Shirley Micallef, Ph.D.

Professor, UM - Department of Plant Science and Landscape Architecture, CFS3
2126 Plant Sciences Building
College Park, MD 20742
United States


My research focuses on the microbiological safety of fresh produce. Main research areas include:

  • (i) assessing the impact of various cropping practices on the persistence of foodborne enteric pathogens in the agricultural environment, including cover crops, soil amendments and mulches
  • (ii) environmental metabolomics of plant surfaces to understand enteric pathogen colonization of plants
  • (iii) studying enteric pathogen-plant responses when associating with each other
  • (iv) crop microbiomes

My current research focuses on microbial food safety of fruits and vegetables, specifically looking at how human pathogens associate with specialty crops and how they interact with the environment. In our lab, we investigate microbial produce safety at all levels of biology, from the molecular responses of pathogen-commodity pairs, to the ecology of enteric pathogens in the agro-environment. We use a multidiscplinary approach and utilize a variety of methods to assess enteric pathogen populations and their ecology, as well as molecular and sequencing technologies to evaluate the plant microbiome and pathogen-plant responses.

Research projects involve investigating Salmonella growth on pre-harvest tomatoes and the influence of plant genetic variation on plant-enteric pathogen relationships. This works also leads to enteric pathogen responses to the vegetarian lifestyle. Another area of investigation is the impact that various cropping methods have on the persistence and dispersal of human pathogens in pre-harvest production areas, as well as the ecology of Salmonella in the environment.

I am also involved in Good Agricultural Practices (GAP) training evaluation in Maryland, assessing the effectiveness of training in driving GAPs implementation on farms.

Funded Projects:

Resistance through diversity: Understanding Salmonella phenotypic plasticity and decision making in response to antimicrobials - Tier 1 Funding Competition 2017, University of Maryland.

CONSERVE: A Center of Excellence at the Nexus of Sustainable Water Reuse, Food, and Health - USDA-NIFA Water for Agriculture

Reducing On-Farm Enteric Pathogens through Cropping Methods and Improved Food Safety Trainings - USDA/NIFA - Agriculture and Food Research Initiative (AFRI)

‘Evaluating the effect of muskmelon cultivar and cover crops on soil biodiversity, and plant and human disease suppression during organic production’ - USDA-NIFA-Organic Transitions Program.

When tomatoes talk back: Salmonella-tomato plant interactions and pathogen growth responses to plant defense activation’. - UMD ADVANCE Interdisciplinary and Engaged Research Seed Grant Program

Microbiological study and development of microbial risk assessment of Listeria monocytogenes on Cucurbitaceae fruits. International Collaborative Research Agreement – Rural Development Administration, South Korea.

Developing Scientifically-based Consensus Food Safety Metrics for Leafy Greens and Tomatoes. Specialty Crop Research Initiative (SCRI), Coordinated Agricultural Project (CAP), USDA.

Quantitative Risk Assessment for Listeria monocytogenes in Cantaloupes. Maryland Agricultural Experiment Station Competitive Grants Program.

Microbiological assessment of organic produce pre- and post-harvest and development of a customized food safety outreach program for organic growers. Maryland Agricultural Experiment Station Competitive Grants Program.

Hsu CK and Micallef SA, 2017. Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria. International Journal of Food Microbiology 2017 Jul 27;259:1-6. doi: 10.1016/j.ijfoodmicro.2017.07.012. [Epub ahead of print] 
Micallef SA and Buchanan RL, 2017.  Regulatory issues associated with pre-harvest food safety - United States perspective. Microbiology Spectrum 2017, 5(4). doi:10.1128/microbiolspec. PFS-0016-2016. 
Pang H, McEgan R, Micallef SA, Pradhan AK, 2017. Evaluation of Meteorological Factors Associated with Pre-harvest Contamination Risk of Generic Escherichia coli in a Mixed Produce and Dairy Farm. Food Control – in press.
Dev Kumar G and Micallef SA, 2017. Susceptibility of Salmonella enterica isolates from tomato farm environments to fatty acids naturally found on tomato fruit.  2017, 14(5):293-301. doi: 10.1089/fpd.2016.2239. PMID: 28398868
Goldstein RR, Kleinfelter L, He X, Micallef SA, George A, Gibbs SG, Sapkota AR, 2017.  Higher prevalence of coagulase-negative staphylococci carriage among reclaimed water spray irrigators.  Sci Total Environ. 2017 Apr 1;595:35-40. doi: 10.1016/j.scitotenv.2017.03.174. [Epub ahead of print]. PMID: 28376426
Sharma M, Dashiell G, Handy ET, East C, Reynnells R, White C, Nyarko E, Micallef SA, Hashem F, and  Millner PD, 2017.  Survival of Salmonella Newport on whole and fresh-cut cucumbers treated with lytic bacteriophages. Journal of Food Protection (2017) 80(4): 668-673. doi:10.4315/0362-028X.JFP-16-449
 Allard SM, Walsh CS, Wallis AE, Ottesen AR, Brown EW, Micallef SA*, 2016.  Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers. Science of the Total Environment (2016) 573:555-563. doi: 10.1016/j.scitotenv.2016.08.157.  PMID: 27580466

Micallef SA*, Callahan MT and Pagadala S, 2016.  Occurrence and dispersal of indicator bacteria on cucumber grown horizontally or vertically on various mulch types.  Journal of Food Protection (2016) 79(10): 1663-1672.

Callahan MT, Micallef SA, Sharma M, Millner PD, Buchanan RL, 2016.  Investigating Metrics Proposed to Prevent the Harvest of Leafy Green Crops Exposed to Floodwater Contaminated with Escherichia coli. Appl Environ Microbiol. 2016 Apr 15. pii: AEM.00052-16. [Epub ahead of print] PMID: 27084022

Han S and Micallef SA*, 2016. Environmental metabolomics of the plant surface provides insights on Salmonella enterica colonization of tomato. Applied and Environmental Microbiology, 82:10 3131-3142; Accepted manuscript posted online 18 March 2016, doi: 10.1128/AEM.00435-16. PMID: 26994076 

Callahan MT, Marine SC, Everts KL and Micallef SA*, 2016. Drip line flushing with chlorine may not be effective in reducing bacterial loads in irrigation water distribution systems. Journal of Food Protection (2016) – accepted 23 February 2016, in press.  doi:10.4315/0362-028X.JFP-16-011

Xu A, Buchanan RL, Micallef SA*, 2016.  Impact of mulches and growing season on indicator bacteria survival during lettuce cultivation.  International Journal of Food Microbiology 224:28-39. doi: 10.1016/j.ijfoodmicro.2016.02.013 [Epub ahead of print]. PMID: 26938806.

Reed-Jones N, Marine SC, Everts K and Micallef SA*, 2016. Effect of cover crop species and season on population dynamics of Escherichia coli and Listeria innocua in soil. Applied and Environmental Microbiology – posted online 4 January 2016, doi: 10.1128/AEM.03712-15. PMID: 26729724

Rainfall intensity effects on removal of fecal indicator bacteria from solid dairy manure applied over grass-covered soil.  Science of the Total Environment 539:583-591. doi: 10.1016/j.scitotenv.2015.07.108. Epub 2015 Sep 18. PMID: 26386449

Xu. A., Pahl, D.M., Buchanan R. and Micallef S.A.*. Comparing the microbiological status of pre- and post-harvest produce from small organic production. Journal of Food Protection 78(6):1072-80. doi: 10.4315/0362-028X.JFP-14-548. PMID: 26038895

Marine S.C.†, Pagadala S.†, Wang F.†, Pahl D.M., Melendez M.V., Kline W. L., Oni R.A., Walsh C.S., Everts K.L., Buchanan R.L. and Micallef S.A.*. Growing season, but not farming system, a food safety risk determinant for leafy greens in the mid-Atlantic region, Applied and Environmental Microbiology (2015) 81(7):2395-407 - online 23 January 2015, doi: 10.1128/AEM.00051-15. PMID: 25616798.   

Pagadala S.†, Marine S.C.†, Micallef S.A.*, Wang F., Pahl D.M., Melendez M.V., Kline W. L., Oni R.A., Walsh C.S., Everts K.L. and Buchanan R.L. "Assessment of region, farming system, irrigation source and sampling time as food safety risk factors for tomatoes and their production areas on small- and medium-sized farms in Maryland, Delaware and New Jersey" Int J Food Microbiol. 2015 Mar 2;196:98-108. doi: 10.1016/j.ijfoodmicro.2014.12.005. Epub 2014 Dec 13. PMID:25540859

Han S. and Micallef S.A.*, 2014. Salmonella Newport and Typhimurium Colonization of Fruit Differs from Leaves in Various Tomato Cultivars –Journal of Food Protection 77(11):1844-50. doi: 10.4315/0362-028X.JFP-13-562.

Rachel E. Rosenberg Goldstein, Shirley A. Micallef, Shawn G. Gibbs, Xin He, Ashish George, Amir Sapkota, Sam W. Joseph, Amy R. Sapkota.  Occupational exposure to Staphylococcus aureus and Enterococcus spp. among spray irrigation workers using reclaimed water. International Journal of Environmental Research and Public Health (2014) 11(4), 4340-4355.

Rosenberg Goldstein R.E., Micallef S.A., Gibbs S.G., George A., Claye E., Sapkota A., Joseph S.W., Sapkota A.R. Detection of Vancomycin-Resistant Enterococci (VRE) at Four U.S. Wastewater Treatment Plants that Provide Effluent for Reuse. Science of the Total Environment (2014) 1;466-467:404-11. PMID:23933428.

Micallef, S.A. and Colón-Carmona, A. (2013) Genetic and Developmental Control of Rhizosphere Bacterial Communities, in Molecular Microbial Ecology of the Rhizosphere: Volume 1 & 2 (ed F.J. de Bruijn), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118297674.ch24

Micallef S.A., Rosenberg Goldstein R.E., George A., Ewing L., Tall B.D., Boyer, M.S., Joseph S.W., Sapkota A.R. Diversity , Distribution abd Antibiotic Resistance of Enterococcus spp. Recovered from Tomatoes, Leaves, Water and Soil on Mid-Atlantic Farms. Food Microbiology (2013) 36(2):465-74. PMID:24010630

Rosenberg Goldstein R.E., Micallef S.A., Gibbs S.G., Davis J.A., He X., George A., Kleinfelter L.M., Schreiber N.A., Mukherjee S., Sapkota A., Joseph S.W., Sapkota A.R. Methicillin-Resistant Staphylococcus aureus (MRSA) Detected at Four U.S. Wastewater Treatment Plants. Environmental Health Perspectives(2012) 120(11):1551-1558. PMID: 23124279

Jean-Gilles Beaubrun, J., Cheng, C.-M., Chen, K.-S., Ewing, L., Wang, H., Agpaoa, M.C., Huang, M.- C.J., Dickey, E., Du, J.M., Williams-Hill, D.M., Hamilton B., Micallef S.A., Rosenberg Goldstein R.E., George A., Joseph, S.W., Sapkota, A.R., Jacobson, A.P., Tall, B.D., Kothary, M.H., Dudley, K., Hanes, D.E. The evaluation of a PCR-based method for identification of Salmonella enterica serotypes from environmental samples and various food matrices. Food Microbiology (2012) 31(2):199-209. PMID: 22608224

Micallef S.A., Rosenberg Goldstein R.E., George A., Kleinfelter L., Boyer M.S., McLaughlin C.R., Estrin A., Ewing L., Jean-Gilles Beaubrun J., Hanes D.E., Kothary M.H., Tall B.D., Razeq J.H., Joseph S.W., Sapkota A.R. Occurrence and Antibiotic Resistance of Multiple Salmonella Serotypes Recovered from Water, Sediment and Soil on Mid-Atlantic Tomato Farms. Environmental Research (2012) 114: 31-39. PMID: 22406288

Micallef S.A., Channer S., Shiaris M.P. and Colón-Carmona A.  Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere.  Plant Signaling and Behavior (2009) 4(8): 777-780.

Micallef S.A., Shiaris M.P. and Colón-Carmona A. Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot (2009) 60 (6): 1729-42.

Awards and Honors:

  • AGNR On-Campus Junior Faculty Award 2016
  • AGNR Alumni Excellence in Research Award, University of Maryland, 2016
  • Award for Outstanding Achievement in Molecular, Cellular and Organismal Biology, University of Massachusetts Boston, 2009
  • National Science Foundation (NSF), Boston Science Partnership Fellowship, 2005-07
  • Community of Mediterranean Universities Scholarship, 1993
Solving food protection problems locally, regionally, and internationally