Agricultural Practices Influence Salmonella Contamination and Survival in Pre-harvest Tomato Production

Serotype Distribution, Antimicrobial Resistance, Virulence Genes, and Genetic Diversity of Salmonella spp. Isolated from small-scale Leafy Green Vegetable Supply Chains in South Africa

Salmonella have been implicated in foodborne disease outbreaks globally and is a pressing concern in the South African small-scale sector due to inadequate hygiene standards and limited regulatory oversight, leading to a higher risk of foodborne diseases. By investigating irrigation water and leafy green vegetables produced by small-scale growers and sold through unregulated supply chains, this study was able to determine the presence, serotype distribution, virulence gene profiles, antibiotic resistance, and genetic diversity of Salmonella isolated from these sources. From 426 samples, 21 Salmonella-positive samples were identified, providing 53 Salmonella isolates. Of these, six different Salmonella serotypes and sequence types (STs) were identified, including Salmonella II 42:r: ST1208 (33.96%; n = 18), Salmonella Enteritidis: ST11 (22.64%; n = 12), Salmonella II 42:z29: ST4395 (16.98%; n = 9), Salmonella Havana: ST1524 (15.09%; n = 8), Salmonella Typhimurium: ST19 (9.43%; n = 5), and Salmonella IIIb 47:i:z: ST7890 (1.89%; n = 1). A total of 92.45% of the isolates were found to be multidrug-resistant, showing high rates of resistance to aztreonam (88.68%; n = 47), ceftazidime (86.79%; n = 46), nalidixic acid (77.36%; n = 41), cefotaxime (75.47%; n = 40), cefepime (71.70%; n = 38), and streptomycin (69.81%; n = 37). All isolates possessed the aac(6')-Iaa antimicrobial resistance gene, with a range of between 9 and 256 virulence genes. Eleven cluster patterns were observed from Enterobacterial Repetitive Intergenic Consensus sequence analyses, demonstrating high diversity among the Salmonella spp., with water and fresh produce isolates clustering, suggesting water as a potential contamination source. Plasmid replicon types were identified in 41.51% (n = 22) of the isolates, including Col(pHAD28) in Salmonella Havana (5.66%; n = 3), Col156 in Salmonella II 42:z29:- (1.89%; n = 1) and both IncFIB(S) and IncFII(S) in Salmonella Enteritidis (22.64; n = 12), Salmonella Typhimurium (9.43%; n = 5), and Salmonella Havana (1.89%; n = 1). This study highlights the presence of multidrug-resistant and multivirulent Salmonella spp. in the small-scale leafy green vegetable supply chains, underscoring the need for the development of a "fit-for-purpose" food safety management system within this system.

Effects of Fumigation on the Reduction of Salmonella enterica in Soil

Due to the phaseout of methyl bromide (MeBr), there is a need for broad-spectrum soil fumigation alternatives for pest management. Little is known about the impact of fumigation alternatives on foodborne pathogens, such as Salmonella, in agricultural soils. This study investigated the effect of MeBr alternative fumigants on Salmonella reduction in soil. Sandy loam soil was collected from a conventional farmed vegetable field and inoculated with either Salmonella Newport J1892 or Typhimurium ATCC 14028 (5.9 ± 0.3 log10 colony-forming unit [CFU]/g). Each of the four fumigants labeled for pest management (1,3-dichloropropene, chloropicrin, dimethyl disulfide, and metam sodium) was applied at labeled maximum application field levels to soil in pots and stored for a 2-week period. Sterile water was used as a control. Following the 2-week period, Salmonella concentrations in soil samples were enumerated at 1, 7, 14, and 21 days postfumigation. The mean concentration of Salmonella Newport was significantly higher than that of Salmonella Typhimurium 1 day after fumigation (p = 0.015). Fumigation using 1,3-dichloropropene or dimethyl disulfide significantly reduced Salmonella Newport and Salmonella Typhimurium concentrations, compared with the sterile water control. The rate of Salmonella reduction in soil treated with dimethyl disulfide was higher (0.17 ± 0.02 log10 CFU/g/day), compared with soil treated with the other fumigants (0.10-0.12 log10 CFU/g/day). Due to the reduction of Salmonella, alternative fumigation treatments may mitigate potential Salmonella contamination in soil within farm environments.

Soil Microclimate and Persistence of Foodborne Pathogens Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica Newport in Soil Affected by Mulch Type

Mulching is a common agricultural practice that benefits crop production through soil moisture retention, weed suppression, and soil temperature regulation. However, little is known about the effect of mulch on foodborne pathogens present in soil. In this study, the influence of polyethylene plastic, biodegradable corn-based plastic, paper, and straw mulches on Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica Newport populations in soil was investigated. Silt loam soil in troughs was inoculated with a cocktail of the pathogens and covered with mulch or left bare, then incubated for 21 days, during which bacteria were enumerated and environmental parameters monitored. Bacterial counts declined in all treatments over time (p < 0.001) but persisted at 21 days at 0.8-0.95 log CFU/g. Pathogens also declined as a factor of mulch cover (p < 0.01). An exponential decay with asymptote model fit to the data revealed slower rates of decline in soil under mulches for all pathogens (p < 0.05) relative to bare soil. Compared to the average for all treatments, rates of decay in bare soil were 0.60 (p < 0.001), 0.45 (p < 0.05), and 0.63 (p < 0.001) log CFU/g/d for E. coli O157:H7, L. monocytogenes, and Salmonella, respectively. Linear multiple regression revealed that soil hydrological parameters were positively correlated (p < 0.05) with bacterial counts, while day soil temperatures were negatively correlated (p < 0.001), suggesting that higher day temperatures and lower moisture content of bare soil contributed to the faster decline of pathogens compared to mulched soil. A microcosm experiment using field soil from lettuce cultivation suggested no influence of prior mulch treatment on pathogens. In summary, pathogen decline in soil was modified by the soil microclimate created under mulch covers, but the effect appeared was restricted to the time of soil cover. Slower decline rates of pathogens in mulched soil may pose a risk for contamination of fresh market produce crops.

Sanitizer Type and Contact Time Influence Salmonella Reductions in Preharvest Agricultural Water Used on Virginia Farms

No Environmental Protection Agency (EPA) chemical treatments for preharvest agricultural water are currently labeled to reduce human health pathogens. The goal of this study was to examine the efficacy of peracetic acid- (PAA) and chlorine (Cl)-based sanitizers against Salmonella in Virginia irrigation water. Water samples (100 mL) were collected at three time points during the growing season (May, July, September) and inoculated with either the 7-strain EPA/FDA-prescribed cocktail or a 5-strain Salmonella produce-borne outbreak cocktail. Experiments were conducted in triplicate for 288 unique combinations of time point, residual sanitizer concentration (low: PAA, 6 ppm; Cl, 2-4 ppm or high: PAA, 10 ppm; Cl, 10-12 ppm), water type (pond, river), water temperature (12°C, 32°C), and contact time (1, 5, 10 min). Salmonella were enumerated after each treatment combination and reductions were calculated. A log-linear model was used to characterize how treatment combinations influenced Salmonella reductions. Salmonella reductions by PAA and Cl ranged from 0.0 ± 0.1 to 5.6 ± 1.3 log10 CFU/100 mL and 2.1 ± 0.2 to 7.1 ± 0.2 log10 CFU/100 mL, respectively. Physicochemical parameters significantly varied by untreated water type; however, Salmonella reductions did not (p = 0.14), likely due to adjusting the sanitizer amounts needed to achieve the target residual concentrations regardless of source water quality. Significant differences (p < 0.05) in Salmonella reductions were observed for treatment combinations, with sanitizer (Cl > PAA) and contact time (10 > 5 > 1 min) having the greatest effects. The log-linear model also revealed that outbreak strains were more treatment-resistant. Results demonstrate that certain treatment combinations with PAA- and Cl-based sanitizers were effective at reducing Salmonella populations in preharvest agricultural water. Awareness and monitoring of water quality parameters are essential for ensuring adequate dosing for the effective treatment of preharvest agricultural water.

Oral Administration of a Phage Cocktail to Reduce Salmonella Colonization in Broiler Gastrointestinal Tract-A Pilot Study

Salmonella contamination in poultry meat products can lead to serious foodborne illness and economic loss from product recalls. It is crucial to control Salmonella contamination in poultry from farm to fork. Bacteriophages (phages) are viruses of bacteria that offer several advantages, especially their specificity to target bacteria. In our study, three Salmonella phages (vB_SenS_KP001, vB_SenS_KP005, and vB_SenS_WP110) recovered from a broiler farm and wastewater treatment stations showed high lysis ability ranging from 85.7 to 96.4% on over 56 serovars of Salmonella derived from several sources, including livestock and a broiler farm environment. A three-phage cocktail reduced S. Enteritidis and S. Typhimurium, in vitro by 3.9 ± 0.0 and 3.9 ± 0.2 log units at a multiplicity of infection (MOI) of 10³ and 3.8 ± 0.4 and 4.1 ± 0.2 log units at MOI of 10⁴ after 6 h post-phage treatment. A developed phage cocktail did not cause phage resistance in Salmonella during phage treatments for three passages. Phages could survive under simulated chicken gastrointestinal conditions in the presence of gastric acid for 2 h (100.0 ± 0.0% survivability), bile salt for 1 h (98.1 ± 1.0% survivability), and intestinal fluid for 4 h (100 ± 0.0% survivability). Each phage was in the phage cocktail at a concentration of up to 9.0 log PFU/mL. These did not cause any cytotoxicity to human fibroblast cells or Caco-2 cells as indicated by the percent of cell viability, which remained nearly 100% as compared with the control during 72 h of co-culture. The phage cocktail was given to broilers raised in commercial conditions at a 9 log PFU/dose for five doses, while naturally occurring Salmonella cells colonized in the gastrointestinal tract of broilers were significantly reduced as suggested by a considerably lower Salmonella prevalence from over 70 to 0% prevalence after four days of phage treatment. Our findings suggest that a phage cocktail is an effective biocontrol agent to reduce Salmonella present in the guts of broilers, which can be applied to improve food safety in broiler production.

Tomato Cultivar Nyagous Fruit Surface Metabolite Changes during Ripening Affect Salmonella Newport

ABSTRACT

Tomatoes are a valuable crop consumed year-round. Ripe fruit is picked for local sale, whereas tomatoes intended for transit may be harvested at late mature green or breaker stages when fruit firmness preserves quality. In this study, we evaluated Solanum lycopersicum cv. BHN602 association with three Salmonella serotypes and S. lycopersicum cv. Nyagous with Salmonella Newport using fruit at two ripeness stages. Counts of Salmonella Javiana and Typhimurium were higher from red ripe fruit surfaces of BHN602, and counts of Salmonella Newport were higher from ripe Nyagous fruit than from mature green fruit (P < 0.05). Aqueous fruit washes containing fruit surface compounds collected from ripe Nyagous fruit supported more Salmonella Newport growth than green fruit washes (P < 0.05). Growth curve analysis showed that between 2 and 6 h, Salmonella Newport grew at a rate of 0.25 log CFU/h in red fruit wash compared with 0.17 log CFU/h in green fruit wash (P < 0.05). The parallel trend in Salmonella interaction between fruit and wash suggested that surface metabolite differences between unripe and ripe fruit affect Salmonella dynamics. Untargeted phytochemical profiling of tomato fruit surface washes with gas chromatography time-of-flight mass spectrometry showed that ripe fruit had threefold-lower amino acid and fourfold-higher sugar (fructose, glucose, and xylose) levels than green fruit. Green fruit had higher levels of lauric, palmitic, margaric, and arachidic acids, whereas red fruit had more capric acid. The phenolics ferulic, chlorogenic, and vanillic acid, as well as tyrosol, also decreased with ripening. Although limitations of this study preclude conclusions on how specific compounds affect Salmonella, our study highlights the complexity of the plant niche for foodborne pathogens and the importance of understanding the metabolite landscape Salmonella encounters on fresh produce. Fruit surface phytochemical profiling generated testable hypotheses for future studies exploring the differential Salmonella interactions with tomato varieties and fruit at various ripeness stages.

HIGHLIGHTS

Salmonella Typhimurium outbreak associated with frozen tomato cubes at a restaurant in western Finland, January to February 2021

Several individuals reported gastrointestinal symptoms following meals consumed in late January 2021 at a restaurant in western Finland. We conducted a retrospective cohort study and defined a case as a person who ate at the lunch restaurant between 27 and 29 January 2021 and had stomach pain, vomiting or diarrhoea and/or a laboratory-confirmed Salmonella Typhimurium infection within 2 weeks after the exposure. We collected faecal and food samples for microbiological analysis. Salmonella isolates were characterised in detail using whole genome sequencing (WGS) and cluster analysis by core genome multilocus sequence typing (cgMLST). Altogether, 393 meals were sold and 101 people (who ate 142 meals) participated in the cohort study. There were 49 cases; 23 were laboratory-confirmed infections with a multidrug-resistant S. Typhimurium. The S. Typhimurium isolates from cases and frozen tomato cubes used uncooked in salads were closely related and clustered together in cgMLST comparison. These salads were consumed by 76% of the cases. Based on the cgMLST clustering, they were the suggested source of the outbreak. Statistical association was not significant between eating the salads and being a case. Following the outbreak investigation, the producer decided to recommend cooking of their frozen tomato products before consumption.

A rapid colorimetric lateral flow test strip for detection of live Salmonella Enteritidis using whole phage as a specific binder

Specific antibodies are essential components of immunoassay, which can be applied for the detection of pathogens. However, producing an antibody specific to live bacterial pathogens by the classical method of immunizing animals with live pathogens can be impractical. Phage display technology is an effective alternative method to obtain antibodies with the desired specificity against selected antigenic molecules. In this study, we demonstrated the power of a microarray-based technique for obtaining specific phage-derived antibody fragments against Salmonella, an important foodborne pathogen. The selected phage-displayed antibody fragments were subsequently employed to develop a lateral flow test strip assay for the detection of live Salmonella. The test strips showed specificity to Salmonella Enteritidis without cross-reactivity to eight serovars of Salmonella or other bacteria strains. The test strip assay requires 15 min, whereas the conventional biochemical and serological confirmation test requires at least 24 h. The microarray screening technique for specific phage-based binders and the test strip method can be further applied to other foodborne pathogens.

A Wash of Ethyl Acetoacetate Reduces Externally added Salmonella enterica on Tomatoes

The continuously high numbers of food-borne disease outbreaks document that current intervention techniques are not yet satisfactory. This study describes a novel wash for tomatoes that can be used as part of the food processing chain and is designed to prevent contamination with serovars of Salmonella enterica. The wash contains ethyl acetoacetate (EAA) at a concentration of 8% in H₂O. This wash reduced live bacterial counts (on Salmonella Shigella agar) of externally added S. Newport MDD14 by 2.3 log, counts of S. Typhimurium ATCC19585 by 1.5 log, and counts of S. Typhimurium FSL R6-0020 by 3.4 log. The naturally occurring background flora of the tomatoes was determined on plate count agar. The log reduction by EAA was 2.1. To mimic organic matter in the wash, we added 1% tomato homogenate to the 8% EAA solution. Prior to using the wash, the tomato homogenate was incubated with the EAA for 2 h. In the presence of the tomato homogenate, the log reductions were 2.4 log for S. Newport MDD14 and 3 log for S. Typhimurium FSL R6-0020. It seems like tomato homogenate did not reduce the efficacy of the EAA wash in the two S. enterica serovars tested. We propose the use of EAA as a wash for tomatoes to reduce bacterial counts of S. enterica well as naturally occurring background flora.

Food Safety Risks of Harvesting Dropped and Drooping Produce: A Review

ABSTRACT

The Produce Safety Rule of the Food Safety Modernization Act (FSMA) sets forth minimum standards for fruit and vegetable production in the United States. One provision states that growers must not harvest dropped produce because damage or ground contact may contaminate produce. In an unpublished survey of 2020 food safety inspections conducted by the Northeast Center to Advance Food Safety, handling of dropped produce covered by the FSMA was a common misunderstood and noncompliance issue among growers in the Northeast. In consideration of this provision's on-farm practicality, this review was conducted to evaluate the risks associated with dropped and drooping produce, to guide growers in making informed risk management decisions, and to answer the following questions: (i) what are the risk factors that influence transferability of pathogens from touching the ground to produce and (ii) what are the risks associated with harvesting dropped or drooping produce covered under the Produce Safety Rule? A search of online databases revealed 12 relevant publications, which highlighted moisture, contact time, and crop features as affecting contamination rates from a ground surface to a crop surface. Soil and mulch posed a differential risk, with bare soil generally presenting a lower risk than plastic mulch. The effects of other mulch types are unclear. Mulches may promote pathogen persistence in soil, although they may also protect produce from contaminated soils. These studies were limited in their scope and applicability and most did not directly address dropped produce. Research is needed to clarify the various effects of dropped and drooping produce, the impact of ground surface type on pathogen survivability and transfer, soil and crop features that facilitate contamination, and postharvest risks of harvesting dropped or drooping produce. A comprehensive understanding of these issues will guide growers in implementing preventive measures and better managing risk in a way practicable to each farm's unique conditions.

HIGHLIGHTS

A Combined Field–Lab Approach for Assessing Salmonella Infantis Persistence in Broiler Litter in a Stockpile and Composting Sleeve

Broiler litter (BL) is often contaminated by a variety of zoonotic pathogens. This study attempts to assess the persistence of Salmonella enterica serovar Infantis (S. Infantis) in BL based on spatial and temporal variation of physicochemical properties in a stockpile and composting sleeve. A single trial of two pilot-scale setups, ~35 m3 each, included an open static pile (stockpile) and composting in a polyethylene sleeve with forced aeration. The initial water content was adjusted only for the sleeve (~50% w/w) as in a common composting practice. Both systems were monitored weekly and then biweekly during 2 months in 47–53 sampling points each on every campaign. Measurements included temperature, water content, pH, electrical conductivity (EC), gas-phase oxygen, and ammonia, and the collected data were used to construct multiple contour grid maps. Of the stockpile volume, 83, 71, and 62% did not reach the commonly required minimum temperature of 55°C for three consecutive days during the first, second, and third weeks, respectively. Oxygen levels showed a strong gradient across the stockpile, while anaerobic conditions prevailed in the core. Variation was also recorded within the sleeve, but due to the water content adjustment and active aeration, the conditions favored more intense degradation and higher temperatures. Combining the grid maps drawn in this study with decay rate constants recently published for S. Infantis in BL under 36 combinations of temperature, water content, and pH, we assessed the spatial persistence of S. Infantis in the stockpile and the sleeve. Temperature was shown as a major factor, while water content and pH had only a small effect, in the stockpile only. Co-correlations between temperature, water content, EC, and oxygen suggest that selected physicochemical properties may be sufficient for such assessments. Up to 3 weeks would be recommended to achieve 7–8 log10 reduction in Salmonella in a stockpile, while this would be fully achieved within 1 week in a sleeve. This approach of combining high-resolution spatial field sampling along with decay rates of pathogens under controlled lab conditions may improve quantitative microbial risk assessments and future regulations of manure utilization.

Anaerobic soil disinfestation, amendment-type, and irrigation regimen influence Salmonella survival and die-off in agricultural soils

AIMS

This study investigated Salmonella concentrations following combinations of horticultural practices including anaerobic soil disinfestation (ASD), soil amendment type and irrigation regimen.

METHODS AND RESULTS

Sandy-loam soil was inoculated with a five-serovar Salmonella cocktail (5.5 ± 0.2 log CFU per gram) and subjected to one of six treatments: (i) no soil amendment, ASD (ASD control), (ii) no soil amendment, no-ASD (non-ASD control) and (iii-vi) soil amended with pelletized poultry litter, rye, rapeseed or hairy vetch with ASD. The effect of irrigation regimen was determined by collecting samples 3 and 7 days after irrigation. Twenty-five-gram soil samples were collected pre-ASD, post-soil saturation (i.e. ASD-process), and at 14 time-points post-ASD, and Salmonella levels enumerated. Log-linear models examined the effect of amendment type and irrigation regimen on Salmonella die-off during and post-ASD. During ASD, Salmonella concentrations significantly decreased in all treatments (range: -0.2 to -2.7 log CFU per gram), albeit the smallest decrease (-0.2 log CFU per gram observed in the pelletized poultry litter) was of negligible magnitude. Salmonella die-off rates varied by amendment with an average post-ASD rate of -0.05 log CFU per gram day (CI = -0.05, -0.04). Salmonella concentrations remained highest over the 42 days post-ASD in pelletized poultry litter, followed by rapeseed, and hairy vetch treatments. Findings suggested ASD was not able to eliminate Salmonella in soil, and certain soil amendments facilitated enhanced Salmonella survival. Salmonella serovar distribution differed by treatment with pelletized poultry litter supporting S. Newport survival, compared with other serovars. Irrigation appeared to assist Salmonella survival with concentrations being 0.14 log CFU per gram (CI = 0.05, 0.23) greater 3 days, compared with 7 days post-irrigation.

CONCLUSIONS

ASD does not eliminate Salmonella in soil, and may in fact, depending on the soil amendment used, facilitate Salmonella survival.

SIGNIFICANCE AND IMPACT OF THE STUDY

Synergistic and antagonistic effects on food safety hazards of implementing horticultural practices should be considered.

Determination of Salmonella enterica Leaf Internalization Varies Substantially According to the Method and Conditions Used to Assess Bacterial Localization

In a previous study, comparing the internalization of S. enterica serovar Typhimurium in various leaves by confocal microscopy, we have demonstrated that the pathogen failed to internalize tomato leaves. Numerous reasons may account for these findings, yet one such factor might be the methodology employed to quantify leaf internalization. To this end, we have systematically studied leaf localization of a Green-fluorescent protein-labeled Salmonella strain in tomato, lettuce, and Arabidopsis leaves by surface sterilization and enumeration of the surviving bacteria, side by side, with confocal microscopy observations. Leaf sterilization was performed using either sodium hypochlorite, silver nitrate, or ethanol for 1 to 7min. The level of internalization varied according to the type of disinfectant used for surface sterilization and the treatment time. Treatment of tomato leaves with 70% ethanol for up to 7min suggested possible internalization of Salmonella, while confocal microscopy showed no internalization. In the case of in lettuce and Arabidopsis leaves, both the plate-count technique and confocal microscopy demonstrated considerable Salmonella internalization thought different sterilization conditions resulted in variations in the internalization levels. Our findings highlighted the dependency of the internalization results on the specific disinfection protocol used to determine bacterial localization. The results underscore the importance of confocal microscopy in validating a particular surface sterilization protocol whenever a new pair of bacterial strain and plant cultivar is studied.

Survival and Persistence of Foodborne Pathogens in Manure-Amended Soils and Prevalence on Fresh Produce in Certified Organic Farms: A Multi-Regional Baseline Analysis

Biological soil amendments of animal origin (BSAAOs), including untreated (e.g., raw or aged manure, or incompletely composted manure) and treated animal products (e.g., compost), are used for crop production and as part of soil health management. Application of BSAAO's must be done cautiously, as raw manure commonly contains enteric foodborne pathogens that can potentially contaminate edible produce that may be consumed without cooking. USDA National Organic Program (NOP) certified production systems follow the 90-or 120-day interval standards between applications of untreated BSAAOs and crop harvest, depending on whether the edible portions of the crops are in indirect or direct contact with the soil, respectively. This study was conducted to evaluate the survival of four foodborne pathogens in soils amended with BSAAOs and to examine the potential for bacterial transfer to fresh produce harvested from USDA NOP certified organic farms (19) from four states. Only 0.4% (2/527) of produce samples were positive for L. monocytogenes. Among the untreated manure and compost samples, 18.0% (42/233) were positive for at least one of the tested and culturable bacterial foodborne pathogens. The prevalence of non-O157 STEC and Salmonella in untreated manure was substantially &gt; that of E. coli O157:H7 and L. monocytogenes. Of the 2,461 soil samples analyzed in this study, 12.9% (318) were positive for at least one pathogen. In soil amended with untreated manure, the prevalence of non-O157 STEC [7.7% (190) and L. monocytogenes (5.0% (122), was &gt; that of Salmonella (1.1% (26)] or E. coli O157 [0.04% (1)]. Foodborne pathogen prevalence in the soil peaked after manure application and decreased significantly 30 days post-application (dpa). However, non-O157 STEC and L. monocytogenes were recovered from soil samples after 90 and 120 dpa. Results indicate that produce contamination by tested foodborne pathogens was infrequent, but these data should not be generalized outside of the specific wait-time regulations for organic crop production and the farms studied. Moreover, other sources of contamination, e.g., irrigation, wildlife, environmental conditions, cropping and management practices, should be considered. This study also provides multi-regional baseline data relating to current NOP application intervals and development of potential risk mitigation strategies to reduce pathogen persistence in soils amended with BSAAOs. These findings contribute to filling critical data gaps concerning occurrence of fecal pathogens in NOP-certified farming systems used for production of fresh produce in different US regions.

Role of soil in the regulation of human and plant pathogens: soils' contributions to people

Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a 'One Health' framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Interactions between Microbial Food Safety and Environmental Sustainability in the Fresh Produce Supply Chain

Improving the environmental sustainability of the food supply chain will help to achieve the United Nations Sustainable Development Goals (SDGs). This environmental sustainability is related to different SDGs, but mainly to SDG 2 (Zero Hunger), SDG 12 (Responsible Production and Consumption), SDG 13 (Climate Action), and SDG 15 (Life on Land). The strategies and measures used to improve this aspect of the food supply chain must remain in balance with other sustainability aspects (economic and social). In this framework, the interactions and possible conflicts between food supply chain safety and sustainability need to be assessed. Although priority must be given to safety aspects, food safety policies should be calibrated in order to avoid unnecessary deleterious effects on the environment. In the present review, a number of potential tensions and/or disagreements between the microbial safety and environmental sustainability of the fresh produce supply chain are identified and discussed. The addressed issues are spread throughout the food supply chain, from primary production to the end-of-life of the products, and also include the handling and processing industry, retailers, and consumers. Interactions of fresh produce microbial safety with topics such as food waste, supply chain structure, climate change, and use of resources have been covered. Finally, approaches and strategies that will prove useful to solve or mitigate the potential contradictions between fresh produce safety and sustainability are described and discussed. Upon analyzing the interplay between microbial safety and the environmental sustainability of the fresh produce supply chain, it becomes clear that decisions that are taken to ensure fresh produce safety must consider the possible effects on environmental, economic, and social sustainability aspects. To manage these interactions, a global approach considering the interconnections between human activities, animals, and the environment will be required.

Factors Influencing the Persistence of Salmonella Infantis in Broiler Litter During Composting and Stabilization Processes and Following Soil Incorporation

Broiler litter (BL), a by-product of broiler meat production, is frequently contaminated with Salmonella and other zoonotic pathogens. To ensure the safety of crop production chains and limit pathogen spread in the environment, a pre-treatment is desired before further agricultural utilization. The objective of this study was to characterize the effect of physico-chemical properties on Salmonella persistence in BL during composting and stabilization and following soil incorporation, toward optimization of the inactivation process. Thirty-six combinations of temperature (30, 40, 50, and 60°C), water content (40, 55, and 70%; w/w), and initial pH (6, 7, and 8.5) were employed in static lab vessels to study the persistence of Salmonella enterica serovar Infantis (S. Infantis; a multidrug-resistant strain) during incubation of artificially-inoculated BL. The effect of aeration was investigated in a composting simulator, with controlled heating and flow conditions. Temperature was found to be the main factor significantly influencing Salmonella decay rates, while water content and initial pH had a secondary level of influence with significant effects mainly at 30 and 40°C. Controlled simulations showed faster decay of Salmonella under anaerobic conditions at mesophilic temperatures (&lt;45°C) and no effect of NH3 emissions. Re-wetting the BL at mesophilic temperatures resulted in Salmonella burst, and led to a higher tolerance of the pathogen at increased temperatures. Based on the decay rates measured under all temperature, water content, and pH conditions, it was estimated that the time required to achieve a 7 log10 reduction in Salmonella concentration, ranges between 13.7–27.2, 6.5–15.6, 1.2–4.7, and 1.3–1.5 days for 30, 40, 50, and 60°C, respectively. Inactivation of BL indigenous microbial population by autoclaving or addition of antibiotics to which the S. Infantis is resistant, resulted in augmentation of Salmonella multiplication. This suggests the presence of microbial antagonists in the BL, which inhibit the growth of the pathogen. Finally, Salmonella persisted over 90 days at 30°C in a Vertisol soil amended with inoculated BL, presumably due to reduced antagonistic activity compared to the BL alone. These findings are valuable for risk assessments and the formulation of guidelines for safe utilization of BL in agriculture.

Cascading effects of composts and cover crops on soil chemistry, bacterial communities and the survival of foodborne pathogens

AIMS

Recent foodborne disease outbreaks have caused farmers to re-evaluate their practices. In particular, concern that soil amendments could introduce foodborne pathogens onto farms and promote their survival in soils has led farmers to reduce or eliminate the application of animal-based composts. However, organic amendments (such as composts and cover crops) could bolster food safety by increasing soil microbial diversity and activity, which can act as competitors or antagonists and reduce pathogen survival.

METHODS AND RESULTS

Leveraging a study of a 27-year experiment comparing organic and conventional soil management, we evaluate the impacts of composted poultry litter and cover crops on soil chemistry, bacterial communities and survival of Salmonella enterica and Listeria monocytogenes. We found that bacterial community composition strongly affected pathogen survival in soils. Specifically, organic soils managed with cover crops and composts hosted more macronutrients and bacterial communities that were better able to suppress Salmonella and Listeria. For example, after incubating soils for 10 days at 20°C, soils without composts retained fourfold to fivefold more Salmonella compared to compost-amended soils. However, treatment effects dissipated as bacterial communities converged over the growing season.

CONCLUSIONS

Our results suggest that composts and cover crops may be used to build healthy soils without increasing foodborne pathogen survival.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our work suggests that animal-based composts do not promote pathogen survival and may even promote bacterial communities that suppress pathogens. Critically, proper composting techniques are known to reduce pathogen populations in biological soil amendments of animal origin, which can reduce the risks of introducing pathogens to farm fields in soil amendments. Thus, animal-based composts and cover crops may be a safe alternative to conventional fertilizers, both because of the known benefits of composts for soil health and because it may be possible to apply amendments in such a way that food-safety risks are mitigated rather than exacerbated.

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.

Correlation of Salmonella enterica and Listeria monocytogenes in Irrigation Water to Environmental Factors, Fecal Indicators, and Bacterial Communities

Outbreaks of foodborne illnesses linked to fresh fruits and vegetables have been key drivers behind a wide breadth of research aiming to fill data gaps in our understanding of the total ecology of agricultural water sources such as ponds and wells and the relationship of this ecology to foodborne pathogens such as Salmonella enterica and Listeria monocytogenes. Both S. enterica and L. monocytogenes can persist in irrigation water and have been linked to produce contamination events. Data describing the abundance of these organisms in specific agricultural water sources are valuable to guide water treatment measures. Here, we profiled the culture independent water microbiota of four farm ponds and wells correlated with microbiological recovery of S. enterica (prevalence: pond, 19.4%; well, 3.3%), L. monocytogenes (pond, 27.1%; well, 4.2%) and fecal indicator testing. Correlation between abiotic factors, including water parameters (temperature, pH, conductivity, dissolved oxygen percentage, oxidation reduction potential, and turbidity) and weather (temperature and rainfall), and foodborne pathogens were also evaluated. Although abiotic factors did not correlate with recovery of S. enterica or L. monocytogenes (p > 0.05), fecal indicators were positively correlated with incidence of S. enterica in well water. Bacterial taxa such as Sphingomonadaceae and Hymenobacter were positively correlated with the prevalence and population of S. enterica, and recovery of L. monocytogenes was positively correlated with the abundance of Rhizobacter and Comamonadaceae (p < 0.03). These data will support evolving mitigation strategies to reduce the risk of produce contamination by foodborne pathogens through irrigation.

Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces

Salmonella enterica can colonize all parts of the tomato plant. Tomatoes have been frequently implicated in salmonellosis outbreaks. In agricultural settings, Salmonella must overcome stress, nutritional and competition barriers to become established on plant surfaces. Knowledge of the genetic mechanisms underlying Salmonella-plant associations is limited, especially when growing epiphytically. A genome-wide transcriptomic analysis of Salmonella Typhimurium (SeT) was conducted with RNA-Seq to elucidate strategies for epiphytic growth on live, intact tomato shoot and root surfaces. Six plasmid-encoded and 123 chromosomal genes were significantly (using Benjamini-Hochberg adjusted p-values) up-regulated; 54 and 110 detected in SeT on shoots and roots, respectively, with 35 common to both. Key signals included NsrR regulon genes needed to mitigate nitrosative stress, oxidative stress genes and host adaptation genes, including environmental stress, heat shock and acid-inducible genes. Several amino acid biosynthesis genes and genes indicative of sulphur metabolism and anaerobic respiration were up-regulated. Some Type III secretion system (T3SS) effector protein genes and their chaperones from pathogenicity island-2 were expressed mostly in SeT on roots. Gene expression in SeT was validated against SeT and also the tomato outbreak strain Salmonella Newport with a high correlation (R ² = 0.813 and 0.874, respectively; both p < 0.001). Oxidative and nitrosative stress response genes, T3SS2 genes and amino acid biosynthesis may be needed for Salmonella to successfully colonize tomato shoot and root surfaces.

Salmonella enterica Elicits and Is Restricted by Nitric Oxide and Reactive Oxygen Species on Tomato

The enteric pathogen Salmonella enterica can interact with parts of the plant immune system despite not being a phytopathogen. Previous transcriptomic profiling of S. enterica associating with tomato suggested that Salmonella was responding to oxidative and nitrosative stress in the plant niche. We aimed to investigate whether Salmonella was eliciting generation of reactive oxygen species (ROS) and nitric oxide (NO), two components of the microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) of plants. We also sought to determine whether this interaction had any measurable effects on Salmonella colonization of plants. Biochemical, gene expression and on-plant challenge assays of tomato vegetative and fruit organs were conducted to assess the elicitation of ROS and NO in response to Salmonella Newport association. The counter bacterial response and the effect of NO and ROS on Salmonella colonization was also investigated. We detected H₂O₂ in leaves and fruit following challenge with live S. Newport (p < 0.05). Conversely, NO was detected on leaves but not on fruit in response to S. Newport (p < 0.05). We found no evidence of plant defense attenuation by live S. Newport. Bacterial gene expression of S. Newport associating with leaves and fruit were indicative of adaptation to biotic stress in the plant niche. The nitrosative stress response genes hmpA and yoaG were significantly up-regulated in S. Newport on leaves and fruit tissue compared to tissue scavenged of NO or ROS (p < 0.05). Chemical modulation of these molecules in the plant had a restrictive effect on bacterial populations. Significantly higher S. Newport titers were retrieved from H₂O₂ scavenged leaves and fruit surfaces compared to controls (p < 0.05). Similarly, S. Newport counts recovered from NO-scavenged leaves, but not fruit, were higher compared to control (p < 0.05), and significantly lower on leaves pre-elicited to produce endogenous NO. We present evidence of Salmonella elicitation of ROS and NO in tomato, which appear to have a restricting effect on the pathogen. Moreover, bacterial recognition of ROS and NO stress was detected. This work shows that tomato has mechanisms to restrict Salmonella populations and ROS and NO detoxification may play an important role in Salmonella adaptation to the plant niche.

Agricultural production systems can serve as reservoir for human pathogens

Food-borne diseases are a threat to human health and can cause severe economic losses. Nowadays, in a growing and increasingly interconnected world, food-borne diseases need to be dealt with in a global manner. In order to tackle this issue, it is essential to consider all possible entry routes of human pathogens into the production chain. Besides the post-harvest handling of the fresh produce itself, also the prevention of contamination in livestock and agricultural soils are of particular importance. While the monitoring of human pathogens and intervening measures are relatively easy to apply in livestock and post-harvest, the investigation of the prevention strategies in crop fields is a challenging task. Furthermore, crop fields are interconnected with livestock via fertilizers and feed; therefore, a poor hygiene management can cause cross-contamination. In this review, we highlight the possible contamination of crop plants by bacterial human pathogens via the rhizosphere, their interaction with the plant and possible intervention strategies. Furthermore, we discuss critical issues and questions that are still open.

Diversity and Dynamics of Salmonella enterica in Water Sources, Poultry Litters, and Field Soils Amended With Poultry Litter in a Major Agricultural Area of Virginia

The Eastern Shore of Virginia (ESV) is a major agricultural region in Virginia and in the past has been linked to some tomato-associated outbreaks of salmonellosis. In this study, water samples were collected weekly from irrigation ponds and wells in four representative vegetable farms (Farms A–D, each farm paired with one pond and one well) and a creek as well. In addition, water samples from two sites in the Chesapeake Bay on the ESV were collected monthly. Poultry litter was sampled monthly from three commercial broiler farms. Soil samples were collected monthly after fertilization with poultry litter from 10 farms in 2014 and another 14 farms in 2015. A most probable number method was used to detect Salmonella enterica presence and concentration in collected samples. Presumptive Salmonella colonies were confirmed by the cross-streaking method. Molecular serotyping was carried out to determine the Salmonella serovars. The average prevalence of Salmonella in pond, well, creek, and bay water samples was 19.3, 3.3, 24.2, and 29.2%, respectively. There were significant spatial and temporal differences for Salmonella incidence in various water sources. The prevalence of S. enterica in four tested ponds from farms A, B, C, and D were 16, 12, 22, and 27%, respectively. While the prevalence of S. enterica in irrigation wells was significantly lower, some well water samples tested positive during the study. Salmonella Newport was found to be the predominant serovar isolated from water samples. All poultry houses of the three tested broiler farms were Salmonella-positive at certain sampling points during the study with prevalence ranging from 14.3 to 35.4%. Salmonella was found to be able to survive up to 4 months in poultry litter amended soils from the tested farms in 2014, and up to 6 months in 2015. This research examined the dynamics of S. enterica in relationship to water source, poultry litter, and amended soil in a major agricultural area, and provides useful information for food safety risk assessments.