Comparative persistence of Salmonella and Escherichia coli O157:H7 in loam or sandy loam soil amended with bovine or swine manure

Survival of Salmonella spp. under varying temperature and soil conditions

Soils can serve as suitable reservoirs for or barriers against microbial contamination of water resources and plant produce. The magnitude of water or food contamination risks through soil depends on several factors, including the survival potential of microorganisms in the soil. This study assessed and compared the survival/persistence of 14 Salmonella spp. strains in loam and sandy soils at 5, 10, 20, 25, 30, 35, 37 °C and under uncontrolled ambient temperature conditions in Campinas Sao Paulo. The ambient temperature ranged from 6 °C (minimum) to 36 °C (maximum). Bacterial population densities were determined by the conventional culture method (plate counts) and monitored for 216 days. Statistical differences among the test parameters were determined by Analysis of Variance, while relationships between temperature and soil type were evaluated using Pearson correlation analysis. Similarly, relationships between time and temperature for survival of the various strains were evaluated using Pearson correlation analysis. Results obtained indicate that temperature and soil type influence the survival of Salmonella spp. in soils. All 14 strains survived for up to 216 days in the organic-rich loam soil under at least three of the temperature conditions evaluated. However, comparatively lower survival rates were recorded in sandy soil, especially at lower temperature. The optimum temperature for survival varied among the strains, where some survived best at 5 °C and others between 30 and 37 °C. Under uncontrolled temperature conditions, the Salmonella strains survived better in loam than in sandy soils. Bacterial growth over post inoculation storage period was overall more impressive in loam soil. In general, the results indicate that temperature and soil type can interact to influence the survival of Salmonella spp. strains in soil. For the survival of some strains, there were significant correlations between soil type and temperature, while for some others, no significant relationship between soil and temperature was determined. A similar trend was observed for the correlation between time and temperature.

Growth Media of Escherichia coli Does Not Affect Its Survival in Soil under Static Conditions

ABSTRACT

Many studies have examined the survival of Escherichia coli and foodborne pathogens in agricultural soils. The results of these studies can be influenced by various growth conditions and growth media used when preparing cultures for an experiment. The objectives of this study were to (i) determine the growth curves of rifampin (R)-resistant E. coli in three types of growth media containing R: tryptic soy agar (TSA-R); tryptic soy broth (TSB-R); and poultry pellet extract (PPE-R) and (ii) evaluate the influence of growth media on the survival of E. coli in agricultural soil. Poultry pellet extract (PPE) was prepared by filter sterilizing a 1:10 suspension of heat-treated poultry pellets in sterile water. Generic E. coli (TVS 353) acclimated to 80 μg/mL of R was grown in TSA-R, TSB-R, and PPE-R at 3.0 to 3.5 log CFU/mL and incubated at 37°C. Growth curves were determined by quantifying E. coli populations at 0, 4, 8, 16, 24, and 32 h. Soil microcosms were inoculated with E. coli (6.0 log CFU/g) previously cultured in one of the three media types and stored at 25°C, and soil samples were quantified for E. coli on days 0, 1, 3, 7, 14, 28, and 42. Growth curves and survival models were generated by using DMFit and GInaFiT, respectively. E. coli growth rates were 0.88, 0.77, and 0.69 log CFU/mL/h in TSA-R, TSB-R, and PPE-R, respectively. E. coli populations in the stationary phase were greater for cultures grown in TSA-R (9.4 log CFU/mL) and TSB-R (9.1 log CFU/mL) compared with PPE-R (7.9 log CFU/mL). The E. coli populations in the soil remained stable up to 3 days before declining. An approximate 2 log CFU/g decline of E. coli in soil was observed for each culture type between days 3 and 7, after which E. coli populations declined more slowly from days 7 to 42. A biphasic shoulder model was used to evaluate E. coli survival in soils on the basis of growth media. Using standardized culture growth preparation may aid in determining the complex interactions of enteric pathogen survival in soils.

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What on earth? The impact of digestates and composts from farm effluent management on fluxes of foodborne pathogens in agricultural lands

The recycling of biomass is the cornerstone of sustainable development in the bioeconomy. In this context, digestates and composts from processed agricultural residues and biomasses are returned to the soil. Whether or not the presence of pathogenic microorganisms in these processed biomasses is a threat to the sustainability of the current on-farm practices is still the subject of debate. In this review, we describe the microbial pathogens that may be present in digestates and composts. We then provide an overview of the current European regulation designed to mitigate health hazards linked to the use of organic fertilisers and soil improvers produced from farm biomasses and residues. Finally, we discuss the many factors that underlie the fate of microbial pathogens in the field. We argue that incorporating land characteristics in the management of safety issues connected with the spreading of organic fertilisers and soil improvers can improve the sustainability of biomass recycling.

Survival and inactivation kinetics of Salmonella enterica serovar Typhimurium in irradiated and natural poultry litter microcosms

The use of poultry litter as a biological soil amendment presents a risk for the preharvest contamination of fresh produce by Salmonella. In order to properly assess this risk, it is important to understand the factors influencing the persistence of Salmonella in poultry litter. This research was performed to investigate the influence of indigenous microflora on the survival of Salmonella Typhimurium in poultry litter. Microcosms of irradiated (sterilized) and natural poultry litter were inoculated with S. Typhimurium, adjusted to pH 8.0, 0.92 water activity (a_w), and stored at 30°C for 6 days. S. Typhimurium populations (log CFU g^-1) declined in both litter treatments and there were no significant differences (P > 0.05) in recovery between litter treatments on any sampling days (0 to 6). The pH of the natural litter significantly increased (P < 0.05) from 8.42 on day 0 to 9.00 on day 6. By day 6, S. Typhimurium populations in both litter treatments fell below the limit of detection (1 log CFU g^-1). The inactivation kinetics of S. Typhimurium in both litter treatments were described by the Weibull model. Under the experimental conditions (pH 8.0, 0.92 a_w, 30°C), the presence or absence of poultry litter microflora did not significantly influence the survival of S. Typhimurium. This study demonstrates that the mere presence of poultry litter microflora will not inhibit Salmonella survival. Instead, inhibitory interactions between various microorganisms in litter and Salmonella are likely dependent on more favorable environmental conditions (e.g., a_w, pH) for growth and competition.

Strain, Soil-Type, Irrigation Regimen, and Poultry Litter Influence Salmonella Survival and Die-off in Agricultural Soils

The use of untreated biological soil amendments of animal origin (BSAAO) have been identified as one potential mechanism for the dissemination and persistence of Salmonella in the produce growing environment. Data on factors influencing Salmonella concentration in amended soils are therefore needed. The objectives here were to (i) compare die-off between 12 Salmonella strains following inoculation in amended soil and (ii) characterize any significant effects associated with soil-type, irrigation regimen, and amendment on Salmonella survival and die-off. Three greenhouse trials were performed using a randomized complete block design. Each strain (~4 log CFU/g) was homogenized with amended or non-amended sandy-loam or clay-loam soil. Salmonella levels were enumerated in 25 g samples 0, 0.167 (4 h), 1, 2, 4, 7, 10, 14, 21, 28, 56, 84, 112, 168, 210, 252, and 336 days post-inoculation (dpi), or until two consecutive samples were enrichment negative. Regression analysis was performed between strain, soil-type, irrigation, and (i) time to last detect (survival) and (ii) concentration at each time-point (die-off rate). Similar effects of strain, irrigation, soil-type, and amendment were identified using the survival and die-off models. Strain explained up to 18% of the variance in survival, and up to 19% of variance in die-off rate. On average Salmonella survived for 129 days in amended soils, however, Salmonella survived, on average, 30 days longer in clay-loam soils than sandy-loam soils [95% Confidence interval (CI) = 45, 15], with survival time ranging from 84 to 210 days for the individual strains during daily irrigation. When strain-specific associations were investigated using regression trees, S. Javiana and S. Saintpaul were found to survive longer in sandy-loam soil, whereas most of the other strains survived longer in clay-loam soil. Salmonella also survived, on average, 128 days longer when irrigated weekly, compared to daily (CI = 101, 154), and 89 days longer in amended soils, than non-amended soils (CI = 61, 116). Overall, this study provides insight into Salmonella survival following contamination of field soils by BSAAO. Specifically, Salmonella survival may be strain-specific as affected by both soil characteristics and management practices. These data can assist in risk assessment and strain selection for use in challenge and validation studies.

Temporal and Agricultural Factors Influence Escherichia coli Survival in Soil and Transfer to Cucumbers

Biological soil amendments of animal origin (BSAAO) increase nutrient levels in soils to support the production of fruits and vegetables. BSAAOs may introduce or extend the survival of bacterial pathogens which can be transferred to fruits and vegetables to cause foodborne illness. Escherichia coli survival over 120 days in soil plots (3 m²) 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 2 years (2018 and 2019) were evaluated. Plots were inoculated with E. coli (8.5 log CFU/m²) and planted with cucumber seedlings (Supremo). The number of days needed to reduce E. coli levels by 4 log CFU (dpi4log) was determined using a sigmoidal decline model. Random forest regression and one-way analysis of variance (ANOVA; P < 0.05) identified predictors (soil properties, nutrients, and weather factors) of dpi4log of E. coli and transfer to cucumbers. The combination of year, amendment, and mulch (25.0% increase in the mean square error [IncMSE]) and year (9.75% IncMSE) were the most prominent predictors of dpi4log and transfer to cucumbers, respectively. Nitrate levels at 30 days and soil moisture at 40 days 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 such as Escherichia 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 or 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, 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.

The progress of type II persisters of Escherichia coli O157:H7 to a non-culturable state during prolonged exposure to antibiotic stress with revival being aided through acid-shock treatment and provision of methyl pyruvate

Persisters are a form of dormancy in bacteria that provide temporary resistance to antibiotics. The following reports on the formation of Escherichia coli O157:H7 E318 type II persisters from a protracted (8 days) challenge with ampicillin. Escherichia coli O157:H7 followed a multiphasic die-off pattern with an initial rapid decline (Phase I) of susceptible cells that transitioned to a slower rate representing tolerant cells (Phase II). After 24 h post-antibiotic challenge, the E. coli O157:H7 levels remained relatively constant at 2 log CFU/mL (Phase III), but became non-culturable within 8-days (Phase IV). The revival of persisters in Phase III could be achieved by the removal of antibiotic stress, although those in Phase IV required an extended incubation period or application of acid-shock. The carbon utilization profile of persister cells was less diverse compared with non-persisters, with only methyl pyruvate being utilized from the range tested. Inclusion of methyl pyruvate in tryptic soy agar revived non-cultural persisters, presumably by stimulating metabolism. The results suggest that persisters could be subdivided into culturable or non-culturable cells, with the former representing a transition state to the latter. The study provided insights into how to revive cells from dormancy to aid enumeration and control.

Survival of Shiga Toxin-Producing Escherichia coli in Various Wild Animal Feces That May Contaminate Produce

ABSTRACT

Domestic and wild animal intrusions are identified as a food safety risk during fresh produce production. The purpose of this study was to evaluate the survival of Shiga toxin-producing Escherichia coli (STEC) in cattle, feral pig, waterfowl, deer, and raccoon feces from sources in California, Delaware, Florida, and Ohio. Fecal samples were inoculated with a cocktail of rifampin-resistant STEC serotypes (O103, O104, O111, O145, and O157) (104 to 106 CFU/g of feces). Inoculated feces were held at ambient temperature. Populations of surviving cells were monitored throughout 1 year (364 days), with viable populations being enumerated by spread plating and enrichment when the bacteria were no longer detected by plating. Representative colonies were collected at various time intervals based on availability from different locations to determine the persistence of surviving STEC serotypes. Over the 364-day storage period, similar survival trends were observed for each type of animal feces from all states except for cattle and deer feces from Ohio. STEC populations remained the highest in cattle and deer feces from all states between days 28 and 364, except for those from Ohio. Feral pig, waterfowl, and raccoon feces had populations of STEC of <1.0 log CFU/g starting from day 112 in feces from all states. E. coli O103 and O104 were the predominant serotypes throughout the entire storage period in feces from all animals and from all states. The survival of both O157 and non-O157 STEC strains in domesticated and wild animal feces indicates a potential risk of contamination from animal intrusion.

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Environmental Drivers for Persistence of Escherichia coli and Salmonella in Manure-Amended Soils: A Meta-Analysis

ABSTRACT

Application of organic amendments to agricultural land improves soil quality and provides nutrients essential for plant growth; however, they are also a reservoir for zoonotic pathogens whose presence poses a significant risk to public health. The persistence of bacteria in manure-amended soil, and differences in manure handling practices, are important issues from a food safety perspective. The primary objective of this study was to quantitatively summarize the variations in the rate of decline of Escherichia coli and Salmonella spp. in manure-amended soil under laboratory and field conditions, and to assess the impact of environmental factors. Available literature data on persistence of E. coli and Salmonella spp. in manure-amended soil from 42 primary research studies were extracted and statistically analyzed using a mixed-effect regression model. The results indicated that temperature (soil and air combined) was the most prominent factor affecting persistence of both E. coli and Salmonella spp. under laboratory conditions (P < 0.001), and of E. coli under field conditions (P < 0.05). The time required for a log reduction of E. coli under field conditions was significantly higher at low temperature (0 to 10°C) than at high temperature (greater than 20°C) (P < 0.05). In addition, application method was identified as a significant factor, with manure incorporation to soil inducing longer survival compared with surface application by approximately 1.2 times. The significant variation observed among primary research studies of bacterial persistence has highlighted that mitigation strategies associated with the use of manures in fresh produce production need to be improved by addressing factors such as climate, soil management, application method, and initial microbial levels. These findings may be used to support guidelines establishing exclusion periods between manure fertilization and the grazing or harvesting of crops, and may be useful for the generation of quantitative microbial risk models for fresh produce.

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Effect of soil type and temperature on survival of Salmonella enterica in poultry manure-amended soils

The effects of soil type and temperature on the survival of a cocktail of five Salmonella enterica serotypes (Enteritidis, Infantis, Montevideo, Typhimurium and Zanzibar) in manure-amended soils under controlled laboratory conditions was assessed. Containers of clay loam or sandy soil, unaltered or amended with 2% (w/w) poultry manure, were inoculated with S. enterica (~5 log₁₀ CFU per gram) and held at 5, 21 or 37°C for 6 weeks. Statistical analysis of the persistence of S. enterica identified a significant three-way interaction between soil type, manure amendment and temperature. Clay loam soils and lower temperatures tended to support S. enterica persistence over 6 weeks with only 1- and 2-log reductions respectively. In contrast, sand and higher temperatures resulted in a 4-log and either 3- to 4-log reductions respectively. Manure amendment had an overarching effect of reducing die-off of S. enterica in comparison with unamended soils. This study highlights that a large component of variation of the rate of S. enterica reduction in soils may be attributed to combinations of environmental factors, in particular, soil type and temperature. It further underscores the importance of risk management strategies and industry guidelines based on local data and that reflect the diversity of prevailing horticultural production environments. SIGNIFICANCE AND IMPACT OF THE STUDY: The persistence of Salmonella enterica in soil environments was shown to be significantly influenced by a range of individual and interacting environmental effects, including temperature, soil type and amendment addition. This indicates that current horticultural food safety management systems which employ a uniform prescribed exclusion period between application of manure and time of harvest may be unfit for purpose under certain conditions by either underestimating or overestimating pathogen die-off. These findings support exclusion periods that account for a range of environmental factors including temperature, soil type and growing region that may be more appropriate to manage microbiological risks associated with soil which has been amended with manure.

High resolution characterisation of E. coli proliferation profiles in livestock faeces

Agricultural intensification can lead to high volumes of livestock faeces being applied to land, either as solid or liquid manures or via direct defecation, and can result in reservoirs of faecal indicator organisms (FIOs) persisting within farmland. Understanding the survival of FIOs, e.g. E. coli, in agricultural environments, and in particular within different livestock faeces, is key to developing catchment management practices for the protection of ecosystem services provided by clean water. Frequently, controlled laboratory studies, under constant temperature regimes, are used to determine the impact of environmental factors on E. coli persistence in livestock faeces; however, such studies oversimplify the diurnal variations and interactions of real world conditions. The aim of this study was to investigate the survival of E. coli using a controlled environment facility, which simulated diurnal variation of temperatures typically experienced during a British spring and summer. The approach provided a comparison of E. coli persistence profiles within faeces of sheep, beef cattle and dairy cattle to allow novel interpretations of E. coli regrowth patterns in contrasting livestock faeces in the period immediately post-defecation. Thus, the coupling of a tightly controlled environment facility with high resolution monitoring enabled the development of a new non-linear, asymptotic description of E. coli proliferation in livestock faeces, with increased potential for E. coli growth observed during warmer temperatures for all livestock types. While this study focused on temperatures typical of the UK, the occurrence of a phase of E. coli regrowth has implications for microbial water quality management worldwide.

Survival of Escherichia coli in Manure-Amended Soils Is Affected by Spatiotemporal, Agricultural, and Weather Factors in the Mid-Atlantic United States

Untreated biological soil amendments of animal origin (BSAAO), such as manure, are commonly used to fertilize soils for growing fruit and vegetable crops and can contain enteric bacterial foodborne pathogens. Little is known about the comparative longitudinal survival of pathogens in agricultural fields containing different types of BSAAO, and field data may be useful to determine intervals between manure application and harvest of produce intended for human consumption to minimize foodborne illness. This study generated 324 survival profiles from 12 different field trials at three different sites (UMES, PA, and BARC) in the Mid-Atlantic United States from 2011 to 2015 of inoculated nonpathogenic Escherichia coli (gEc) and attenuated O157 E. coli (attO157) in soils which were unamended (UN) or amended with untreated poultry litter (PL), horse manure (HM), or dairy manure solids (DMS) or liquids (DML). Site, season, inoculum level (low/high), amendment type, management (organic/conventional), and depth (surface/tilled) all significantly (P < 0.0001) influenced survival duration (dpi100mort). Spatiotemporal factors (site, year, and season) in which the field trial was conducted influenced survival durations of gEc and attO157 to a greater extent than weather effects (average daily temperature and rainfall). Initial soil moisture content was the individual factor that accounted for the greatest percentage of variability in survival duration. PL supported greater survival durations of gEc and attO157, followed by HM, UN, and DMS in amended soils. The majority of survival profiles for gEc and attO157 which survived for more than 90 days came from a specific year (i.e., 2013). The effect of management and depth on dpi100mort were dependent on the amendment type evaluated.IMPORTANCE Current language in the Food Safety Modernization Act Produce Safety Rule states no objection to a 90- or 120-day interval between application of untreated BSAAO and harvest of crops to minimize transfer of pathogens to produce intended for human consumption with the intent to limit potential cases of foodborne illness. This regional multiple season, multiple location field trial determined survival durations of Escherichia coli in soils amended with manure to determine whether this interval is appropriate. Spatiotemporal factors influence survival durations of E. coli more than amendment type, total amount of E. coli present, organic or conventional soil management, and depth of manure application. Overall, these data show poultry litter may support extended survival of E. coli compared to horse manure or dairy manure, but spatiotemporal factors like site and season may have more influence than manure type in supporting survival of E. coli beyond 90 days in amended soils in the Mid-Atlantic United States.