Biological soil amendments of animal origin (BSAAO) increase nutrient levels in soils to support production of fruits and vegetables. BSAAOs may introduce or extend survival of bacterial pathogens which can transfer to fruits and vegetables to cause foodborne illness. Escherichia coli survival over 120 days in soil plots (3m2) covered with (mulched) or without plastic mulch (not mulched), amended with either poultry litter, composted poultry litter, heat treated poultry pellets, or chemical fertilizer and transfer to cucumbers in two years (2018, 2019) was evaluated. Plots were inoculated with E. coli (8.5 log CFU/m2) and planted with cucumber seedlings (Supremo). The number of days (d) needed to reduce E. coli levels by 4 log CFU (dpi4log) was determined using a sigmoidal decline model. RandomForest regression and one-way ANOVA (p < 0.05) identified predictors (soil properties and nutrients, weather factors) of dpi4log of E. coli and transfer to cucumbers. The combination of year, amendment and mulch (25.0%IncMSE) and year (9.75%IncMSE) were the most prominent predictors of dpi4log and transfer to cucumbers, respectively. Nitrate levels at 30d and soil moisture at 40d were also impactful predictors of dpi4log. Differing rainfall amounts in 2018 (24.9 in) and 2019 (12.6 in) affected E. coli survival in soils and transfer to cucumbers. Salmonella spp. were recovered sporadically from various plots, but were not recovered from cucumbers in either year. Greater transfer of E. coli to cucumbers was also shown to be partially dependent on dpi4log of E. coli in plots containing BSAAO. IMPORTANCE Poultry litter and other biological soil amendments are commonly used fertilizers in fruit and vegetable production and can introduce enteric pathogens like E. coli O157:H7 or Salmonella previously associated with outbreaks of illness linked to contaminated produce. E. coli survival duration in soils covered with plastic mulch or uncovered and containing poultry litter, heat-treated poultry litter pellets were evaluated. Nitrate levels on day 30 and moisture content in soils on day 40 on specific days were good predictors of E. coli survival in soils; however, knowledge of the combination of year, amendment and mulch type was a better predictor. Different cumulative rainfall totals from year to year most likely affected the transfer of E. coli from soils to cucumbers and survival durations in soil. E. coli survival in soils can be extended by the addition of several poultry litter based soil amendments commonly used in organic production of fruits and vegetables and is highly dependent on temporal variation in rainfall.

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The COVID-19 pandemic is a global crisis and continues to impact communities as the disease spreads. Clinical testing alone provides a snapshot of infected individuals but is costly and difficult to perform logistically across whole populations. The virus which causes COVID-19, SARS-CoV-2, is shed in human feces and urine and can be detected in human waste. SARS-CoV-2 can be shed in high concentrations (>107 genomic copies/mL) due to its ability to replicate in the gastrointestinal tract of humans through attachment to the angiotensin-converting enzyme 2 (ACE-2) receptors there. Monitoring wastewater for SARS-CoV-2, alongside clinical testing, can more accurately represent the spread of disease within a community. This protocol describes a reliable and efficacious method to recover SARS-CoV-2 in wastewater, quantify genomic RNA levels, and evaluate concentration fluctuations over time. Using this protocol, viral levels as low as 10 genomic copies/mL were successfully detected from 30 mL of wastewater in more than seven-hundred samples collected between August 2020 and March 2021. Through the adaptation of traditional enteric virus methods used in food safety research, targets have been reliably detected with no inhibition of detection (RT-qPCR) observed in any sample processed. This protocol is currently used for surveillance of wastewater systems across New Castle County, Delaware.