Research Project: Improving Pre-harvest Produce Safety through Reduction of Pathogen Levels in Agricultural Environments and Development and Validation of Farm-Scale Microbial Quality Model for Irrigation Water Sources

Location: Environmental Microbial & Food Safety Laboratory

2023 Annual Report

Accomplishments
1. Improved methods for monitoring antibiotic resistant Escherichia coli in irrigation ponds. Irrigation waters may facilitate the spread of emerging antibiotic-resistant bacteria or genes to humans through contaminated fruits and vegetables. In groundbreaking work, ARS scientists from Beltsville, Maryland, researched spatiotemporal variation of tetracycline-resistant E. coli in irrigation ponds and established the existence of persistent spatial. The percentage of tetracycline-resistant E. coli levels were predicted by levels of nitrate, dissolved organic matter, and dissolved oxygen concentrations. Results of this work benefit farmers and water resource managers by indicating that antibiotic-resistant E. coli can be predicted by water quality parameters and a modified microbial testing regimen.

2. Established a database using microbial indicators for water quality monitoring. Escherichia coli and Enterococcus spp. are common indicators for microbial quality of irrigation water. ARS scientists in Beltsville, Maryland, established a unique database coupling E. coli and enterococci levels in sediment and the water column of the Conococheague creek in Pennsylvania. Results for this study emphasize that land use, seasonality, and sediment texture should be taken into account during water quality monitoring efforts.

3. Growth media does not affect persistence of Escherichia coli in soils. Examining the duration of E. coli survival in soils containing biological soil amendments of animal origin (BSAAO) is an important produce safety objective. Establishing the duration between planting of fruit and vegetable crops and harvest minimizes the transfer of pathogens from untreated BSAAO to fruit and vegetable crops. In a collaboration between ARS scientists in Beltsville, Maryland, and University of Florida scientists, it was determined that the microbiological method of preparing the E. coli culture (on agar plates, in liquid growth media, or in sterilize manure extract) did not affect the survival duration of E. coli. These findings provide flexibility to scientists in different U.S. regions looking to determine appropriate interval to minimize foodborne contamination between planting and harvest of fruits and vegetables. These efforts also support farmers in recycling nutrients from manure or composted manure in fruit and vegetable production.

4. Antibiotic resistant Escherichia coli percentages were low in surface and reclaimed waters in the Mid-Atlantic region of the U.S. Escherichia coli is a common indicator of the microbial quality of irrigation water. Extended spectrum beta-lactamase producing- (ESBL-) E. coli is an emerging pathogen. ARS scientists in Beltsville, Maryland, collaborated with scientists from multiple universities on a two-year survey conducting over 12 different sites to show that percentage of ESBL-producing E. coli was low (less than 3%) of the total E. coli recovered. These results indicate that ESBL-producing E. coli are not prominent in surface (river or pond) or reclaimed water sources, and are not currently a prominent hazard for irrigation water in the Mid-Atlantic region of the U.S.

5. Water from a first flush rainwater harvesting system did not contain bacterial foodborne pathogens. Rainwater harvesting is one of the sustainable agricultural practices that may benefit smaller or urban farmers. A first-flush system delivers water collected from rooftops into beds containing soil used to grow vegetables and produce. ARS scientists in Beltsville, Maryland, in collaboration with University of Maryland and Hood College investigators, analyzed 30 samples from this collection system at regular intervals. These results revealed that the prominent foodborne pathogens, Salmonella enterica and Listeria monocytogenes, were not detected. Results presented here indicated that harvested rainwater may be a useful source of irrigation water for small-scale growers.

Review Publications
Pyo, J., Pachepsky, Y.A., Kim, S., Abbas, A., Kim, M., Kwon, J., Ligaray, M., Cho, K. 2022. AI4Water v1.0: an open-source python package for modeling hydrological time series using data-driven methods. Geoscientific Model Development. 15(7):3021-3039.
Kim, S., Pachepsky, Y.A., Micallef, S., Rosenberg-Goldstein, R., Hashem, F., Parveen, S., Kniel, K., Sapkota, A., Sharma, M. 2023. Temporal stability of Salmonella enterica and Listeria monocytogenes in surface waters used for irrigation in the Mid-Atlantic United States. Journal of Food Protection. 86(4). Article 100058. https://doi.org/10.1016/j.jfp.2023.100058.
Kim, S., Paul, M., Negahban-Azar, M., Micallef, S., Rosengerg Goldstein, R., Hashem, F., Parveen, S., Sapkota, A., Kniel, K., Sapkota, A., Pachepsky, Y.A., Sharma, M. 2022. Persistent spatial patterns of Listeria monocytogenes and Salmonella enterica concentrations in surface waters: Empirical orthogonal function analysis of data from Maryland. Applied Sciences. 12:7526. https://doi.org/10.3390/app12157526.
Pachepsky, Y.A., Harriger, D.M., Panko Graff, C., Stocker, M.D., Smith, J.E. 2023. Coupled dynamics of fecal indicator bacteria in sandy sediments and the water column: a three-year high-frequency study at a Pennsylvania creek. Water, Air, and Soil Pollution. 234:398. https://doi.org/10.1007/s11270-023-06371-z.
Smith, J., Hill, R., Wolny, J., Stocker, M., Pachepsky, Y.A. 2022. Estimating phytoplankton concentrations in agricultural irrigation ponds from water quality measurements: a machine learning application. Journal of Phycology. 9(11):142.
Stocker, M.D., Smith, J.E., Pachepsky, Y.A. 2022. Depth-dependent concentrations of E. coli in agricultural irrigation ponds. Water. 14(14):2276. https://doi.org/10.3390/w14142276.
Stocker, M.D., Smith, J., Pachepsky, Y.A. 2023. Spatial variation of tetracycline-resistant E. coli and relationships with water quality variables in irrigation water: A pilot study. Journal of Applied Microbiology. 3(2):504-518. https://doi.org/10.3390/applmicrobiol3020036.
Solaiman, S., Handy, E., Brinks, T., Good, K., Bollinger, C., Sapkota, A.R., Sharma, M., Micallef, S.A. 2022. Escherichia coli phylogroup distribution and prevalence of extended spectrum ß-lactamase (ESBL) producers in U.S. Mid-Atlantic surface and reclaimed water. Environmental Microbiology. https://doi.org/10.1128/AEM.00837-22.
Morgado, M.E., Hudson, C.L., Chattopadhay, S., Ta, K., East, C.L., Purser, N., Allard, S., Ferrier, D.M., Sapokata, A.R., Sharma, M., Rosenburg-Goldstien, R. 2022. The effect of a first-flush rainwater harvesting irrigation system on E. coli and pathogen concentrations in irrigation water, soil, and produce. Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2022.156976.
Malayil, L., Ramachandran, P., Chattopadhyay, S., Allard, S.M., Bui, A., Butron, J., Callahan, M., Craddock, H., Murray, R., East, C.L., Sharma, M., Kniel, K.E., Micallef, S.A., Hashem, F., Gerba, C., Ravishankar, S., Parveen, S., May, E., Handy, E.T., Kulkarni, P., Anderson-Coughlin, B., Craighead, S., Gartley, S., Vanore, A., Duncan, R., Foust, D., Haymaker, J., Betancourt, W., Zhu, L., Mongodin, E., Sapkota, A., Sapkota, A.R. 2022. Variations in bacterial diversity and antibiotic resistance genes across diverse recycled and surface waters used for irrigation in the Mid-Atlantic and Southwest United States: A CONSERVE two-year field study. Journal of Environmental Science and Technology. https://doi.org/10.1021/acs.est.2c02281 .
Vikram, A., Callahan, M.L., Woolston, J.W., Sharma, M., Sulakvelidze, A. 2022. Phage biocontrol for reducing bacterial foodborne pathogens in produce and other foods. Current Opinion in Biotechnology. 78. Article 102805. https://doi.org/10.1016/j.copbio.2022.102805.