Progress 10/01/19 to 09/30/20
Outputs
Target Audience:Target audiences that were reached by my research program efforts since May 2018 were undergraduate and graduate students, industry representatives, and government agencies. Changes/Problems:The research activities have been substantially slowed down in Spring 2020 due to the COVID-19 pandemic. What opportunities for training and professional development has the project provided?Five graduate students and ten undergraduate students have been mentored in research, science communication, and scientific writing. Additionally, approximately 50 students have been taught topics that are aligned with this project. Specifically, I trained graduate and undergraduate students in research. Throughout the year, I trained five graduate students and ten undergraduate students. I mentored students in scientific and grant writing and guided them through the process of their research or fellowship proposal submission, as well as research presentations at local, regional, and international conferences. Two of the mentored food science students graduated in Spring 2020, and one of them assumed a position of an Associate R&D Scientist in Food Safety in the food industry, while another one assumed a position of a PhD student. I also instructed two courses that are aligned with the goals of this project. The first course, FDSC 409 - Laboratory in Food Microbiology, is a core course in a Food Science major. As part of my effort to train the next generation of food scientists in traditional microbiological, molecular, as well as omics methods, I developed and taught a lab that introduced students to food processing environmental microbiomes. Students learned what microbiomes are, how they could be leveraged in food science, and how to analyze and interpret microbiome information. The second course I taught was FDSC 497 - Foodborne Pathogen Genomic Epidemiology. In this course, I train students in the application of whole-genome sequencing data analyses tools to answer epidemiological questions relevant to food safety and outbreak investigation. After gaining analytical skills by working through a case study, students apply these skills in a group project by working on a real-life sequence dataset. In Spring 2020, students analyzed sequences of Salmonella from a wastewater treatment system and published a peer-reviewed resource announcement paper reporting the results of their findings. As part of this course, students work on a final project in which they develop an outreach/extension video wherethey communicate the application and impact of applying whole-genome sequencing in the context of food safety. Through this, students learn analytical skills, as well as science communication skills. FDSC 497 course was approved as a standing course FDSC 517 in Fall 2020. How have the results been disseminated to communities of interest?The results of the research have been disseminated through published peer-reviewed papers and conference presentations in the form of posters and oral presentations, as well as seminars. In this funding period, I was working with the Pennsylvania tree fruit industry on monitoring Listeria monocytogenes in packing houses. In Fall 2020, I initiated a project that will evaluate the efficacy of select cleaning and sanitizing procedures to help the industry improve control of L. monocytogenes and improve food safety. Furthermore, I collaborated with scientists from FDA CFSAN on the evaluation of L. monocytogenes occurrence and microbiome characterization in tree fruit packinghouses. In addition to that, I collaborated with scientists from the CDC on the characterization of the cytotoxic capacity of the Bacillus cereus group isolates from food and other sources. Lastly, I worked with an epidemiologist from the Pennsylvania State Department of Health on a genomic epidemiology project focused on improving the understanding of Campylobacter epidemiology. I also provided technical support in the application of whole-genome sequence analyses programs and the interpretation of analyses results. What do you plan to do during the next reporting period to accomplish the goals?1. Complete characterization of B. cereus group isolates' cytotoxic capacity and develop analytical tools for assessment of the level of cytotoxicity based on genomic data. 2. Establish correlations between B. cereus antimicrobial resistance phenotypes and genotypes. 3. Evaluate cleaning and sanitizing protocols on the reduction of Listeria monocytogenes and the composition of microbiomes in tree fruit packing houses.
Impacts
What was accomplished under these goals?
1. The research focused on this goal resulted in several publications, including (i) the proposal of a taxonomic framework for Bacillus cereus group that reconciles genomic definitions of species with industrial and clinical phenotypes, (ii) development and publication of a bioinformatics tool BTyper that adopts the new taxonomic framework, (iii) characterization of phylogenetic relatedness, serotypes and virulotypes of Salmonella isolated from untreated and treated wastewater. 2. A collection of 300 Bacillus cereus group isolates has been whole-genome sequenced, characterized in terms of phylogenetic relatedness and virulence gene presence. Isolates growth curves were determined to identify early stationary phase and a subset of isolates has been harvested in the early stationary phase and characterized for cytotoxicity towards human CaCo-2 cells. 3. Two projects focused on characterizing the relationship between genetic and phenotypic antimicrobial resistance are taking place; one focused on Campylobacter and another one focused on Bacillus cereus. The occurrence of genetic resistance determinants for Campylobacter has been presented in conferences. Approximately 90 Bacillus cereus isolates have been phenotypically characterized using disk diffusion to establish ecological resistance cut-offs. Additionally, a novel antimicrobial susceptibility testing method that utilizes dynamic laser speckle imaging coupled with machine learning has been developed using E. coli and S. aureus as model strains in the proof-of-concept experiments. 4. Tree fruit processing facilities were monitored for the presence of L. monocytogenes and its relationship with environmental microbiota and mycobiota in 2017/18. In this funding period, the microbiota and mycobiota data have been analyzed, and Nanopore sequencing has been applied as a proof-of-concept approach to the direct detection of L. monocytogenes DNA in food processing environmental samples.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Carroll, L.M., Wiedmann, M., Kovac, J.* 2020. Proposal of a taxonomic nomenclature for the Bacillus cereus group which reconciles genomic definitions of bacterial species with clinical and industrial phenotypes. mBio, doi: 10.1128/mBio.00034-20
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Simunovic, K., Sahin, O., Kovac, J., Shen, Z., Klancnik, A., Zhang, Q., Smole Mozina S. 2020. (-)-alpha-Pinene reduces quorum sensing and Campylobacter jejuni colonization in broiler chickens. PLoS One, doi:10.1371/journal.pone.0230423.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Keba, A., Rolon, M. A., Temene, A., Dessie, K., Vipham, J., Kovac, J., Zewdu, A. 2020. Review of the prevalence of foodborne pathogens in milk and dairy products in Ethiopia. International Dairy Journal, https://doi.org/10.1016/j.idairyj.2020.104762.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Sullivan, G., Guo, X., Tokman, J.I., Roo, F. S., Trmcic, A., Baker, R.C., Tang, S., Markwell, P., Wiedmann, M., Kovac, J.* 2020. Extended enrichment procedures can be used to define false-negative probabilities for cultural gold standard methods for Salmonella detection, facilitating comparisons between gold standard and alternative methods. J Food Prot. 83(6):1030-1037. doi:10.4315/0362-028X.JFP-19-422.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Connolly, C.J., Kaminsky, L., Pinto, G.N., Sinclair, P.C., Bajracharya, G., Yan, R., Nawrocki, E.M., Dudley, E.G., Kovac, J.* 2020. Whole-genome sequences of Salmonella isolates from an ecological wastewater treatment system. Microbiol Resour Announc. 9(23):e00456-20. doi: 10.1128/MRA.00456-20.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Chung. T., Weller, D.L., Kovac, J*. The composition of microbial communities in six streams, and Its association with environmental conditions, and foodborne pathogen isolation. Front Microbiol. 2020 Jul 29;11:1757. doi: 10.3389/fmicb.2020.01757.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Zhou, K., Zhou, C., Sapre, A., Pavlock, J.H., Weaver, A., Muralidharan, R., Noble, J., Chung, T., Kovac, J., Liu, Z., Ebrahimi, A. 2020. Dynamic Laser Speckle Imaging Meets Machine Learning to Enable Rapid Antibacterial Susceptibility Testing (DyRAST). ACS Sens. 2020 Sep 18. doi: 10.1021/acssensors.0c01238.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Liu MM, Coleman S, Wilkinson L, Smith ML, Hoang T, Niyah N, Mukherjee M, Huynh S, Parker CT, Kovac J, Hancock REW, Gaynor EC. Unique inducible filamentous motility identified in pathogenic Bacillus cereus group species. ISME J. 2020 Aug 7. doi: 10.1038/s41396-020-0728-x.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Carroll, L. M., Cheng, R.A., Kovac, J.* 2020. No assembly required: Using BTyper3 to assess the congruency of a proposed taxonomic framework for the Bacillus cereus group with historical typing methods. Frontiers in Microbiology, https://doi.org/10.3389/fmicb.2020.580691.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
G. Bajracharya, R. Yan, B. Roman, L. LaBorde, R. Brennan, J. Kovac. Microbiological Quality of Penn State Wastewater Before and After Recycling Through the EcoMachineTM. ABASM Annual Meeting. Loretto, PA, November 8-9, 2019. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
Feng, J., A. Padin-Lopez, P. Sinclair, L. LaBorde, J. Kovac. Combating Listeria monocytogenes growth in apple packing house biofilms. ABASM Annual Meeting. Loretto, PA, November 8-9, 2019. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
Pinto, G., Yan, R., Luyster, C., Koestler, A., Yeung, E., Chung, T., Taylor-Roseman, R., Cogan, K., Dalesandre, G., Kovac, J. Heat resistance of Salmonella in cocoa bean roasting by dry-heat treatment. ABASM Annual Meeting, Loretto, PA, November 8-9, 2019. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
Yan, R., E. Mills, L.K. Hudson, N.M. M'ikanatha, I. Nachamkin, T. G. Denes, J. Kovac. Whole genome sequencing-based analysis of Campylobacter from clinical samples and retail meat. ABASM Annual Meeting, Loretto, PA, November 8-9, 2019. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Hudson, L.K., Yan, R., Golwalkar, M., M'ikanatha, N., Nachamkin, I., Thomas, L., Moore, C., Qian, X., Garman, K.N., Dunn, J.R., Kovac, J., Denes, T.G. Phylogenetic analysis reveals source attribution patterns for Campylobacter spp. in Tennessee and Pennsylvania. ASM Microbe Summer of Science, Summer 2020. Online version of ASM Microbe in response to COVID-19. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Niyah, N., Prince, C., Chung, T., Johler, S., Kovac, J. Genotyping and growth rate characterization of B. cereus group Isolates from diverse sources. ASM Microbe Summer of Science, Summer 2020. Online version of ASM Microbe in response to COVID-19. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Yan, R., M'ikanatha, N., Hudson, L.K., Nachamkin, I., Denes, T.G., Kovac, J. The occurrence of genetic antimicrobial resistance determinants in Campylobacter isolated from poultry meat and clinical samples in Pennsylvania. ASM Microbe Summer of Science, Summer 2020. Online version of ASM Microbe in response to COVID-19. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Carroll, L.M., Wiedmann, M., Kovac, J. Keeping up with the Bacillus cereus group: leveraging genomic data to fight bacterial taxonomic ambiguity from farm to clinic. IAFP 2020 (online), October 26-28, 2020. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Chung, T., Prince, C., Niyah, N., Johler, S., Kovac, J. Genomic characterization and growth rates of B. cereus group isolates from diverse sources. IAFP 2020 (online), October 26-28, 2020. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Connoly, C., Kovac, J., Cutter Nettles C. Effect of DNA extraction method on qPCR efficiency for pathogens in ground beef. IAFP 2020 (online), October 26-28, 2020. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Pinto, G., Yan, R., Luyster, C., Koestler, A., Yeung, E., Chung, T., Hopfer, H., Ziegler, G., Taylor Roseman, R., Cogan, K., DAlesandre, G., Kovac, J. Thermal inactivation of Salmonella on cocoa beans during dry-heat roasting. IAFP 2020 (online), October 26-28, 2020. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Rolon, M.L., Tan., X., Chung, T., Gonzalez Escalona, N., Chen, Y., Macarasin, D., LaBorde, L.F., Kovac, J. Two-year monitoring of environmental microbial communities in three apple packing facilities and their association with the presence of Listeria monocytogenes. IAFP 2020 (online), October 26-28, 2020. Oral presentation.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Yan, R., Mills, E., Hudson, L.K., Mikanatha, N., Nachamkin, I., Denes, T.G., Kovac, J. Whole genome sequencing-based analyses of Campylobacter isolates from clinical samples and retail poultry meats. IAFP 2020 (online), October 26-28, 2020. Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Kovac, J. Diversity of microbial communities and their co-occurrence with foodborne pathogens in surface waters. IAFP 2020 (online), October 26-28, 2020. Invited oral presentation.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Kovac, J. Microbiota of built tree fruit processing environments: their potential role in Listeria monocytogenes persistence. IAFP 2020 (online), October 26-28, 2020. Invited oral presentation.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Kovac, J. Machine learning: to reveal potential pathogen indicators when other approaches cannot. IAFP 2020 (online), October 26-28, 2020. Invited oral presentation.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Rolon, M.L., Tan., X., Chung, T., Gonzalez Escalona, N., Chen, Y., Macarasin, D., LaBorde, L.F., Kovac, J. Two-year monitoring of environmental microbial communities in three apple packing facilities and their association with the presence of Listeria monocytogenes. 34th ISME World Conference, August 2-7, 2020. Abstract accepted, conference canceled due to COVID-19.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Niyah, N, Prince, C, Chung, T., Johler, S., Gomez, G., Getz, E., Luquez, C., Halpin, J., Kovac, J. Population structure and virulence gene distribution among B. cereus group Isolates from diverse sources. 2020 Society for Advancement of Chicanos/Hispanics and Native Americans in Science Conference, October 14 24 (online). Poster.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Niyah, N, Prince, C, Chung, T., Johler, S., Gomez, G., Getz, E., Luquez, C., Halpin, J., Kovac, J. Population structure and virulence gene distribution among B. cereus group Isolates from diverse sources. American Indian Science and Engineering Society National Conference, October 15 17, 2020. Poster.
|
Progress 10/01/18 to 09/30/19
Outputs
(N/A)
Impacts
What was accomplished under these goals?
Goal 1: a. We sequenced 123 Campylobacter isolates from foodborne infections in PA. We carried out comparative analyses with meat isolates obtained from food in PA, in order to identify clusters of potentially epidemiologically linked isolates. The results of this study, which is the first Campylobacter comparative genomics study on PA isolates, will be presented at AB ASM meeting in November 2019. b. We completed a study investigating microbiome dynamics throughout the Campylobacter enrichment in meat samples and presented the study results at IAFP. The study helped in identifying the diversity of microbiota on poultry meat samples and its changes during the enrichment of Campylobacter. Furthermore, the study helped identify the necessary sequencing depth and the level of host (chicken) DNA contamination one can expect when conducting shotgun sequencing using meat samples. c. We completed the characterization of B. cereus group outbreak isolates and published a study that provides guidelines on approaches to studying B. cereus group genomic epidemiology and benchmarks several bioinformatics tools for whole genome sequence analyses on our dataset. Goal 2: a. We started a USDA NIFA-funded B. cereus group exposure assessment project. Thus far, we obtained a diverse collection of B. cereus group isolates from a collaborator at the University of Zurich, characterized the growth curves for 300 isolates, whole-genome sequenced them and initiated cytotoxicity assessment. b. We carried out experiments on closely related clade IV isolates with various level of cytotoxicity to comparatively investigate the expression of virulence factors between cytotoxic and non-cytotoxic isolates using proteomics. Proteomics characterization is underway. Goal 3: We finalized antimicrobial resistance phenotyping on 100 B. cereus group isolates. The phenotypic data is currently being analyzed to determine the ecological cut-off values for resistance to individual tested antibiotics. Furthermore, the phenotypic data is being analyzed in relation to genomic data to identify the correlations between genotypes and phenotypes. Goal 4: a. We published the results from a study in which we surveyed apple packinghouse microbiota over a harvesting and packing season and investigated associations between microbial composition and Listeria monocytogenes in the environmental samples. We also collected samples throughout the second season and sequenced the environmental microbiota from collected samples. b. We completed the data analyses of agricultural water microbiomes and their associations with the isolation of foodborne pathogens. The manuscript describing results is in the final revision stage before submission to a journal. c. We began the assessment of the effectivenes of the cological wastewater treatment in terms of microbial safety and microbial diversity in recycled water.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Chung, T., Weller D. L., Kovac J. Factors associated with surface water microbial community structure in Northeast US. ASM Conference on Next Generation Sequencing, Tyson, VA (DC area), September 23-26, 2018. Poster.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Tan, X., Chung, T., Kovac, J., LaBorde, L. Diversity of Built Environment Microbiomes and their Association with the Occurrence of Listeria monocytogenes in three Fruit Packing Houses. Annual Penn State Microbiome Center Meeting. University Park, October 2, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
11. Chung, T., Weller D. L., Kovac J. Factors associated with surface water microbial community structure in Northeast US. Allegheny Branch American Society for Microbiology Annual Meeting. Gettysburg, November 9-10, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
10. Tan, X., Chung, T., Kovac, J., LaBorde, L. Diversity of Built Environment Microbiomes and their Association with the Occurrence of Listeria monocytogenes in three Fruit Packing Houses. Annual Penn State Microbiome Center Meeting. Allegheny Branch American Society for Microbiology Annual Meeting. Gettysburg, November 9-10, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Weaver, A., Zhou, K., Zhou, C., Chung, T., Condello, M., Noble, J., Liu, Z., Ebrahimi, A., Kovac, J. Susceptibility of E. coli and Salmonella enterica strains used as model microorganisms in development of a rapid antimicrobial susceptibility testing method. Allegheny Branch American Society for Microbiology Annual Meeting. Gettysburg, November 9-10, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Nwanosike, H., Taejung, C., Xiaoli, L., Condello, M., Dudley, E., Lamandella, G., Kovac, J. Investigating the Virulence Potential of E. coli Isolates Obtained from Cocoa Beans, Using Whole Genome Sequence Analyses, Orlando, April 6-9, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Mills, E., Kovac, J. Determining the ecological resistance cut-off values for a population of dairy Bacillus cereus group Isolates. Gamma Sigma Delta Research Expo. University Park, PA, March 26, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Fitzgerald, T., Kovac, J. Variability in insecticidal crystal protein production among dairy-associated Bacillus cereus group Isolates. Gamma Sigma Delta Research Expo. University Park, PA, March 26, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Weaver, A. Prince, C., Sapre, A., Zhou, K., Zhou, C., Noble, J., Liu, Z., Ebrahimi, A., Kovac, J. Susceptibility of E. coli and Salmonella enterica strains used as model microorganisms in development of a rapid antimicrobial susceptibility testing method. Gamma Sigma Delta Research Expo. University Park, PA, March 26, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Tan, Q., Chung, T., Chen, Y., Macarasin, D., LaBorde, L., Kovac, J. Diversity of built environment microbiomes and their association with the occurrence of Listeria monocytogenes in three fruit packing houses. Gamma Sigma Delta Research Expo. University Park, PA, March 26, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Feng, J., Pacchia, J., LaBorde, L., Kovac, J. Ability of Bacillus subtilis to inhibit Listeria monocytogenes in casing soil used as a substrate for mushroom growing. Gamma Sigma Delta Research Expo. University Park, PA, March 26, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Shi, X., Feng, B., Kovac, J. Factors associated with persister cell formation frequency in Listeria monocytogenes. Gamma Sigma Delta Research Expo. University Park, PA, March 26, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Chung, T., Weller D. L., Kovac J. Factors associated with surface water microbial community structure in Northeast US. Gamma Sigma Delta Research Expo. University Park, PA, March 26, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Yan, R., Pinto, G., Yeung, E., Luyster, C., Chung, T., Taylor-Roseman, R., Cogan, K., Dalesandre, G. Kovac, J. Inactivation of Salmonella on cocoa beans using dry-heat treatment. Gamma Sigma Delta Research Expo. University Park, PA, March 26, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Chung, T., Weller D. L., Kovac J. Factors associated with surface water microbial community structure in Northeast US. Penn State Graduate Exhibition. University Park, PA, March 27-29, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Mukherjee, M., Lambert, J., Kovac, J. Cytotoxicity of clade IV dairy-associated isolates on CaCo-2 cells. Penn State Graduate Exhibition. University Park, PA, March 27-29, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Tan, Q., Chung, T., Chen, Y., Macarasin, D., LaBorde, L., Kovac, J. Diversity of built environment microbiomes and their association with the occurrence of Listeria monocytogenes in three fruit packing houses. Penn State Graduate Exhibition. University Park, PA, March 27-29, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Tan, Q., Chung, T., Chen, Y., Macarasin, D., LaBorde, L., Kovac, J. Diversity of built environment microbiomes and their association with the occurrence of Listeria monocytogenes in three fruit packing houses. IAFP Annual meeting. July Louisville, KY, July 21-24, 2019. Poster.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Chung, T., Weller D. L., Kovac J. Factors associated with surface water microbial community structure in Northeast US. IAFP Annual meeting. July Louisville, KY, July 21-24, 2019. Poster.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Tan, Q., Chung, T., Chen, Y., Macarasin, D., LaBorde, L., Kovac, J. Diversity of built environment microbiomes and their association with the occurrence of Listeria monocytogenes in three fruit packing houses. ASM Microbe 2019. San Francisco, CA, June 20-24, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Yan, R., A. Ottesen, P. Ramachandran, E. Strain, E. Reed, J. Kovac. Dynamics of microbiome composition during enrichment of Campylobacter in poultry samples. IAFP Annual meeting. July Louisville, KY, July 21-24, 2019. Poster.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Liao, J., Hohl Orsi, R., Carroll, L. M., Kovac, J., Ou, H., Zhang, H., Wiedmann, M. 2019. Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evolutionary Biology, doi.org/10.1186/s12862-019-1457-5.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Kovac, J. Precision food safety: a paradigm shift in detection and control of foodborne pathogens. 2019. mSystems, doi.org/10.1128/mSystems.00164-19.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Harrand, A. S., Kovac, J., Carroll, L. M., Guariglia-Oropeza, V., Kent, D. J., Wiedmann, M. 2019. Assembly and characterization of a pathogen strain collection for produce safety applications: Pre-growth conditions have a larger effect on peroxyacetic acid tolerance than strain diversity. Frontiers in Microbiology, doi.org/10.3389/fmicb.2019.01223.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Reichler, S. J., Martin, N. H., Evanowski, R. L., Kovac, J., Wiedmann, M., Orsi, R. H. 2019. A century of gray: a genomic locus found in 2 distinct Pseudomonas spp. is associated with historical and contemporary color defects in dairy products worldwide. Journal of Dairy Science, doi: 10.3168/jds.2018-16192.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Bell, T. H., Hockett, K., Alcala-Briseno, R. I., Barberchek, M., Beattie, G. A., Bruns, M. A., Carlson, J., Chung, T., Collins, A., Emmett, B., Esker, P., Garrett, K., Glenna, L., Gugino, B. K., del Mar Jimenez Gasco, M., Kinkel, L., Kovac, J., Kowalski, K., Kuldau, G., Leveau, J., Mischalska-Smith, M., Myrick, J., Peter, K., Vivanco Salazar, Shade, A., Stopinske, N., Tan, X., Wickings, K., Tergeau, E. Manipulating wild and tamed phytobiomes: Challenges and opportunities. Phytobiomes, doi:10.1094/PBIOMES-01-10-0006-W.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Beno, S. B., Orsi, R. H., Cheng, R. A., Kent, D. J., Kovac, J., Duncan, D. R., Martin, N. H., Wiedmann, M. 2019. Genes associated with psychrotolerant Bacillus cereus group isolates. Frontiers in Microbiology, doi:10.3389/fmicb.2019.00662.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Tan, X., Chung, T., Chen, Y., Macarisin, D., LaBorde, L., Kovac., J. 2019. The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities. Microbiome, doi.org/10.1186/s40168-019-0726-2.
|
Progress 05/01/18 to 09/30/18
Outputs
Target Audience:Target audiences that were reached by my research program efforts since May 2018 were following: Students: I have improved the laboratory exercises in FDSC 409: Laboratory in Food Microbiology course that I have developed last year. This is a required course for Food Science majors. The improved lab workflows have been introduced in the (i) Predictive Microbiology class where students are validating Combase predictions of microbial growth by carrying out wet laboratory experiments in foods, (ii) Isolation and identification of a food spoilage microorganism where students are working on naturally contaminated foods to isolate and identify the spoilage microorganism using 16S rRNA PCR amplification, Sanger sequencing and BLAST and (iii) Listeria monocytogenes traceback analyses where students are conducting environmental pathogen sampling in a wet pilot plant and later on work on a simulated pathogen traceback using vector swabbing approach and sigB phylogenetic sequence analyses traceback. This is the first time that Food Science students are learning how to analyze sequences and how to apply them in practical situations in food industry. I have introduced these labs with the goal of equipping Food Science students with bioinformatics skills needed to keep up with the advances in molecular methods used in the industry. These curriculum changes are expected to have a positive impact in terms of broader use of molecular methods for detection, tracing and mitigation of food safety hazard in the food supply chains. I have mentored and continue mentoring 10 undergraduate students that are working on food safety projects in my laboratory. Two of them have secured the Penn State College of Agricultural Sciences research grants in Fall 2018. Two that had graduated in Spring 2018 had secured QA/QC jobs in food industry immediately after graduation. I have hosted and mentored two undergraduate students in my lab this summer - a latin female student from University of Puerto Rico who has decided to pursue an MS degree in Food Science at UPR after the summer research experience and hopes to pursue a PhD degree at Penn State after graduation; and a female African student from Juniata College who is graduating in Fall 2018 and is planning to pursue a graduate degree next Fall after gaining work experience in industry. Both of these students have written scientific papers based on their research in my lab that are currently in preparation for submission to International Journal of Systematic and Evolutionary Microbiology (new bacterial species report) and ASM Microbiology Resource Announcement (report of food E. coli isolates genomic sequences and sequence analyses). I have developed and given a one-day workshop on basic food microbiology techniques and a short workshop on how to review a scientific paper to a group of 13 undergraduate students that have visited Penn State Department of Food Science as part of the summer REEU experience funded by the USDA. Students were from University of Puerto Rico and small colleges from Pennsylvania; a number of them were from underrepresented groups and more than half of them were female. Industry: I have given two lectures and a laboratory practical session to attendees of a Penn State Food Microbiology Short Course that was held at the Department of Food Science on May 24th, 2018. The lectures covered immunological and advanced molecular methods for foodborne pathogen detection in the food supply chain. The practical laboratory session taught attendees how to carry out a PCR-based detection of foodborne pathogens. These efforts are a direct investment in extension education that is expected to result in improved food safety due to better understanding of detection and tracing of microbiological food hazards. Government agencies: I have secured a travel grant to attend the 2018 annual GenomeTrakr meeting organized by the FDA CFSAN and Association of Public Health Laboratories (APHL). I have established new collaborations that led to the collaborative submission of an IAFP symposium proposal focused on using metagenomics methods to identify microbiological hazards in the food supply chain. The graduate student that had accompanied me has started a new collaboration with the FDA CFSAN researchers that is expected to lead to better understanding of the foodborne pathogen enrichment microbiomes and improved approaches to foodborne pathogen isolation methods. Despite the ample advantages of molecular methods, pathogen isolates are still critically needed to study their phenotypes for functional genomics inference validation. Changes/Problems:Identifying associations between production, processing and sanitizing procedures and microbiomes/resistomes in the food supply chain (Objective 4) is challenging in food processing facilities that do not have proper record keeping in place. Inference of associations between sanitizing procedures that are self-reported and facility environmental microbiomes may therefore be biased. For this reason, we are proposing to focus on collection of facility microbiomes and study the effects of sanitizers on L. monocytogenes grown in these natural biofilms in a controlled laboratory environment in Year 2 of this project. What opportunities for training and professional development has the project provided?These projects have provided an opportunity for two Food Science MS graduate students to develop advanced bioinformatics skills through two agricultural microbiome projects. Both students have started the program with no prior bioinformatics experience. One of these students is now proficient in R programming language and has established a weekly Microbiome Study Group for graduate students in Food Science that are interested in developing their data analyses skills. This student has also presented their research at ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatics Pipelines conference and got an opportunity to establish new collaborations. Student that has been collecting samples in tree fruit packinghouses got an opportunity to develop thorough understanding of food safety challenges in this type of food processing operation. They have presented their research in the Penn State Microbiome Center Annual Networking Event and won a best poster award. Ten undergraduate students involved in food safety research in my lab have gotten an opportunity to develop research, study design, laboratory methods and data analyses skills that had helped them obtain jobs and internships in reputable companies, and fellowships in collaborative projects between government agencies and academic institutions (e.g., Christian Hanses, Ecolab, CONSERVE Project, REEU projects). Two of the undergraduate students have drafted their first first-author scientific papers and two are co-authors on these papers. Two MS students are drafting their first papers and developing scientific writing skills. The project has provided students with grant writing training under my mentorship. Two of the undergraduate students have been successful in securing the College of Agricultural Science and the Department of Food Science competitive research funding to pursue their independent studies. How have the results been disseminated to communities of interest?The results of the packinghouse facilities monitoring have been communicated to the stakeholders with recommendations for corrective actions, scientific papers have been published and sequences have been made publicly available through NCBI. What do you plan to do during the next reporting period to accomplish the goals?1. Investigate genomic similarity between sporadic and outbreak clinical, food and environmental isolates of Campylobacter from Pennsylvania. 2. Screen our B. cereus group collection for cytotoxicity and use genomics and proteomics methods to identify links between genotypes and/or secretomes and cytotoxicity phenotypes. 3. Study temporal changes in antimicrobial resistance of Campylobacter in Pennsylvania using genomic sequencing data. 4. Study the interactions between environmental microbiome and pathogens in food processing facilities and characterize the effects of microbiomes on resistance of L. monocytogenes to sanitizers when grown in natural biofilms.
Impacts
What was accomplished under these goals?
1. We have, for the first time, investigated a B. cereus group outbreak using whole genome sequences and have identified a recently published new species B. paranthracis as a causative agent of a foodborne outbreak. We have reported the important epidemiological, microbiological and bioinformatics considerations for investigation of outbreaks associated with closely related species complexes (https://www.biorxiv.org/content/early/2018/08/24/399287). 2. We have optimized and used a high-throughput cytotoxicity assay optimized to screen for cytotoxic potential of diarrheagenic Bacillus cereus group isolates. The method is described in a paper that is under review in Frontiers in Microbiology and is available on BioRxiv https://www.biorxiv.org/content/early/2018/08/24/399287. 3. We have initiated a collaboration between University of Pennsylvania, Pennsylvania Department of Health and Tennessee Integrated Food Safety Center of Excellence/University of Tennessee. We are currently sequencing over 50 human clinical isolates of Campylobacter for comparative genomics analyses with publicly available Pennsylvania retail meet isolate genomes to study Campylobacter population structure and antimicrobial resistance (AMR). Additionally, we have screened our >100 B. cereus group dairy isolate collection for antimicrobial resistance and are in the process of analyzing associations between genetic antimicrobial resistance gene determinants and antimicrobial resistance phenotypes to facilitate genome-based AMR prediction. 4. We have completed first season of longitudinal monitoring of tree fruit packinghouse environmental microbiomes and cultured Listeria monocytogenes, and identified distinct microbiomes in a facility with persisting L. monocytogenes genotype. Publication is in preparation and the second season monitoring will be launched in November. Further studies aimed at understanding the interactions between L. monocytogenes and environmental microbiomes are underway. We have also identified distinct microbiomes in surface waters that have livestock operations upstream the sampling sites. Water in these streams is commonly used for agricultural irrigation and may present food safety risk. We are in the process of data analyses to identify potential new indicators of food safety hazards.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2018
Citation:
Laura M Carroll, Martin Wiedmann, Manjari Mukherjee, David C Nicholas, Lisa A Mingle, Nellie B Dumas, Jocelyn A Cole, Jasna Kovac. Characterization of emetic and diarrheal Bacillus cereus strains from a 2016 foodborne outbreak using whole-genome sequencing: addressing the microbiological, epidemiological, and bioinformatic challenges.
bioRxiv 399287; doi: https://doi.org/10.1101/399287
Under review in Frontiers in Microbiology.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Kovac, J. (July 9, 2018). "Re-classification of Bacillus cereus group dairy isolates and characterization of their pathogenic potential," Talk - Annual meeting of International Association for Food Protection, IAFP, Salt Lake City, UT.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Kovac, J. (June 26, 2018). "Applying whole genome sequencing to illuminate dairy sporeformers," Invited talk - Annual Meeting of the American Dairy Science Association, ADSA, Knockville, TN.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Chung, T., Weller, D., Kovac, J. (September 23, 2018 - September 26, 2018). "Factors associated with surface water microbial community structure in Northeast US," Poster presentation - The ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines, American Society for Microbiology, Washington DC area.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Kovac, J. (May 10, 2018 - June 11, 2018). "Pathogenic potential of the Bacillus cereus group in the context of phylogeny and taxonomy," Poster presentation - 2nd conference on preparing winning grants, Delaware State University in collaboration with USDA/NIFA-Institute of Food Safety and Nutrition, Dover, DE.
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