Research

Reference:

Chandross-Cohen, T., Chung, T., Watson, S.C., Rolon, M.L., Kovac, J. (2025). Precision food safety: Advances in omics-based surveillance for proactive detection and management of foodborne pathogens. Trends in Food Science & Technology, 163:105186. https://doi.org/10.1016/j.tifs.2025.105186

Research Areas

1. Environmental Microbiota and Foodborne Pathogen Persistence in Food Processing Facilities

Our lab investigates the environmental microbiota of food processing facilities and how these resident microbial communities shape the survival, persistence, and antimicrobial tolerance of foodborne pathogens, with a primary focus on Listeria monocytogenes. Using tree fruit packing facilities as a model system, we combine longitudinal environmental sampling, culturing, amplicon and shotgun metagenomic sequencing, and controlled biofilm assays to track how microbiota composition changes across facilities and seasons, and to identify bacterial and fungal taxa associated with L. monocytogenes contamination (Rolon et al., 2023). We have also evaluated how improved sanitation standard operating procedures affect total microbial populations and pathogen occurrence in these environments (Rolon et al., 2025).

A core line of our work examines how co-occurring environmental bacteria, including Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae, form multi-species biofilms that protect L. monocytogenes from common sanitizers such as benzalkonium chloride and peroxyacetic acid (Rolon et al., 2024; Voloshchuk et al., 2025). In parallel, we use whole-genome sequencing to characterize sanitizer resistance, antimicrobial resistance and virulence genes, and long-term strain persistence in facility environments (Méndez Acevedo et al., 2024). Together, this research supports evidence-based sanitation and environmental monitoring strategies to reduce pathogen persistence and improve food safety in produce processing environments.

Select papers:

Rolon, M.L. et al. (2023). The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination. Microbiome, 11:128. https://doi.org/10.1186/s40168-023-01544-8

Rolon, M.L. et al. (2025). Impact of improved sanitation standard operating procedures on microbial populations at three tree fruit packing facilities. Journal of Food Protection, 88:100436. https://doi.org/10.1016/j.jfp.2024.100436

Méndez Acevedo, M. et al. (2024). Sanitizer resistance and persistence of Listeria monocytogenes isolates in tree fruit packing facilities. Journal of Food Protection, 87:100354. https://doi.org/10.1016/j.jfp.2024.100354

Voloshchuk, O. et al. (2025). Pseudomonadaceae increased the tolerance of Listeria monocytogenes to sanitizers in multi-species biofilms. Food Microbiology, 128:104687. https://doi.org/10.1016/j.fm.2024.104687

Rolon, M.L. et al. (2024). Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride. Biofilm, 7:100177. https://doi.org/10.1016/j.bioflm.2024.100177

2. Genomic Subtyping and Risk Prediction of Foodborne Pathogens Using Bacillus cereus Group as a Model System

Our lab integrates whole-genome sequencing, bioinformatics, cell-based cytotoxicity assays, and traditional microbiological methods to characterize foodborne pathogens at the subtype (strain, lineage, and genomospecies) level and to translate genomic data into food safety risk predictions. We use the Bacillus cereus group,  a genomically diverse species complex spanning industrial biopesticide strains, the bioterrorism agent B. anthracis, and toxin-producing foodborne pathogens, as a model system, since its taxonomic complexity and phenotypic heterogeneity make it a stringent test case for linking genotype to phenotype and risk.

A first thread of this work has focused on resolving the group's taxonomy so that genomic classification remains interpretable and actionable for clinicians, industry, and regulators. This includes proposing a genomospecies-subspecies-biovar nomenclatural framework reconciling genomic species definitions with clinical and industrial phenotypes (Carroll et al., 2020), describing a novel psychrotolerant, cytotoxic species (Bacillus wiedmannii) isolated from dairy environments (Miller et al., 2016), evaluating whether low-cost typing methods remain congruent with genomics-based taxonomy (Carroll et al., 2020), benchmarking bioinformatics tools for identifying insecticidal biovar Thuringiensis strains (Chung et al., 2024), and synthesizing the field's taxonomic progress in a comprehensive review (Carroll et al., 2022).

A second thread applies genomic and phenotypic subtyping to understand and predict pathogenic potential and food safety risk, including antimicrobial resistance. This includes demonstrating that toxin gene presence alone is a poor predictor of cytotoxicity, and that phylogenetic clade better explains variability in toxin production across strains (Miller et al., 2018; Kovac et al., 2016), applying whole-genome sequencing to reconstruct a real-world foodborne outbreak (Carroll et al., 2019), characterizing how temperature and food matrix modulate virulence gene expression and toxin stability in psychrotolerant, dairy-relevant strains (Chandross-Cohen et al., 2026), building a quantitative exposure assessment model to predict the risk of cytotoxic strains growing to hazardous levels during HTST milk storage (Su, Chandross-Cohen et al., 2024), evaluating improved detection methods for B. cereus group contamination in powdered infant formula and infant cereal (Nguyen et al., 2026), and showing that antimicrobial resistance genotypes correlate poorly with phenotypic resistance, while disk diffusion susceptibility testing is unreliable for this group compared to broth microdilution (Mills et al., 2022). 

Underpinning this experimental work, we have also synthesized the field's understanding of the complex regulatory networks controlling enterotoxin expression, highlighting why enterotoxin gene presence alone is insufficient to predict toxicoinfection and identifying knowledge gaps that need to be closed to develop reliable genetic markers of virulence (Prince and Kovac, 2022). Together, this research aims to move B. cereus group risk assessment beyond simple presence/absence testing toward subtype- and genotype-informed, quantitative food safety decision-making.

Select papers:

Carroll, L.M. et al. (2019). Characterization of emetic and diarrheal Bacillus cereus strains from a 2016 foodborne outbreak using whole-genome sequencing. Frontiers in Microbiology, 10:144. https://doi.org/10.3389/fmicb.2019.00144

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, 11. https://doi.org/10.1128/mbio.00034-20

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, 11:580691. https://doi.org/10.3389/fmicb.2020.580691

Mills, E., Sullivan, E., Kovac, J. (2022). Comparative analysis of Bacillus cereus group isolates' resistance using disk diffusion and broth microdilution and the correlation between antimicrobial resistance phenotypes and genotypes. Applied and Environmental Microbiology, 88:e02302-21. https://doi.org/10.1128/aem.02302-21

Prince, C., Kovac, J. (2022). Regulation of enterotoxins associated with Bacillus cereus sensu lato toxicoinfection. Applied and Environmental Microbiology, 88:e00405-22. https://doi.org/10.1128/aem.00405-22

Carroll, L.M., Cheng, R.A., Wiedmann, M., Kovac, J. (2022). Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond. Critical Reviews in Food Science and Nutrition, 62:7677–7702. https://doi.org/10.1080/10408398.2021.1916735

Chung, T., Salazar, A., Harm, G., Johler, S., Carroll, L.M., Kovac, J. (2024). Comparison of the performance of multiple whole-genome sequence-based tools for the identification of Bacillus cereus sensu stricto biovar Thuringiensis. Applied and Environmental Microbiology, 90:e01778-23. https://doi.org/10.1128/aem.01778-23

Su, J., Chandross-Cohen, T. et al. (2024). Assessment of the exposure to cytotoxic Bacillus cereus group genotypes through high-temperature, short-time milk consumption. Journal of Dairy Science. https://doi.org/10.3168/jds.2024-24703

Chandross-Cohen, T. et al. (2026). Environmental modulation of cytotoxicity and virulence factor stability in psychrotolerant Bacillus cereus group isolates. Food Microbiology, 140:105166. https://doi.org/10.1016/j.fm.2026.105166

Nguyen, P.T., Chandross-Cohen, T., Kovac, J., Restaino, L. (2026). Isolation and characterization of Bacillus cereus group species in powdered infant formula and infant cereal using a newly developed detection system. Journal of Food Protection, 89:100677. https://doi.org/10.1016/j.jfp.2025.100677

3. Campylobacter jejuni Ecology, Antimicrobial Resistance, and Viable but Nonculturable State on Poultry Meat

Our lab studies Campylobacter jejuni prevalence, antimicrobial resistance, and the biotic and abiotic factors that drive it into a viable but nonculturable (VBNC) state on chicken meat, a state in which cells remain intact and potentially infectious but fail to grow on standard culture media, causing culture-based methods to underestimate true pathogen burden. We combine culture-based enumeration, viability qPCR, whole-genome sequencing, and controlled challenge studies to characterize how C. jejuni survives processing, storage, and antimicrobial interventions, and to determine when culturability data alone can be misleading for food safety risk assessment.

One thread of this work characterizes C. jejuni occurrence and resistance in the field. This includes surveying retail chicken breasts and finding Campylobacter prevalence and concentrations to be low but detectable, with viability qPCR revealing a VBNC subpopulation missed by culture-based testing (Navarre et al., 2025), and comparing antimicrobial resistance and its underlying genetic determinants between Campylobacter isolated from human clinical cases and poultry meat in Pennsylvania, showing higher fluoroquinolone resistance in human isolates and generally good, but imperfect, genotype-phenotype concordance (Yan et al., 2023).

A second thread investigates how chicken meat microbiota and antimicrobial treatments jointly shape C. jejuni survival and culturability. We showed that psychrotolerant spoilage bacteria naturally present on chicken meat (e.g., Pseudomonas, Brochothrix, Acinetobacter) can enhance C. jejuni culturability during refrigerated aerobic storage, while culture-based methods substantially underestimated viable cell concentrations relative to viability qPCR (Yan et al., 2026). We also evaluated peroxyacetic acid (PAA), a poultry processing antimicrobial, and found that it significantly reduced C. jejuni culturability without proportionally reducing viability, inducing a portion of the population into a VBNC state and causing culture-based plating to overestimate PAA's true antimicrobial effect by up to 1 log (Navarre et al., 2026). Together, this research highlights that pairing culture-based and molecular viability methods is necessary to accurately assess Campylobacter die-off and persistence, and it informs more reliable antimicrobial intervention and risk assessment strategies for poultry products.

Select papers:

Yan, R., M'ikanatha, N.M., Nachamkin, I., Hudson, L.K., Denes, T.G., Kovac, J. (2023). Prevalence of ciprofloxacin resistance and associated genetic determinants differed among Campylobacter isolated from human and poultry meat sources in Pennsylvania. Food Microbiology, 116:104349. https://doi.org/10.1016/j.fm.2023.104349

Navarre, A., Rupert, K., Chandross-Cohen, T., Kovac, J. (2025). Low prevalence and concentrations of Campylobacter detected on retail chicken breasts. Journal of Food Protection, 88:100635. https://doi.org/10.1016/j.jfp.2025.100635

Navarre, A., Quintana-Pérez, F.M., Kovac, J. (2026). Peroxyacetic acid treatment significantly reduced Campylobacter jejuni culturability but not viability on chicken breasts. Food Control, 180:111652. https://doi.org/10.1016/j.foodcont.2025.111652

Yan, R., Watson, S.C., Wei, X., Kovac, J. (2026). Psychrotolerant spoilage bacteria enhanced Campylobacter jejuni culturability on refrigerated chicken meat. Food Microbiology, 138:105051. https://doi.org/10.1016/j.fm.2026.105051

4. Microbial Ecology and Foodborne Pathogen Persistence in Soilless (Hydroponic) Farming Systems

As controlled environment agriculture expands to improve food security and resource efficiency, our lab studies how hydroponic system design shapes the microorganisms present in these production environments and the food safety risks that result. We investigate how factors like system type, nutrient solution chemistry, and growing cycle affect microbial community composition and load, characterize the persistence of foodborne pathogens across different hydroponic system designs, evaluate the efficacy of control strategies applied at different stages of hydroponic production, and study the genetic basis underlying pathogen survival in these systems.

Our first study in this area compared five common soilless system types (deep water culture, Kratky, nutrient film technique, ebb and flow, and drip irrigation) over two bok choy growing cycles. We found that microbial load and bacterial community composition in the nutrient solution varied significantly by system type, growing cycle, and sampling day, with drip irrigation systems showing the highest aerobic plate counts and nutrient solution pH negatively associated with microbial load. Core microbiota analysis identified Acidovorax, Legionella, and Caulobacter as core and hub taxa across systems, with Acidovorax detected in every sample, warranting further investigation into their roles in plant health and food safety (Bywater et al., 2026). This foundational work establishes how system design drives microbial dynamics in hydroponic production and sets the stage for our ongoing studies of pathogen persistence, intervention efficacy, and the genetic determinants of survival across these engineered growing environments.

Select papers:

Bywater, A., Novaski Seffrin, A., Bisanz, J.E., Di Gioia, F., Kovac, J. (2026). Soilless farming system design impacts the diversity and composition of microbiota. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.01167-26

5. Food Safety in Low- and Middle-Income Country Dairy and Produce Supply Chains (Focus on Ethiopia and Cambodia)

We collaborate on food safety research in international, resource-limited settings. To date, our focus was on the Ethiopian dairy value chain and the Cambodian fresh produce supply chain to generate the baseline prevalence, risk factor, and genomic data needed to design context-appropriate interventions in low- and middle-income countries (LMICs). This work combines cross-sectional and longitudinal field sampling, standard culture-based pathogen detection, epidemiological risk-factor analysis, and whole-genome sequencing to characterize foodborne pathogen occurrence, transmission, and persistence, as well as the social dimensions of food safety, in settings where surveillance and intervention resources are limited.

In Ethiopia, we collaborated on work that systematically characterized foodborne pathogen contamination across the dairy value chain, from producers to collectors, processors, and retailers of raw milk, pasteurized milk, and cottage cheese. In a review of the literature, we established baseline prevalence estimates for Salmonella, Listeria monocytogenes, and E. coli O157:H7 in Ethiopian dairy products and identified major gaps, including a complete absence of Campylobacter data at the time (Keba et al., 2020). We subsequently filled that gap and others through large cross-sectional studies (n = 912 samples) documenting the prevalence and farm- and facility-level risk factors for Campylobacter (Admasie et al., 2022), Salmonella (Bedassa et al., 2023), and Listeria (Hassen et al., 2025) contamination, along with a broader assessment of microbial hygiene indicators (aerobic plate counts, coliforms, generic E. coli) showing widespread noncompliance with Ethiopian food safety standards (Mengstu et al., 2023). Seasonal follow-up studies further showed that Salmonella prevalence was higher in the dry season (Nahusenay et al., 2024) while Campylobacter prevalence and antimicrobial resistance varied regionally by season, with high resistance to tetracycline, erythromycin, and ciprofloxacin (Admasie et al., 2024).

At the genomic level, whole-genome sequencing and SNP-based phylogenetics of L. monocytogenes and L. innocua isolates from the dairy supply chain revealed low intra-sequence-type genetic diversity consistent with strain selection and persistence within the supply chain (Wei, Hassen et al., 2024). Recognizing that food safety interventions need to account for social context, we also collaborated on examining the gendered dimensions of dairy handling in Ethiopia, showing that women's central role in milking and animal husbandry disproportionately exposes them to milk-, water-, and animal-borne pathogens, and arguing for gender-sensitive food safety interventions (Garsow et al., 2022).

In Cambodia, we extended this genomics-driven approach to the fresh produce sector, sequencing Salmonella enterica and E. coli isolates collected from farms, distribution centers, and markets along the vegetable supply chain in two provinces. SNP-based relatedness analysis identified closely related isolates of the same serotype recovered from different supply chain stages, provinces, and time points, providing genomic evidence of Salmonella transmission and persistence within the Cambodian vegetable supply chain and informing where targeted control measures could have the greatest impact (Salazar et al., 2025).

Select papers:

Keba, A. et al. (2020). Review of the prevalence of foodborne pathogens in milk and dairy products in Ethiopia. International Dairy Journal, 109:104762. https://doi.org/10.1016/j.idairyj.2020.104762

Garsow, A.V. et al. (2022). Exploring the relationship between gender and food safety risks in the dairy value chain in Ethiopia. International Dairy Journal, 124:105173. https://doi.org/10.1016/j.idairyj.2021.105173

Admasie, A. et al. (2023). Prevalence of Campylobacter species and associated risk factors for contamination of dairy products collected in a dry season from major milk sheds in Ethiopia. Food Microbiology, 109:104145. https://doi.org/10.1016/j.fm.2022.104145

Mengstu, B. et al. (2023). Evaluation of microbial hygiene indicators in raw milk, pasteurised milk and cottage cheese collected across the dairy value chain in Ethiopia. International Dairy Journal, 136:105487. https://doi.org/10.1016/j.idairyj.2022.105487

Bedassa, A. et al. (2023). Prevalence and associated risk factors for Salmonella enterica contamination of cow milk and cottage cheese in Ethiopia. Food Safety and Risk, 10:2. https://doi.org/10.1186/s40550-023-00101-3

Admasie, A. et al. (2024). Seasonal variation in the prevalence and antimicrobial resistance of Campylobacter species in milk and milk products in Ethiopia. International Dairy Journal, 149:105826. https://doi.org/10.1016/j.idairyj.2023.105826

Nahusenay, H. et al. (2024). Seasonal variation of Salmonella enterica prevalence in milk and cottage cheese along the dairy value chain in three regions of Ethiopia. Food Safety and Risk, 11:2. https://doi.org/10.1186/s40550-024-00108-4

Wei, X., Hassen, A. et al. (2024). Genomic characterization of Listeria monocytogenes and Listeria innocua isolated from milk and dairy samples in Ethiopia. BMC Genomic Data, 25:12. https://doi.org/10.1186/s12863-024-01195-0

Hassen, A. et al. (2025). Prevalence of Listeria monocytogenes and Listeria species and associated risk factors for contamination of milk and cottage cheese along the value chains in Ethiopia. International Journal of Food Microbiology, 429:111021. https://doi.org/10.1016/j.ijfoodmicro.2024.111021

Salazar, A. et al. (2025). Genomic diversity and potential transmission and persistence of Salmonella in the Cambodian vegetable supply chain. Journal of Food Protection, 88:100447. https://doi.org/10.1016/j.jfp.2024.100447

6. Collaborative Innovations in Diagnostics, Genomics, and Outbreak Surveillance

Beyond our core food safety research areas, our lab collaborates with engineers, computational biologists, and public health partners to develop new tools and methods with applications spanning diagnostics, pathogen genomics, and outbreak detection.

Rapid antimicrobial susceptibility testing (AST). Working with electrical engineers at Penn State, we have helped develop dynamic laser speckle imaging (DLSI) as a label-free, machine-learning-driven approach to AST that determines minimum inhibitory concentrations in hours rather than days. This began with a benchtop proof of concept that predicted ampicillin and gentamicin MICs for E. coli in 60 minutes (Zhou et al., 2020), advanced to a holographic variant capable of testing at low bacterial concentrations across Gram-positive and Gram-negative organisms (Yang et al., 2025, Biosensors and Bioelectronics), and most recently produced a 3D-printed, portable, cellphone-camera-based device designed for point-of-care use in resource-limited settings (Yang et al., 2025, ECS Sensors Plus).

Microbial genome evolution and horizontal gene transfer. In collaboration with Dr. Stefanic at the University of Ljubljana, we contribute to studying the evolutionary forces shaping bacterial genomes using Bacillus subtilis as a model. This work showed that kin discrimination (i.e., the antagonistic killing that occurs when genetically distinct B. subtilis swarms meet) actually promotes horizontal gene transfer between unrelated strains, with dying donor cells releasing DNA that surviving, stress-responsive recipient cells take up via natural transformation (Stefanic et al., 2021). A follow-up study characterized the diversity and distribution of prophages (integrated bacteriophage elements) across global and local B. subtilis isolates, finding that phylogenetic relatedness predicts a strain's prophage repertoire better than geographic origin, and that carrying more prophages is associated with heightened host stress responses (Stefanic et al., 2025). Together, these studies inform our understanding of how mobile genetic elements and social interactions between strains shape bacterial genome evolution, providing a foundational perspective relevant to how pathogens acquire and spread traits like virulence and antimicrobial resistance.

Genomic taxonomic markers and pathogen identification. With computational biology collaborators, we have contributed to the development of kmerDB, a public database and web interface cataloguing species-specific genomic and proteomic sequence signatures ("quasi-primes") across tens of thousands of reference genomes and proteomes, to support taxonomic classification and comparative genomics (Mouratidis et al., 2024). Building on this concept, we helped apply "genomic quasi-G-primes" (short, species-specific DNA signatures) to distinguish septic from healthy patients using blood-derived sequencing data, offering a space-efficient alternative to conventional metagenomic classification for infection diagnostics (Sha et al., 2026).

Wastewater epidemiology for outbreak detection. In collaboration with Dudley lab and the Pennsylvania Department of Health, we evaluated sewage monitoring as a complement to traditional foodborne disease surveillance. Screening wastewater from two central Pennsylvania treatment plants, this research recovered Salmonella isolates that were genomically indistinguishable from strains involved in a concurrent multistate Salmonella Baildon outbreak, demonstrating that wastewater surveillance can detect outbreak-associated strains circulating in a community even without matching clinical cases (Goldblum et al., 2024; M'ikanatha et al., 2024).

Select papers:

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 Sensors, 5:3140–3149. https://doi.org/10.1021/acssensors.0c01238

Stefanic, P., Belcijan, K., Kraigher, B., Kostanjšek, R., Nesme, J., Madsen, J.S., Kovac, J., Sørensen, S.J., Vos, M., Mandic-Mulec, I. (2021). Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis. Nature Communications, 12:3457. https://doi.org/10.1038/s41467-021-23685-w

Goldblum, Z.S., M'ikanatha, N.M., Nawrocki, E.M., Cesari, N., Kovac, J., Dudley, E.G. (2024). Salmonella sp. tied to multistate outbreak isolated from wastewater, United States, 2022. Emerging Infectious Diseases, 30:2695. https://doi.org/10.3201/eid3012.240443

M'ikanatha, N.M., Goldblum, Z.S., Cesari, N., Nawrocki, E.M., Fu, Y., Kovac, J., Dudley, E.G. (2024). Outbreak-associated Salmonella Baildon found in wastewater demonstrates how sewage monitoring can supplement traditional disease surveillance. Journal of Clinical Microbiology, 62:e00825-24. https://doi.org/10.1128/jcm.00825-24

Mouratidis, I., Baltoumas, F.A., Chantzi, N., Patsakis, M., Chan, C.S.Y., Montgomery, A., Konnaris, M.A., Aplakidou, E., Georgakopoulos, G.C., Das, A., Chartoumpekis, D.V., Kovac, J., Pavlopoulos, G.A., Georgakopoulos-Soares, I. (2024). kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species. Computational and Structural Biotechnology Journal, 23:1919–1928. https://doi.org/10.1016/j.csbj.2024.04.050

Yang, J., Zhou, K., Sapre, A., et al., Kovac, J., Liu, Z., Ebrahimi, A. (2025). Label-free rapid antimicrobial susceptibility testing with machine-learning based dynamic holographic laser speckle imaging. Biosensors and Bioelectronics, 278:117312. https://doi.org/10.1016/j.bios.2025.117312

Yang, J., Zhou, K., Hernandez, L., Zhou, C., Voloshchuk, O., Kovac, J., Ebrahimi, A., Liu, Z. (2025). Portable dynamic laser speckle imaging for rapid antimicrobial susceptibility testing. ECS Sensors Plus, 4:044601. https://doi.org/10.1149/2754-2726/ae1e10

Stefanic, P., Stare, E., Floccari, V.A., Kovac, J., Hertel, R., Rocha, U., Kovács, Á.T., Mandic-Mulec, I., Strube, M.L., Dragoš, A. (2025). Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales. Cell Reports, 44:115197. https://doi.org/10.1016/j.celrep.2024.115197

Sha, C.M., Patsakis, M., Mouratidis, I., Wei, X., Chung, T., Kovac, J., Georgakopoulos-Soares, I. (2026). Doing more with less: Genomic quasi-G-primes differentiate septic from healthy patients. PLOS ONE, 21:e0341828. https://doi.org/10.1371/journal.pone.0341828

Mission

The mission of our lab is to create environment and resources conducive to

1. Innovative, productive, responsible and reproducible undergraduate and graduate research with positive societal impact;
2. Promotion of STEM among women and diversity groups and
3. Training of a new generation of food scientists equipped with microbiological and bioinformatics skills and broad understanding of societal challenges related to food safety.

Values

Our lab's values are aligned with Penn State's core values.

Integrity: We act with integrity and honesty in accordance with the highest academic, professional, and ethical standards.

Respect: We respect and honor the dignity of each person, embrace civil discourse, and foster a diverse and inclusive community.

Responsibility: We act responsibly, and we are accountable for our decisions, actions, and their consequences.

Discovery: We seek and create new knowledge and understanding and foster creativity and innovation for the benefit of our communities, society, and the environment.

Excellence: We strive for excellence in all our endeavors as individuals, an institution, and a leader in higher education.

Community: We work together for the betterment of our University, the communities we serve, and the world.

Publications

The list of publications is available at the bottom of the directory page.