISPR spacer presence. A manuscript has received peer-review requiring minor revisions. Obj 2. To facilitate improve mycotoxin sorting, the MS student on the project has analyzed nearly 400 kernels from inoculated and control corn and developed a classification algorithm that is > 90% accurate to identify aflatoxin contamination. This manuscript has been published in a peer-reviewed journal. In addition, we have begun to receive yearly shipments of contaminated commercial corn from Texas and have a new student developing classifications for both aflatoxin and fumonisin contaminated kernels. Over 500 kernels have been analyzed from 2017 harvest corn. Obj 3. We finished analysis of Champaign County Public Health Department (CUPHD) data of over 10 years of restaurant inspections. We have analyzed the historic inspections records as if they were scored under the new system FDA Model Food Code inspection report to determine the relationships between the new inspection systems. This manuscript is in preparation.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2018
Citation:
Cheng, X., A. Vella, and M.J. Stasiewicz. 2018. Classification of aflatoxin contaminated single corn kernels by ultraviolet to near infrared spectroscopy. Food Cont. (In Press). https://doi.org/10.1016/j.foodcont.2018.11.037.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2018
Citation:
Taylor, A.J. and M.J. Stasiewicz. 2018. CRISPR-based subtyping using whole genome sequence data does not improve differentiation of persistent and sporadic Listeria monocytogenes strains. J. Food Sci. (Reviewed, Minor Revisions Requested).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Stasiewicz, M.J. 2018. Single-kernel detection of mycotoxins in corn: Foundations for high-throughput sorting. Corn Utilization and Technology Conference. St. Louis, MO. Jun. 4-6, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Stasiewicz, M.J. 2018. Whole-genome sequencing for pathogen environmental monitoring: Focus on Listeria. ADSA Annual Meeting. Knoxville, TN. Jun. 24-27, 2018.
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:This project has provided research training to the students working on the project, including two MS students (Obj. 1 and 2), one non-thesis MS student (Obj. 3), and one undergraduate student (Obj 2). The PI also presented work related to this project at two industry conferences and one invited academic retreat. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?During the course of the reporting period the PI was invited to present project results to three professional meetings, two industry focused and one a small-academic conference. These provided important contacts and collaborative opportunities (Texas corn project, Obj 2). In addition, this period the project has provided projects for two MS students and two short-term students (non-thesis MS, undergrad). Students have learned to perform Biosafety Level Two microbiology work, keep digital laboratory notebooks, and perform code-based statistical analysis. How have the results been disseminated to communities of interest?Two invited presentations to industry conferences, the Peanut and Tree Nut Processors Conference and the Global Food Safety Initiative, both focused on Obj 1 work. Obj 3 work has been published. What do you plan to do during the next reporting period to accomplish the goals?For the next reporting period, Obj 1 work will includescreening persistent and sporadic strains for ability to grow on different food associated carbon sources and preparing both screening and CRISPR work for publication.Obj 2 work will includedeveloping robust calibrations for Texas corn kernels, then validating these methods by installing a sorting mechanism and then actually sorting corn during the 2018 harvest. Obj 3 work will include finishing the analysis of CUPHD restaurant inspection data, working with the CUPHD to use these data to inform their inspection process, and preparing this work for publication.
Impacts
What was accomplished under these goals?
The long-term goal of setting up an applied food safety laboratory has been accomplished. In May the Stasiewicz lab moved into a 2,000 square footlab space shared with two other food science microbiology faculty, with an associated media room, waste processing room, cold room, and instrument room. The entire laboratory suite operates at the BL2 level. Stasiewicz has secured Institutional Biosafety Committee approval for the novel mycotoxin sorting work as of January 2017. Progress on each individual objective is described below: Obj 1. To facilitate persistent pathogen identification and control, the MS student that started just prior to this reporting period has made significant progress on distinct project. We have developed a high-throughput phenotyping protocol for pre-growth, growth in the Bioscreen C, and data analysis. We have also screened the panel of 80 previously identified persistent and sporadic isolates for their ability to growth under pH stress, salt stress, and sanitizer stress. Initial results suggest persistent strains may be more resistant to food industry sanitizers, compared to closely related but sporadic isolates (the control group is an innovation of this work). To determine if CRISPR spacers may be used for further subtyping persistent strains, we have also analyzed whole genome sequences of a panel of 175 Listeria monocytogenes from previous retail deli work for CRISPR spacer presence. Initial results suggest that spacers are vertically transmitted, and therefore not useful for subtyping persistent strains. We are preparing a manuscript to report these negative results. Obj 2. To facilitate improve mycotoxin sorting, the MS student on the project has develop SOP for kernel picking, scanning using custom UV-VIS-NIR spectrometry systems, wet chemistry, and data analysis. We have used this pipeline to analyze nearly 400 kernels from inoculated and control corn and developed a classification algorithm that is > 90% accurate to identify aflatoxin contamination. We are now writing up this manuscript. In addition, we have setup a collaboration to source commercial corn from Texas and develop robust classifications for both aflatoxin and fumonisin contaminated kernels. Obj 3. We have published our analysis of 22 years of FSIS meat and poultry recall data. In addition, we have started a collaboration with the Champaign County Public Health Department (CUPHD) to analyze over 10 years of restaurant inspection data. Illinois will be adopting the FDA model food code in 2018 and begin to inspect restaurants using that system. We are working to re-analyze the historic inspections records as if they were scored under the new system to determine the relationships between the new inspection systems. This will have the potential to determine if the new system is likely to be more stringent than the old, and inform food safety communications with local stakeholders.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Stasiewicz, M.J. 2017. Understanding Whole Genome Sequencing For Food Safety. Peanut and Tree Nut Processors Association Convention 2017. Scottsdale, AZ. January 13-16, 2017.
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Progress 12/22/15 to 09/30/16
Outputs
Target Audience:This project has provided research training to the students working on the project, including two MS students, one PhD student semester project, and two shorter-term students (one undergraduate, one non-thesis Masters) starting after this reporting period. The PI also presented this work at the Multistate Hatch project S-1056 annual meeting, providing knowledge to food safety researchers from 17 institutions. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?During the course of the reporting period, the PI presented preliminary work on the spectral sorting to the Corn Utilization and Technology Conference in St. Louis, MO, Summer of 2016. Participation in the conference provided important networking opportunities to expand the work previously conducted in Kenya to the US context. After that conference, the PI was able to follow up with scientists in Mississippi to source field-inoculated corn likely contaminated with aflatoxins. Once the biosafety infrastructure is in place to study these kernels, collaborators will be able to send these samples and further work can begin. As described above, two new MS students have been recruit to this project as of Fall 2016. They have begun their first year of coursework. They have also worked through safety trainings required to perform food safety work at Biosafety Level 2 (BL2). These are important skills for their development as future food safety professionals. How have the results been disseminated to communities of interest?While the work is still in the start-up phase, the food recall work has been submitted for publication in a peer-reviewed journal. The PI has also presented plans for the lab's work, including this Hatch project, at numerous departmental seminars, including to the full department, the graduate student association, and an undergraduate research course. What do you plan to do during the next reporting period to accomplish the goals?For the next reporting period, the PI anticipates finishing setup of the BL2 food safety laboratory, including getting project protocols approved by the Division of Research Safety. Mr. Taylor will being work phenotyping persistent and sporadic strains using high-throughput growth curve equipment available to the department. Mr. Cheng will continue optical scanning work of US corn, using the higher-resolution UV-VIS-NIR spectrometer. He will use those spectral data to develop algorithms to classify kernels as contaminated above 100 ppb aflatoxin, or uncontaminated below 10 ppb. We will also try to recruit students to work on short term projects following up on the food recall data, possibly to include data on FDA recalls of human foods not regulated by the FSIS and on OASIS data on import refusals.
Impacts
What was accomplished under these goals?
Significant progress has been made setting up the applied food safety laboratory. A 270 sq ft laboratory space has been cleaned out and equipped for the single-kernel sorting and mycotoxin removal work. This effort includes furnishing a custom single-kernel spectrometer, biosafety cabinet, and basic microbiology equipment necessary to scan, grind, and analyze corn kernels for aflatoxin levels. Objective 1: To facilitate the genomics analysis for persist pathogen identification the project has setup a network-ready UNIX computer with all the open-source software to perform modern whole-genome-sequence (WGS) analysis. We have begun two collaborations to better understand persistent Salmonella in food associated environments. These include: (i) a project to analyze 50+ Salmonella Newport genomes from produce growing regions of the Virgina shore to identify the possible harborage points of the pathogen in those produce production systems, and (ii) a international project to analyze the 20+ Salmonella Infantis genomes from isolates gathered from poultry production facilities in Turkey and compare them to Salmonella Infantis isolates in the NCBI GenomeTrakr database. Finally, the PI has recruited an MS student, Alexander Tayor, to begin MS thesis work on metabolic determinants of pathogen persistence. At the end of this reporting period Mr. Taylor has selected a set of 80+ persistent and sporadic strains that have been sequenced in previous persistence work for a statistically rigorous comparison of metabolic phenotypes. We are currently sourcing those strains from domestic collaborators and developing the growth screening protocols for the experimental work. Objective 2: To facilitate improved sorting to remove mycotoxin contaminated cereals from bulk lots, we have built capacity to begin improving sorting to identify and remove aflatoxin contaminated kernels from bulk US corn. The PI has worked with local engineers to develop a custom-built single-kernel light source that provides continuous spectral illumination from 350 to 1,050 nm, spanning UV, visible, and near infrared (NIR) spectra, using discrete LED components. This illumination tube interfaces with a UV-VIS-NIR spectrometer to capture continuous reflectance or emission spectra across those wavelengths. The PI has also recruited an MS student, Xianbin (Eric) Cheng, to begin MS thesis work on this project. At the end of this reporting period Eric has begun to develop protocols to scan non-hazardous corn kernels using the new instrumentation. We are currently working to compare those results to the existing 9 LED sorting system used previously for the discrimination of corn kernels of different visible colors (white, yellow, purple corn). Objective 3: To being work to value reductions of pathogen contamination, the PI advised a PhD student on a semester project to organize data from FSIS coordinated recalls of meat, poultry, and egg products. The student, Acton Gorton, scraped 22 years of food recalls data from the online Recall Case Archive, cleaned the data, and began statistical analysis. This work has found that the median size of FSIS recalls has not increased over the analyzed time period, while the number of recalls has varied without any clear temporal trend. At the end of this reporting period, these results were being written up in a manuscript for submission to the Journal of Food Protection. Since that time we have received peer-review feedback to publish the paper after revisions, and are in the process of revising the manuscript
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2016
Citation:
Gorton, A and M.J. Stasiewicz. 2016. 22-Years of U.S. Meat and Poultry Product Recalls: Implications for Food Safety and Food Waste. Journal of Food Protection.
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