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Center for Food Safety and Security Systems 5825 University Research Court Suite 1400 College Park, Maryland 20740

Associate Professor

Plant Science & Landscape Architecture 2102 Plant Sciences Building 4291 Fieldhouse Drive College Park, Maryland 20742


  • Microbiological safety of fresh produce
  • 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
  • Environmental metabolomics of plant surfaces to understand enteric pathogen colonization of plants
  • Studying enteric pathogen-plant responses
  • Crop microbiomes



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   

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


Areas of Interest: 

  • Food safety of fresh produce

  • Rhizosphere and phyllosphere bacterial interactions

  • Microbial ecology

  • Plant exudate biology

  • Environmental detection of human pathogens

Current Research: 

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.


Courses Taught: 

PLSC115 SAFETY OF FRESH PRODUCE Fall 2012, Fall 2013, Fall 2014, Fall 2015, Fall 2016
PLSC399 SPECIAL PROBLEMS PLSC Spring 2014, Spring 2015, Spring 2016, Summer 2016
PLSC489Q MICROBIO AGRCLTR SYSTEMS Spring 2013, Spring 2014
PLSC689A PLNT SCI & LNDSCP ARCH Fall 2015, Spring 2016


Selected Publications: 

Solaiman S., Micallef SA, 2021. Aeromonas spp. diversity in U.S. mid-Atlantic surface and reclaimed water, seasonal dynamics, virulence gene patterns and attachment to lettuce. STOTEN Volume 779, 20 July 2021, 146472.DOI:


Han S, Lin Sh-Sh, Ferelli AMC, Micallef SA, 2020. Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces. Heliyon 6 (9), e04952 11 Sep 2020. DOI: 


Solaiman S#, Allard SM, Callahan MT, Jiang C, Handy ET, East C, Haymaker J, Bui A, Craddock H, Murray R, Kulkarni P, Anderson-Coughlin B, Craighead S, Gartley S, Vanore A, Duncan R, Foust D, Taabodi M, Sapkota A, May E, Hashem F, Parveen S, Kniel KE, Sharma M, Sapkota AR, Micallef SA, 2020. A longitudinal assessment of Escherichia coli, total coliforms, Enterococcus and Aeromonas spp. dynamics in alternative irrigation water sources: A CONSERVE study. Applied and Environmental Microbiology, AEM.00342-20; DOI:


Melotto M, Brandl MT, Jacob C, Jay-Russell MT, Micallef SA, Warburton ML, Van Deynze A, 2020. Breeding Crops for Enhanced Food Safety. Frontiers in Plant Science 2020, 11, 428.


Ferelli AMC, Bolten S, Szczesny B#, Micallef SA, 2020. Salmonella enterica elicits and is restricted by nitric oxide and reactive oxygen species on tomato.  Frontiers in Microbiology 2020, 11, 391.


Sharma M, Handy E, East CL, Kim S, Jiang, Callahan MT, Allard SM, Micallef SA, Craighead S, Anderson B, Gartley S, Vanore A, Kniel KE, Haymaker J, Duncan R, Foust D, White C, Taabodi M, Hashem F, Parveen S, May EB, Bui A, Craddock H, Kulkarni P, Murray RY, Sapkota A. 2020. Prevalence of Salmonella and Listeria monocytogenes in non-traditional irrigation waters in the mid-Atlantic United States is affected by water type, season, and recovery method. PLOS ONE 15(3): e0229365.


Allard SM, Ottesen AR, Micallef SA, 2020. Rain induces temporary shifts in epiphytic bacterial communities of cucumber and tomato fruit. Scientific Reports (2020) 10:1765.


Todd-Searle J, Friedrich LM, Oni RA, Shenge K, LeJeune JT, Micallef SA, Danyluk MD, Schaffner D, 2020. Quantification of Salmonella enterica transfer between tomatoes, soil and plastic mulch. International Journal of Food Microbiology, 2020, 316: 108480.


Chopyk J, Daniel J Nasko DJ, Allard S, Callahan MT#, Bui A, Ferelli AMC, Chattopadhyay S, Mongodin EF, Pop M, Micallef SA, Sapkota AR, 2020. Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics. STOTEN 706, 1 March 2020, 135395. 


Korir RC#, Everts KL, Micallef S, 2020. Interactions between Salmonella enterica Newport, Fusarium spp. and melon cultivars. Foodborne Pathogens and Disease 2020, 17 (6), 388-395. 


Bolten S, Gu G, Luo Y, Van Haute S, Zhou B, Millner P, Micallef SA, Nou X, 2020. Salmonella inactivation and cross-contamination on cherry and grape tomatoes under simulated wash conditions. Food Microbiology 2020, 87:103359.


Callahan MT#, Micallef SA*, 2019. Waxing and the absence of trichomes favor Salmonella persistence on cucumber (Cucumis sativus L.) fruit – accepted to International Journal of Food Microbiology 9 Sept 2019 – in press. DOI: 10.1016/j.ijfoodmicro.2019.108359


anthi S, Sapkota AR, Raspanti G, Allard S; Bui A, Craddock H, MurrayR, Zhu L, East C, Handy E, Callahan MT, HaymakerJ, Kulkarni P, Anderson B, Craighead S, Gartley S, Vanore A, Betancourt WQ, Duncan R, Foust D, Sharma M, Micallef SA, Gerba C, Parveen S, Hashem F, May EB, Kniel KE, Pop M, Ravishankar S, Sapkota A. Pharmaceuticals, herbicides and disinfectants in agricultural water sources. Environmental Research 2019 April 12; 174:1-8.

Allard SM, Sultana S#, Callahan MT#, Bui A, Craddock H, Haymaker J, Foust D, Duncan R, Smyth E, Mongodin EF, Hashem F, May E, Micallef SA, Sapkota AR, 2019. Quenching by sodium thiosulfate does not influence 16S rRNA gene sequencing profiles of reclaimed water from three sites in the Mid-Atlantic United States. Environmental Research 2019 Feb 15; 172:296-300. DOI: 10.1016/j.envres.2019.02.022

Haymaker J, Sharma M, Parveen S, Hashem F, May EB, Handy ET, White C, East C, Bradshaw R, Micallef SA, Callahan MT#, Allard S, Anderson B, Craighead S, Gartley S, Vanore A, Kniel K, Solaiman S#, Bui A, Murray R, Craddock HA, Kulkarni P, Foust D, Duncan R, TaabodMi , Sapkota AR, 2019. Prevalence of Shiga-toxigenic and atypical enteropathogenic Escherichia coli in untreated surface water and reclaimed water in the mid-Atlantic US. Environmental Research, 172:630-636.

Allard SM, Callahan MT#, Bui A, Ferelli AMC#, Chopyk J, Chattopadhyay S, Mongodin EF, Micallef SA*, Sapkota AR*, 2019. Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens and total bacterial communities from irrigation water to kale and radish crops. STOTEN 2019 May 20; 666:461-471

Zhu L, Torres M, Betancourt WQ; Sharma M, Micallef SA, Gerba C, Sapkota AR, Sapkota A, Parveen S, Hashem F, May E, Kniel KE, Pop M., Ravishankar S, 2019.  Incidence of fecal indicator and pathogenic bacteria in reclaimed and return flow waters in Arizona, USA. Environmental Research 2019 Mar;170: 122-127. doi: 10.1016/j.envres.2018.11.048. Epub 2018 Dec 1.

Dev Kumar Govindaraj#, Macarisin D, Micallef SA*, 2019Salmonella enterica filamentation induced by pelargonic acid is a transient morphotype. Applied Environmental Microbiology 2019 Jan 9; 85(2). pii: e02191-18. doi:10.1128/AEM.02191-18

Callahan MT#, Van Kessel JA, Micallef SA*2019Salmonella enterica recovery from river waters of the Maryland Eastern Shore reveals high serotype diversity and some multidrug resistance. Environmental Research168:7-13; online 12 Sept 2018.

Allard SM#, Ottesen A, Brown EW, Micallef SA*2018. Insect exclusion limits variation in bacterial microbiomes of tomato flowers and fruit. Journal of Applied Microbiology 125:1749-1760.  doi:10.1111/jam.14087

Park E, Luo Y, Marine SC, Everts KE, Micallef SA,  Bolten S#, Stommel J, 2018. Consumer Preference and physicochemical evaluation of organically grown melons. Postharvest Biology and Technology, 2018, 141:77-85. doi:10.1016/j.postharvbio.2018.03.001

Dev Kumar G#, Ravi S, Micallef SA, Brown EW, Macarisin D, 2018. Aeolian contamination of fruit by enteric pathogens: An unexplored paradigm. Current Opinion in Food Science 2018, 19:138-144. doi:10.1016/j.cofs.2017.12.003

Pang H, McEgan R#, Micallef SA, Pradhan AK, 2018. Evaluation of meteorological factors associated with pre-harvest contamination risk of generic Escherichia coli in a mixed produce and dairy farm. Food Control 85:135-143. doi:10.1016/j.foodcont.2017.08.003

Pang H, McEgan R#, Micallef SA, Pradhan AK, 2017. Identifying and Modeling Meteorological Risk Factors Associated with Pre-harvest Contamination of Listeria Species in a Mixed Produce and Dairy Farm. Food Research International 102 (2017) 355–363.doi:10.1016/j.foodres.2017.09.029 


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): 668-673doi: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 entericaserotypes 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.