Climate change and extreme weather events (e. g. exceptionally heavy rainfall in a short duration of time) may cause the contamination of soils and surface waters with potential human pathogens originating from septic tanks, sewers, livestock on elevated land and livestock waste stores (Gil et al., 2015). Soils that are unusually dry can become compacted (e. g. capped) and subsequent heavy rainfall after a period of drought can result in more severe run-off and an increased risk of some types of contamination (Gil et al., 2015). Furthermore, temperature changes caused by extreme precipitation can also directly influence the safety of the food chain by changing pathogen survival time or even by promoting the multiplication of some pathogens (Gil et al., 2015).

Flooding of the ground used to cultivate crops can usually be classified into one of two categories. First, and most common, is when sustained, heavy rainfall saturates land and water begins to pool on the surface of soil being used to cultivate crops. Flooding caused by soil saturation may cause a reduction in crop yield and potentially may even kill crops. However, the saturated soil flood water is essentially rainwater and therefore it is unlikely to contain toxic chemicals or pathogenic biological agents that can cause human illness (US-FDA, 2011). However, please note that saturated floodwater is not guaranteed to be clear of harmful substances.

A less common form of more-severe flooding occurs when surface waters such as streams or rivers are unable to contain the water from heavy, sustained rainfall and overflow across land that is being used for crop cultivation. Surface water overflows are quite likely to contain contaminants that can cause human illness (Geldriech, 1996). Sources of pathogenic microorganisms include livestock manures on pastures washed into surface waters, the release of incompletely treated sewage by water companies whose treatment plants are swamped by excessive volumes of rainfall, overflows from domestic septic tanks and livestock manure stores (Bergholz et al., 2016). Castro-Ibanez et al. (2015a) report there is an enhanced likelihood of Salmonella isolations from crops, water, and soil when leafy greens were flooded. It is important to note that if the contamination source is livestock or wildlife, then the principle human health hazard is bacterial in nature. However, if the contamination includes human faeces, then it is possible the contamination will also include viruses such as norovirus that can also cause illness. Norovirus is the single most common cause of gastroenteritis and foodborne illness worldwide (Patel et al., 2009). In addition to biological hazards, flood water can contain toxic chemicals such as heavy metals, pesticides, fuel residues and industrial process wastes carried from upstream (Casteel et al., 2006).

Gil and colleagues (2015) advise against the use of land that is prone to flooding, or that gullies and drains be constructed as interventions to protect the land. A secondary strategy could be to limit the cultivation to crops where the fruit is raised from the ground and so less affected by flooding (Gil et al., 2015). There are publications that show an increase in the numbers of Salmonella and pathogenic E. coli and other enteric pathogen contamination when land floods (Ceuppens et al 2015; Castro-Ibanez 2015b).

Gil et al. (2015) also discuss pathogen testing of pre-harvest leafy greens. Generally, pathogen testing can be like trying to find a needle in a haystack and for that reason, none of the tools currently ask about pathogen testing. Recognising the issue, a general conclusion of the pathogen testing section is that full adherence to a statistically valid design for sampling fields of produce is impractical and non-economical. Advice was provided that the prevailing adage is that one cannot test their way to food safety and the successful approach is more likely to be adherence to the previously described set of intervention strategies.

There have been very few studies that have determined the duration of contamination in flooded soils. Bergholz et al. (2016) determined that contamination declined slowly over 238 days since the flood cleared. The prevalence of E. coli on swabs dropped by around 75% over the winter but remained quite stable during milder temperatures from day 44 to day 238. In contrast, E. coli was difficult to isolate from soils shortly after a flood event in North Carolina (Casteel et al., 2006). It is not clear from the papers whether differences in testing methodology was the reason for the apparently contradictory reports.

During the discussion of their findings, Bergholz et al. (2016) noted that there is a limited amount of research describing the survival of biological agents and other hazards on crops that have been exposed to flood water. Bergholz et al. (2016) believe this lack of information is the reason why the current advice of the United States Food and Drug Administration is that if an edible part of a crop has come in contact with flood water, the crop should be considered contaminated and unsuitable for human consumption (US-FDA, 2011). There are no specific regulations in the EU for flooding, however there is advice provided in the Commission notice on guidance document on addressing microbiological risks in fresh fruits and vegetables at primary production through good hygiene. The advice is “Fresh fruit and vegetables for which the edible part has come into contact with flood waters close to harvest (less than two weeks) should not be consumed as raw product. If the flooding event takes place more than two weeks before harvest or if these products are processed, a case-by-case (site-specific) risk assessment should be performed”.


Bergholz, P.W., Strawn, L.K., Ryan, G.T., Warchocki, S. and Wiedmann, M. 2016. Spatiotemporal Analysis of microbiological contamination in New York State produce fields following extensive flooding from Hurricane Irene. Journal of Food Protection. 79, 384-391.

Casteel, M. J., M. D. Sobsey, and J. P. Mueller. 2006. Fecal contamination of agricultural soils before and after hurricane-associated flooding in North Carolina. J. Environ. Sci. Health A Tox. Hazard. Subst. Environ. Eng. 41, 173–184.

Ceuppens,S., Johannessen,G.S., Allende,A., Tondo,E.C., El-Tahan,F., Sampers,I., Jacxsens,L. and Uyttendaele,M. (2015) Risk factors for Salmonella, Shiga toxin-producing Escherichia coli and Campylobacter Occurrence in primary production of leafy greens and strawberries. International Journal of Environmental Research and Public Health 12, 9809-9831.

Gil,M.I., Selma,M.V., Suslow,T., Jacxsens,L., Uyttendaele,M. and Allende,A. (2015) Pre- and postharvest preventive measures and intervention strategies to control microbial food safety hazards of fresh leafy vegetables. Critical Reviews in Food Science and Nutrition 55, 453-468.

Castro-Ibanez, I., Gil, M. I., Tudela, J. A. and Allende, A. 2015a. Microbial safety considerations of flooding in primary production of leafy greens: A case study. Food Research International, 68, 62-69.

Castro-Ibanez I., Gil M.I., Tudela J.A., Ivanek R., Allende A. 2015b. Assessment of microbial risk factors and impact of meteorological conditions during production of baby spinach in the southeast of Spain. Food Microbiol. 49, 173–181.

Food Safety Alliance. 2015. Food safety for flooded farms in the aftermath of flooding, fruit and vegetable crops may pose a food safety risk. Available online. Accessed 25/05/2016.

Geldreich, E.E. 1996. Pathogenic agents in freshwater resources. Hydrological Processes. 10, 315-333.

Patel, M. M., Hall, A. J., Vinjé, J. and Parashar, U. D. 2009. Noroviruses: a comprehensive review. J. Clin. Virol. 44, 1-8.

U.S. Food and Drug Administration. 2011. Guidance for industry: evaluating the safety of flood-affected food crops for human consumption. U.S. Food and Drug Administration, Silver Spring, MD.