Salmonella Establishment in Agricultural Soil and Colonization of Crop Plants Depend on Soil Type and Plant Species

Factors Associated with the Prevalence of Salmonella, Generic Escherichia coli, and Coliforms in Florida's Agricultural Soils

Limited data exist on the environmental factors that impact pathogen prevalence in the soil. The prevalence of foodborne pathogens, Salmonella and Listeria monocytogenes, and the prevalence and concentration of generic E. coli in Florida's agricultural soils were evaluated to understand the potential risk of microbial contamination at the preharvest level. For all organisms but L. monocytogenes, a longitudinal field study was performed in three geographically distributed agricultural areas across Florida. At each location, 20 unique 5 by 5 m field sampling sites were selected, and soil was collected and evaluated for Salmonella presence (25 g) and E. coli and coliform concentrations (5 g). Complementary data collected from October 2021 to April 2022 included: weather; adjacent land use; soil properties, including macro- and micro-nutrients; and field management practices. The overall Salmonella and generic E. coli prevalence was 0.418% (1/239) and 11.3% (27/239), respectively; with mean E. coli concentrations in positive samples of 1.56 log CFU/g. Farm A had the highest prevalence of generic E. coli, 22.8% (18/79); followed by Farm B, 10% (8/80); and Farm C 1.25% (1/80). A significant relationship (p < 0.05) was observed between generic E. coli and coliforms, and farm and sampling trip. Variation in the prevalence of generic E. coli and changes in coliform concentrations between farms suggest environmental factors (e.g. soil properties) at the three farms were different. While Salmonella was only detected once, generic E. coli was detected in Florida soils throughout the duration of the growing season meaning activities that limit contact between soil and horticultural crops should continue to be emphasized. Samples collected during an independent sampling trip were evaluated for L. monocytogenes, which was not detected. The influence of local environmental factors on the prevalence of indicator organisms in the soil presents a unique challenge when evaluating the applicability of more global models to predict pathogen prevalence in preharvest produce environments.

A Review on Microbiological Source Attribution Methods of Human Salmonellosis: From Subtyping to Whole-Genome Sequencing

Salmonella is one of the main causes of human foodborne illness. It is endemic worldwide, with different animals and animal-based food products as reservoirs and vehicles of infection. Identifying animal reservoirs and potential transmission pathways of Salmonella is essential for prevention and control. There are many approaches for source attribution, each using different statistical models and data streams. Some aim to identify the animal reservoir, while others aim to determine the point at which exposure occurred. With the advance of whole-genome sequencing (WGS) technologies, new source attribution models will greatly benefit from the discriminating power gained with WGS. This review discusses some key source attribution methods and their mathematical and statistical tools. We also highlight recent studies utilizing WGS for source attribution and discuss open questions and challenges in developing new WGS methods. We aim to provide a better understanding of the current state of these methodologies with application to Salmonella and other foodborne pathogens that are common sources of illness in the poultry and human sectors.

Colonization of Raphanus sativus by human pathogenic microorganisms

Contamination of vegetables with human pathogenic microorganisms (HPMOs) is considered one of the most important problems in the food industry, as current nutritional guidelines include increased consumption of raw or minimally processed organic vegetables due to healthy lifestyle promotion. Vegetables are known to be potential vehicles for HPMOs and sources of disease outbreaks. In this study, we tested the susceptibility of radish (Raphanus sativus) to colonization by different HPMOs, including Escherichia coli PCM 2561, Salmonella enterica subsp. enterica PCM 2565, Listeria monocytogenes PCM 2191 and Bacillus cereus PCM 1948. We hypothesized that host plant roots containing bactericidal compounds are less prone to HPMO colonization than shoots and leaves. We also determined the effect of selected pathogens on radish growth to check host plant-microbe interactions. We found that one-week-old radish is susceptible to colonization by selected HPMOs, as the presence of the tested HPMOs was demonstrated in all organs of R. sativus. The differences were noticed 2 weeks after inoculation because B. cereus was most abundant in roots (log10 CFU - 2.54), S. enterica was observed exclusively in stems (log10 CFU - 3.15), and L. monocytogenes and E. coli were most abundant in leaves (log10 CFU - 4.80 and 3.23, respectively). The results suggest that E. coli and L. monocytogenes show a higher ability to colonize and move across the plant than B. cereus and S. enterica. Based on fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) approach HPMOs were detected in extracellular matrix and in some individual cells of all analyzed organs. The presence of pathogens adversely affected the growth parameters of one-week-old R. sativus, especially leaf and stem fresh weight (decreased by 47-66 and 17-57%, respectively). In two-week-old plants, no reduction in plant biomass development was noted. This observation may result from plant adaptation to biotic stress caused by the presence of HPMOs, but confirmation of this assumption is needed. Among the investigated HPMOs, L. monocytogenes turned out to be the pathogen that most intensively colonized the aboveground part of R. sativus and at the same time negatively affected the largest number of radish growth parameters.

From field to plate: How do bacterial enteric pathogens interact with ready-to-eat fruit and vegetables, causing disease outbreaks?

Ready-to-eat fruit and vegetables are a convenient source of nutrients and fibre for consumers, and are generally safe to eat, but are vulnerable to contamination with human enteric bacterial pathogens. Over the last decade, Salmonella spp., pathogenic Escherichia coli, and Listeria monocytogenes have been linked to most of the bacterial outbreaks of foodborne illness associated with fresh produce. The origins of these outbreaks have been traced to multiple sources of contamination from pre-harvest (soil, seeds, irrigation water, domestic and wild animal faecal matter) or post-harvest operations (storage, preparation and packaging). These pathogens have developed multiple processes for successful attachment, survival and colonization conferring them the ability to adapt to multiple environments. However, these processes differ across bacterial strains from the same species, and across different plant species or cultivars. In a competitive environment, additional risk factors are the plant microbiome phyllosphere and the plant responses; both factors directly modulate the survival of the pathogens on the leaf's surface. Understanding the mechanisms involved in bacterial attachment to, colonization of, and proliferation, on fresh produce and the role of the plant in resisting bacterial contamination is therefore crucial to reducing future outbreaks.

Bidirectional Comparisons Revealed Functional Patterns in Interaction between Salmonella enterica and Plants

Plants may harbor the human pathogen Salmonella enterica. Interactions between S. enterica and different plant species have been studied in individual reports. However, disparities arising from the distinct experimental conditions may render a meaningful comparison very difficult. This study explored interaction patterns between different S. enterica strains including serovars Typhimurium 14028s and LT2 and serovar Senftenberg, and different plants (Arabidopsis, lettuce, and tomato) in one approach. Better persistence of S. enterica serovar Typhimurium strains was observed in all tested plants, whereas the resulting symptoms varied depending on plant species. Genes encoding pathogenesis-related proteins were upregulated in plants inoculated with Salmonella. Furthermore, transcriptome of tomato indicated dynamic responses to Salmonella, with strong and specific responses already 24 h after inoculation. By comparing with publicly accessible Arabidopsis and lettuce transcriptome results generated in a similar manner, constants and variables were displayed. Plants responded to Salmonella with metabolic and physiological adjustments, albeit with variability in reprogrammed orthologues. At the same time, Salmonella adapted to plant leaf-mimicking media with changes in biosynthesis of cellular components and adjusted metabolism. This study provides insights into the Salmonella-plant interaction, allowing for a direct comparison of responses and adaptations in both organisms.

Intraspecies competition among Salmonella enterica isolates in the lettuce leaf apoplast

Multiple Salmonella enterica serovars and strains have been reported to be able to persist inside the foliar tissue of lettuce (Lactuca sativa L.), potentially resisting washing steps and reaching the consumer. Intraspecies variation of the bacterial pathogen and of the plant host can both significantly affect the outcome of foliar colonization. However, current understanding of the mechanisms underlying this phenomenon is still very limited. In this study, we evaluated the foliar fitness of 14 genetically barcoded S. enterica isolates from 10 different serovars, collected from plant and animal sources. The S. enterica isolates were vacuum-infiltrated individually or in pools into the leaves of three- to four-week-old lettuce plants. To estimate the survival capacity of individual isolates, we enumerated the bacterial populations at 0- and 10- days post-inoculation (DPI) and calculated their net growth. The competition of isolates in the lettuce apoplast was assessed through the determination of the relative abundance change of barcode counts of each isolate within pools during the 10 DPI experimental period. Isolates exhibiting varying apoplast fitness phenotypes were used to evaluate their capacity to grow in metabolites extracted from the lettuce apoplast and to elicit the reactive oxygen species burst immune response. Our study revealed that strains of S. enterica can substantially differ in their ability to survive and compete in a co-inhabited lettuce leaf apoplast. The differential foliar fitness observed among these S. enterica isolates might be explained, in part, by their ability to utilize nutrients available in the apoplast and to evade plant immune responses in this niche.

Broad time-dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature

In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11Φcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11Φcu in soils is associated with a complex interplay of metabolic networks.

Effect of Different Pre-Growth Temperatures on the Survival Kinetics of Salmonella enterica and Listeria monocytogenes in Fresh-Cut Salad during Refrigerated Storage

The effect of the pre-growth temperature of bacterial cultures on their subsequent survival kinetics in fresh-cut produce during refrigerated storage was investigated in this study. Three-strain cocktails of Listeria monocytogenes and Salmonella enterica, cultured at different growth temperatures (4, 21, and 37 °C) were inoculated on fresh-cut mixed salad and on individual produce in the mixed salad. The inoculated samples were stored at 4 °C and 80 ± 2% relative humidity (RH) for up to 72 h and the growth, survival, or death kinetics were determined at regular intervals. The results indicate that depending upon the type of pathogen tested, the pre-growth temperature(s) and the type of produce showed a significant (p ≤ 0.05) effect on the survival kinetics. Among the tested produce, mixed salad showed the highest reduction in L. monocytogenes pre-grown at 37 °C (1.33 log CFU/g) followed by red cabbage (0.56 log CFU/g), iceberg lettuce (0.52 log CFU/g), and carrot (-0.62 log CFU/g), after 72 h, respectively. In the case of Salmonella, carrot showed the highest reduction (1.07 log CFU/g for 37 °C pre-grown culture) followed by mixed salad (0.78 log CFU/g for 37 °C pre-grown culture), cabbage (0.76 log CFU/g for 21 °C pre-grown culture), and lettuce (0.65 log CFU/g for 4 °C pre-grown culture), respectively. Among the tested ComBase predictive models, the Baranyi-Roberts model better fitted the experimental data. These findings indicate that the appropriate selection of pre-growth environmental conditions is critical to better understand the kinetics of foodborne pathogens.

Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves

Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.

Exposing Salmonella Senftenberg and Escherichia coli Strains Isolated from Poultry Farms to Formaldehyde and Lingonberry Extract at Low Concentrations

European Union (EU) countries strive to improve the quality and safety of food of animal origin. Food production depends on a good microbiological quality of fodder. However, feed can be a reservoir or vector of pathogenic microorganisms, including Salmonella or Escherichia coli bacteria. Salmonella spp. and E. coli are the two most important food-borne pathogens of public health concern. Contamination with these pathogens, mainly in the poultry sector, can lead to serious food-borne diseases. Both microorganisms can form biofilms on abiotic and biotic surfaces. The cells that form biofilms are less sensitive to disinfectants, which in turn makes it difficult to eliminate them from various surfaces. Because the usage of formaldehyde in animal feed is prohibited in European countries, the replacement of this antibacterial with natural plant products seems very promising. This study aimed to assess the inhibitory effectiveness of Vaccinium vitis-idaea extract against biofilm produced by model Salmonella enterica and E. coli strains. We found that formaldehyde could effectively kill both species of bacterial cells in biofilm, while the lingonberry extract showed some antibiofilm effect on S. enterica serovar Senftenberg. In conclusion, finding natural plant products that are effective against biofilms formed by Gram-negative bacteria is still challenging.

Salmonella enterica relies on carbon metabolism to adapt to agricultural environments

Salmonella enterica, a foodborne and human pathogen, is a constant threat to human health. Agricultural environments, for example, soil and plants, can be ecological niches and vectors for Salmonella transmission. Salmonella persistence in such environments increases the risk for consumers. Therefore, it is necessary to investigate the mechanisms used by Salmonella to adapt to agricultural environments. We assessed the adaptation strategy of S. enterica serovar Typhimurium strain 14028s to agricultural-relevant situations by analyzing the abundance of intermediates in glycolysis and the tricarboxylic acid pathway in tested environments (diluvial sand soil suspension and leaf-based media from tomato and lettuce), as well as in bacterial cells grown in such conditions. By reanalyzing the transcriptome data of Salmonella grown in those environments and using an independent RT-qPCR approach for verification, several genes were identified as important for persistence in root or leaf tissues, including the pyruvate dehydrogenase subunit E1 encoding gene aceE. In vivo persistence assay in tomato leaves confirmed the crucial role of aceE. A mutant in another tomato leaf persistence-related gene, aceB, encoding malate synthase A, displayed opposite persistence features. By comparing the metabolites and gene expression of the wild-type strain and its aceB mutant, fumarate accumulation was discovered as a potential way to replenish the effects of the aceB mutation. Our research interprets the mechanism of S. enterica adaptation to agriculture by adapting its carbon metabolism to the carbon sources available in the environment. These insights may assist in the development of strategies aimed at diminishing Salmonella persistence in food production systems.

Sporadic Detection of Escherichia coli O104:H4 Strain C227/11Φcu in the Edible Parts of Lamb's Lettuce Cultured in Contaminated Agricultural Soil Samples

In the current study, we demonstrate that E. coli O104:H4 strain C227/11Φcu, a derivative of the 2011 enterohemorrhagic/enteroaggregative (EHEC/EAEC) E. coli outbreak strain, migrated into the edible portion of lamb's lettuce plants upon contamination of the surrounding soil. Seeds were surface-sterilized and cultivated on Murashige-Skoog agar or in autoclaved agricultural soil. Migration into the edible portions was investigated by inoculating the agar or soil close to the plants with 108 colony-forming units (CFU). The edible parts, which did not come into contact with the contaminated medium or soil, were quantitatively analyzed for the presence of bacteria after 2, 4 and 8 weeks. Strain C227/11Φcu could colonize lamb's lettuce when contamination of medium or soil occurs. The highest recovery rate (27%) was found for lettuce cultivated in agar, and up to 1.6 × 103 CFU/g lettuce was detected. The recovery rate was lower for the soil samples (9% and 13.5%). Although the used contamination levels were high, migration of C227/11Φcu from the soil into the edible parts was demonstrated. This study further highlights the risk of crop plant contamination with pathogenic E. coli upon soil contamination.

Microplastics in agriculture - a potential novel mechanism for the delivery of human pathogens onto crops

Mulching with plastic sheeting, the use of plastic carriers in seed coatings, and irrigation with wastewater or contaminated surface water have resulted in plastics, and microplastics, becoming ubiquitous in agricultural soils. Once in the environment, plastic surfaces quickly become colonised by microbial biofilm comprised of a diverse microbial community. This so-called 'plastisphere' community can also include human pathogens, particularly if the plastic has been exposed to faecal contamination (e.g., from wastewater or organic manures and livestock faeces). The plastisphere is hypothesised to facilitate the survival and dissemination of pathogens, and therefore plastics in agricultural systems could play a significant role in transferring human pathogens to crops, particularly as microplastics adhering to ready to eat crops are difficult to remove by washing. In this paper we critically discuss the pathways for human pathogens associated with microplastics to interact with crop leaves and roots, and the potential for the transfer, adherence, and uptake of human pathogens from the plastisphere to plants. Globally, the concentration of plastics in agricultural soils are increasing, therefore, quantifying the potential for the plastisphere to transfer human pathogens into the food chain needs to be treated as a priority.

Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize

Pseudomonads are metabolically flexible and can thrive on different plant hosts. However, the metabolic adaptations required for host promiscuity are unknown. Here, we addressed this knowledge gap by employing RNAseq and comparing transcriptomic responses of Pseudomonas donghuensis P482 to root exudates of two plant hosts: tomato and maize. Our main goal was to identify the differences and the common points between these two responses. Pathways upregulated only by tomato exudates included nitric oxide detoxification, repair of iron-sulfur clusters, respiration through the cyanide-insensitive cytochrome bd, and catabolism of amino and/or fatty acids. The first two indicate the presence of NO donors in the exudates of the test plants. Maize specifically induced the activity of MexE RND-type efflux pump and copper tolerance. Genes associated with motility were induced by maize but repressed by tomato. The shared response to exudates seemed to be affected both by compounds originating from the plants and those from their growth environment: arsenic resistance and bacterioferritin synthesis were upregulated, while sulfur assimilation, sensing of ferric citrate and/or other iron carriers, heme acquisition, and transport of polar amino acids were downregulated. Our results provide directions to explore mechanisms of host adaptation in plant-associated microorganisms.

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.

Novel method to recover Salmonella enterica cells for Tn-Seq approaches from lettuce leaves and agricultural environments using combination of sonication, filtration, and dialysis membrane

Salmonella enterica in agricultural environments has become an important concern, due to its potential transmission to humans and the associated public health risks. To identify genes contributing to Salmonella adaptation to such environments, transposon sequencing has been used in recent years. However, isolating Salmonella from atypical hosts, such as plant leaves, can pose technical challenges due to low bacterial content and the difficulty to separate an adequate number of bacteria from host tissues. In this study, we describe a modified methodology using a combination of sonication and filtration to recover S. enterica cells from lettuce leaves. We successfully recovered over a total of 3.5 × 106Salmonella cells in each biological replicate from two six-week old lettuce leaves, 7 days after infiltration with a Salmonella suspension of 5 × 107 colony forming units (CFU)/mL. Moreover, we have developed a dialysis membrane system as an alternative method for recovering bacteria from culture medium, mimicking a natural environment. Inoculating 107 CFU/mL of Salmonella into the media based on plant (lettuce and tomato) leaf and diluvial sand soil, a final concentration of 109.5 and 108.5 CFU/mL was obtained, respectively. One millilitre of the bacterial suspension after 24 h incubation at 28 °C using 60 rpm agitation was pelleted, corresponding to 109.5 and 108.5 cells from leaf- or soil-based media. The recovered bacterial population, from both lettuce leaves and environment-mimicking media, can adequately cover a presumptive library density of 106 mutants. In conclusion, this protocol provides an effective method to recover a Salmonella transposon sequencing library from in planta and in vitro systems. We expect this novel technique to foster the study of Salmonella in atypical hosts and environments, as well as other comparable scenarios.

Computational assessment of phytochemicals of medicinal plants from Mexico as potential inhibitors of Salmonella enterica efflux pump AcrB protein

The AcrAB-TolC efflux pump (EP) confers multidrug resistance to Salmonella enterica, a major etiological agent of foodborne infections. Phytochemicals that inhibit the functions of AcrAB-TolC EP present ideal candidates for reversal of antibiotic resistance. Progressive technological advancements, have facilitated the development of computational methods that offer a rapid low-cost approach to screen and identify phytochemicals with inhibitory potential against EP. In this study, 71 phytochemicals derived from plants used for medicinal purposes in Mexico were screened for their potential as inhibitors of Salmonella AcrB protein using in silico approaches including molecular docking and molecular dynamics (MD) simulation. Consequently, naringenin, 5-methoxypsoralen, and licarin A were identified as candidate inhibitors of AcrB protein. The three phytochemicals bound distal/deep pocket (DP) and hydrophobic trap (HPT) residues of AcrB protein critical for interactions with inhibitors, with estimated binding free energies of -95.5 kJ/mol, -97.4 kJ/mol, and -143.8 kJ/mol for naringenin, 5-methoxypsoralen, and licarin A, respectively. Data from the 50 ns MD simulation study revealed stability of the protein-ligand complex and alterations in the AcrB protein DP conformation upon binding of phytochemicals to the DP and HPT regions. Based on the estimated binding free energy and interactions with three out of five residues lining the hydrophobic trap, licarin A demonstrated the highest inhibitory potential, supporting its further application as a candidate for overcoming drug resistance in pathogens. Communicated by Ramaswamy H. Sarma.

Factors Required for Adhesion of Salmonella enterica Serovar Typhimurium to Lactuca sativa (Lettuce)

Salmonella enterica serovar Typhimurium is a major cause of foodborne gastroenteritis. Recent outbreaks of infections by S. enterica serovar Typhimurium are often associated with non-animal-related food, i.e., vegetables, fruits, herbs, sprouts, and nuts. One main problem related to the consumption of fresh produce is the minimal processing, especially for leafy green salads. In this study, we focused on butterhead lettuce (Lactuca sativa) to which S. enterica serovar Typhimurium adheres at higher rates compared to Valerianella locusta, resulting in prolonged persistence. Here, we systematically analyzed factors contributing to adhesion of S. enterica serovar Typhimurium to L. sativa leaves. Application of a reductionist, synthetic approach, including the controlled surface expression of specific adhesive structures of S. enterica serovar Typhimurium, one at a time, enabled the identification of relevant fimbrial and nonfimbrial adhesins, the O-antigen of lipopolysaccharide, the flagella, and chemotaxis being involved in binding to L. sativa leaves. The analyses revealed contributions of Lpf fimbriae, Sti fimbriae, autotransported adhesin MisL, T1SS-secreted BapA, intact lipopolysaccharide (LPS), and flagella-mediated motility to adhesion of S. enterica serovar Typhimurium to L. sativa leaves. In addition, we identified BapA as a potential adhesin involved in binding to V. locusta and L. sativa leaf surfaces. IMPORTANCE The number of produce-associated outbreaks by gastrointestinal pathogens is increasing and underlines the relevance to human health. The mechanisms involved in the colonization of, persistence on, and transmission by, fresh produce are poorly understood. Here, we investigated the contribution of adhesive factors of S. enterica serovar Typhimurium in the initial phase of plant colonization, i.e., the binding to the plant surface. We used the previously established reductionist, synthetic approach to identify factors that contribute to the surface binding of S. enterica serovar Typhimurium to leaves of L. sativa by expressing all known adhesive structures by remote control expression system.

Serratia marcescens DUF1471-Containing Protein SrfN Is Needed for Adaptation to Acid and Oxidative Stresses

Bacteria can quickly adapt to constantly changing environments through a number of mechanisms, including secretion of secondary metabolites, peptides, and proteins. Serratia marcescens, an emerging pathogen with growing clinical importance due to its intrinsic resistance to several classes of antibiotics, can cause an array of infections in immunocompromised individuals. To better control the spread of S. marcescens infections, it is critical to identify additional targets for bacterial growth inhibition. We found that extracellular metabolites produced by the wild-type organism in response to peroxide exposure had a protective effect on an otherwise-H₂O₂-sensitive ΔmacAB indicator strain. Detailed analysis of the conditioned medium demonstrated that the protective effect was associated with a low-molecular-weight heat-sensitive and proteinase K-sensitive metabolite. Furthermore, liquid chromatography-tandem mass spectrometry analysis of the low-molecular-weight proteins present in the conditioned medium led to identification of the previously uncharacterized DUF1471-containing protein TBU67220 (SrfN). We found that loss of the srfN gene did not have an impact on the production of extracellular enzymes. However, the S. marcescens mutant lacking SrfN was significantly more sensitive to growth in medium with a low pH and to exposure to oxidative stress. Both defects were fully rescued by complementation. Thus, our results indicate that SrfN, a low-molecular-weight DUF1471-containing protein, is involved in S. marcescens SM6 adaptation to adverse environmental conditions. IMPORTANCE Serratia marcescens is ubiquitous in the environment and can survive in water, soil, plants, insects, and animals, and it can also cause infections in humans. In the face of disturbances such as oxidative or low-pH stress, bacteria adapt, survive, and recover through several mechanisms, including changes in their secretome. We show that a hydrogen peroxide-exposed S. marcescens milieu contains a small previously uncharacterized DUF1471-containing protein similar to the SrfN protein in Salmonella enterica serovar Typhimurium, and we illustrate the role of this protein in bacterial survival during acid and oxidative stresses.

Persistence of Salmonella Typhimurium and antibiotic resistance genes in different types of soil influenced by flooding and soil properties

Salmonella is a zoonotic foodborne bacterial pathogen that can seriously harm health. Persistence of Salmonella and antibiotic resistance genes (ARGs) in different types of soil under flooding and natural conditions are rare explored. This study investigated the dynamic changes of the Salmonella, ARGs and bacterial communities in three types of soils applied with pig manure in lab scale. Abundance of the Salmonella Typhimurium in soils reduced to the detection limit varied from 40 to 180 days, most of the Salmonella did not survive in soil for more than 90 days. Flooding and soil texture (content of sand) promote the decline rate of Salmonella. No Salmonella was found have acquired resistance gene from the soil or manure after 90 days. 64 ARGs and 11 MGEs were quantified, abundance of these genes and risky ARGs both gradually decline along with the extension of time. Most of the extrinsic ARGs cannot colonize in soil, cellular protection and antibiotic deactivation were their main resistance mechanism. Multidrug resistance and efflux pump were the dominant class and mechanism of soil intrinsic ARGs. Flooding can affect the ARGs profiles by reducing the types of extrinsic ARGs invaded into soil and inhibit the proliferation of intrinsic genes. Soil sand content, soil moisture and nutrition concentrations had significant direct effect on the abundance or profile of ARGs. Soil bacterial community structures also changed along with the extension of time and affected by flooding. Network analyses between ARGs and bacteria taxa revealed that Actinobacteria and Myxococcia were the main hosts of intrinsic ARGs, some taxa may play a role in inhibiting extrinsic ARGs colonization in the soils. These findings unveil that saturate soil with water may play a positive role in reducing potential risk of Salmonella and ARGs in the farmland environment.

Effects of sterilization methods on the survival of pathogenic bacteria in potting soil stored at various temperatures

Fresh food products can be contaminated with pathogenic bacteria in various agricultural environments. Potting soil is sterilized by heat sterilization and then reused. This study evaluated the effects of three sterilization methods (non-sterilized, pasteurized, and sterilized) on the survival of pathogenic bacteria in potting soil during storage for 60 days at 5, 15, 25, and 35 °C. The reduction in Escherichia coli O157:H7, Salmonella Typhimurium, and Staphylococcus aureus in potting soil was higher at higher temperatures (25 and 35 °C) than at lower temperatures (5 and 15 °C). The population of pathogenic bacteria in pasteurized and sterilized potting soil was reduced below the detectable levels within 30 days at 35 °C. In contrast, the population of Bacillus cereus did not change in potting soil during storage for 60 days at all temperatures. These results indicate that sterilization and storage temperature of potting soil are critical factors influencing the survival of pathogenic bacteria.

Quantifying intra- and inter-species contact rates at supplemental feeding sites in Ethiopia to inform rabies maintenance potential of multiple host species

Rabies, a multi-host pathogen responsible for the loss of roughly 59,000 human lives each year worldwide, continues to impose a significant burden of disease despite control efforts, especially in Ethiopia. However, how species other than dogs contribute to rabies transmission throughout Ethiopia remains largely unknown. In this study, we quantified interactions among wildlife species in Ethiopia with the greatest potential for contributing to rabies maintenance. We observed wildlife at supplemental scavenging sites across multiple landscape types and quantified transmission potential. More specifically, we used camera trap data to quantify species abundance, species distribution, and intra- and inter-species contacts per trapping night over time and by location. We derived a mathematical expression for the basic reproductive number (R₀ ) based on within- and between-species contract rates by applying the next generation method to the susceptible, exposed, infectious, removed model. We calculated R₀ for transmission within each species and between each pair of species using camera trap data in order to identify pairwise interactions that contributed the most to transmission in an ecological community. We estimated which species, or species pairs, could maintain transmission ( R 0 > 1 ${R_0} &gt; 1$ ) and which species, or species pairs, had contact rates too low for maintenance ( R 0 < 1 ${R_0} &lt; 1$ ). Our results identified multiple urban carnivores as candidate species for rabies maintenance throughout Ethiopia, with hyenas exhibiting the greatest risk for rabies maintenance through intra-species transmission. Hyenas and cats had the greatest risk for rabies maintenance through inter-species transmission. Urban and peri-urban sites posed the greatest risk for rabies transmission. The night-time hours presented the greatest risk for a contact event that could result in rabies transmission. Overall, both intra- and inter-species contacts posed risk for rabies maintenance. Our results can be used to target future studies and inform population management decisions.

Critical control point-based assessment and intervention of ochratoxin A risk in Angelicae Gigantis Radix production

Improperly practiced postharvest procedures can pose mycotoxin-related risks during medicinal herb production. As a health food material with pharmacological activities, Angelicae Gigantis Radix (AGR) has been extensively used in oriental medicine or functional foods. Compared with the official protocol, conventional practices were investigated for provisional critical control points (CCPs) in terms of ochratoxin A (OTA) contamination. Conventional practices include field-drying, which was associated with increased fungal exposure. Compared with conventional methods, the washing process in the official protocol was not advantageous for reducing OTA contamination in final products. Instead, drying was examined to assess the fungal growth risk during AGR production. To reduce the energy cost, product overload and shortened drying time could lead to failure in controlling fungal overgrowth and subsequent OTA production. In particular, inner parts of the load contained a higher OTA content than outer parts close to the heat outlet of the dryer. Improper thermal drying of loads allowed the growth of ochratoxigenic species during AGR production. Collectively, non-field-drying and optimally loaded thermal drying are easy preventive actions in key CCPs that need to be well maintained to attenuate any further microbial risk. These assessments provide insights into good practice-based mycotoxin risk management in producing herbal medicinal crops and new cost-efficient appropriate interventions for small-scale farms.

Impact of temperature, soil type and compost amendment on the survival, growth and persistence of Listeria monocytogenes of non-environmental (food-source associated) origin in soil

Listeria monocytogenes of varied sources including food-related sources may reach the soil. Associated food safety and environmental health risks of such contamination depend significantly on the capacity of L. monocytogenes to survive in the soil. This study assessed the survival of 13 L. monocytogenes strains isolated from food and food processing environments and a cocktail of three of the strains in two types of soils (loam and sandy) under controlled temperature conditions: 5, 10, 20, 25, 30℃ and 'uncontrolled' ambient temperature conditions in a tropical region. The impact of compost amendment on the survival of L. monocytogenes in the two different types of soils was also assessed. Soil type, temperature and compost amendment significantly (P <0.001) impacted the survival of L. monocytogenes in soil. Temperature variations affected the survival of L. monocytogenes in soil, where some strains such as strain 732, a L. monocytogenes 1/2a strain survived better at lower temperature (5°C), for which counts of up to 10.47 ± 0.005 log CFU/g were recovered in compost-amended sandy soil, 60 days post-inoculation. Some other strains such as strain 441, a L. monocytogenes 1/2a survived best at intermediate temperature (25 and 30 °C), while others such as 2739 (L. monocytogenes 1/2b) thrived at higher temperature (between 30 °C - 37 °C). There were significant correlations between the influence of temperature and soil type, where lower temperature conditions (5°C - 20°C) were generally more suitable for survival in sandy soil compared to higher temperature conditions. For some of the strains that thrived better in sandy soil at lower temperature, Pearson correlation analysis found significant correlations between temperature and soil type. Steady, controlled temperature generally favored the survival of the strains compared to uncontrolled ambient temperature conditions, except for the cocktail. The cocktail persisted until the last day of post-inoculation storage (60th day) in all test soils and under all incubation temperature conditions. Loam soil was more favorable for the survival of L. monocytogenes and compost amendment improved the survival of the strains, especially in compost-amended sandy soil. Listeria monocytogenes may exhibit variable survival capacity in soil, depending on conditions such as soil type, compost amendment and temperature.

Whole genome sequencing reveals antimicrobial resistance determinants (AMR genes) of Salmonella enterica recovered from raw chicken and ready-to-eat leaves imported into England between 2014 and 2019

AIMS

To compare the antimicrobial resistance (AMR) genes in a genetically diverse group of Salmonella enterica recovered from foods imported into England between 2014 and 2018.

METHODS AND RESULTS

Whole genome sequence was used to detect AMR genes or chromosomal mutations associated with AMR in Salmonella recovered from edible leaves imported from Asia (n = 115) as compared to Salmonella (n = 231) isolated from raw chicken, 74% originated from South America. Among isolates from edible leaves, three (3%) showed resistance to at least one antimicrobial agent, two (2%) of which were multidrug resistant (MDR, resistance to three or more antimicrobial classes). Resistance to at least one antimicrobial agent was detected in 214 (93%) in the chicken isolates, with 164 (71%) showing MDR. Genetic diversity and AMR profiles were highly heterogeneous across the different serovars.

CONCLUSIONS

Resistance was rare among the Salmonella isolates from edible leaves but common (including MDR) among those from raw chicken.

SIGNIFICANCE AND IMPACT OF THE STUDY

Surveillance of AMR in imported foods is essential for monitoring the risk of transmission of resistance from the food chain to humans and provides added public health value to pre-existing controls of the food chain.

Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria

Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.

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.

Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health

The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.

Salmonella enterica changes Macrosteles quadrilineatus feeding behaviors resulting in altered S. enterica distribution on leaves and increased populations

Hemipteran insects are ubiquitous inhabitants of the phyllosphere. Changes in microbial phyllosphere communities have recently been demonstrated following infestation by Macrosteles quadrilineatus (Aster Leafhopper). Although epiphytic Salmonella enterica populations naturally decline in the phyllosphere of plants, M. quadrilineatus infestation facilitated the growth of the bacterial pathogen populations. Here, we demonstrate that cellular damage by insect stylet penetration results in a localized beneficial niche on the leaf surface, leading to enhanced S. enterica populations. We measured S. enterica populations and colonization patterns on plants infested with Hemipterans with distinct feeding behaviors. M. quadrilineatus infestation resulted in higher solute leakage and significantly greater bacterial populations than plants absent of insects. Following immigration via contaminated irrigation water, the highest populations of S. enterica are naturally found on the tips of tomato leaflets. We discovered M. quadrilineatus feeding preference altered the natural distribution of S. enterica populations, and that the presence of S. enterica altered the distribution of probing attempts. These findings elucidate how cellular damage resulting from insect feeding drives changes in bacterial colonization of the phyllosphere.

Spread of Nontyphoidal Salmonella in the Beef Supply Chain in Northern Tanzania: Sensitivity in a Probabilistic Model Integrating Microbiological Data and Data from Stakeholder Interviews

East Africa is a hotspot for foodborne diseases, including infection by nontyphoidal Salmonella (NTS), a zoonotic pathogen that may originate from livestock. Urbanization and increased demand for animal protein drive intensification of livestock production and food processing, creating risks and opportunities for food safety. We built a probabilistic mathematical model, informed by prior beliefs and dedicated stakeholder interviews and microbiological research, to describe sources and prevalence of NTS along the beef supply chain in Moshi, Tanzania. The supply chain was conceptualized using a bow tie model, with terminal livestock markets as pinch point, and a forked pathway postmarket to compare traditional and emerging supply chains. NTS was detected in 36 (7.7%) of 467 samples throughout the supply chain. After combining prior belief and observational data, marginal estimates of true NTS prevalence were 4% in feces of cattle entering the beef supply and 20% in raw meat at butcheries. Based on our model and sensitivity analyses, true NTS prevalence was not significantly different between supply chains. Environmental contamination, associated with butchers and vendors, was estimated to be the most likely source of NTS in meat for human consumption. The model provides a framework for assessing the origin and propagation of NTS along meat supply chains. It can be used to inform decision making when economic factors cause changes in beef production and consumption, such as where to target interventions to reduce risks to consumers. Through sensitivity and value of information analyses, the model also helps to prioritize investment in additional research.

Proteome Expression and Survival Strategies of a Proteorhodopsin-Containing Vibrio Strain under Carbon and Nitrogen Limitation

Photoheterotrophy is a widespread mode of microbial metabolism, notably in the oligotrophic surface ocean, where microbes experience chronic nutrient limitation. One especially widespread form of photoheterotrophy is based on proteorhodopsin (PR), which uses light to generate proton motive force that can drive ATP synthesis, flagellar movement, or nutrient uptake. To clarify the physiological benefits conferred by PR under nutrient stress conditions, we quantified protein-level gene expression of Vibrio campbellii CAIM 519 under both carbon and nitrogen limitation and under both light and dark conditions. Using a novel membrane proteomics strategy, we determined that PR expression is higher under C limitation than N limitation but is not light regulated. Despite expression of PR photosystems, V. campbellii does not exhibit any growth or survival advantages in the light and only a few proteins show significant expression differences between light and dark conditions. While protein-level proteorhodopsin expression in V. campbellii is clearly responsive to nutrient limitation, photoheterotrophy does not appear to play a central role in the survival physiology of this organism under these nutrient stress conditions. C limitation and N limitation, however, result in very different survival responses: under N-limited conditions, viability declines, cultivability is lost rapidly, central carbon flux through the Entner-Doudoroff pathway is increased, and ammonium is assimilated via the GS-GOGAT pathway. In contrast, C limitation drives cell dwarfing with maintenance of viability, as well as utilization of the glyoxylate shunt, glutamate dehydrogenase and anaplerotic C fixation, and a stringent response mediated by the Pho regulon.

IMPORTANCE Understanding the nutrient stress responses of proteorhodopsin-bearing microbes like Vibrio campbellii yields insights into microbial contributions to nutrient cycling, lifestyles of emerging pathogens in aquatic environments, and protein-level adaptations implemented during times of nutrient limitation. In addition to its broad taxonomic and geographic prevalence, the physiological role of PR is diverse, so we developed a novel proteomics strategy to quantify its expression at the protein level. We found that proteorhodopsin expression levels in this wild-type photoheterotroph under these experimental conditions, while higher under C than under N limitation, do not afford measurable light-driven growth or survival advantages. Additionally, this work links differential protein expression patterns between C- and N-limited cultures to divergent stationary-phase survival phenotypes.

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.

Internalisation of Salmonella spp. by Typha latifolia and Cyperus papyrus in vitro and implications for pathogen removal in Constructed Wetlands

ABSTRACTFreshwater contamination by enteric pathogens is implicated in the high frequency of diarrhoeal diseases in low to middle income countries, typically due to poor wastewater management. Constructed Wetlands are a cost-effective and sustainable alternative to conventional/mechanical treatment technologies, but the pathogen removal mechanisms in Constructed Wetlands are not fully understood. This study investigated for the first time the internalisation of Salmonella spp. by Typha latifolia and Cyperus papyrus in hydroponic microcosms. Presence of Salmonella spp. within roots, rhizomes and shoots was assayed using agar-based methods over a period of 12 days. Concentration of Salmonella spp. in growth media showed 2.7 and 4.8 log unit reduction with T. latifolia and C. papyrus, respectively, and 1.8 and 6.0 log unit in unplanted units. Salmonella spp. was recovered from root and rhizome tissues of T. latifolia (up to 4.4 logCFU/g) and C. papyrus (up to 3.4 logCFU/g), and the bacteria were highly concentrated in the epidermis and cortex. However, Salmonella spp. was not detected in the stems and leaves of the two plant species. The present study demonstrates for the first time that these macrophytes internalise cells of Salmonella spp., which could be one pathogen removal mechanism employed by wetland plants.

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.

Occurrence of Fecal Bacteria and Zoonotic Pathogens in Different Water Bodies: Supporting Water Quality Management

Water contaminated with microbiological and chemical constituents can cause a variety of diseases. Water bodies may become contaminated by wild and domestic animal feces, agricultural runoff or sewage, and are often overlooked as a reservoir and source of human infection by pathogenic microorganisms. The objectives of this study were to evaluate the presence of the zoonotic pathogens, Salmonella spp. and Listeria monocytogenes, in various water bodies located in urban and rural areas in the north of Portugal. Water samples were collected from six sites, including natural and artificial ponds, in two different time periods. Several water quality physicochemical parameters, as well as fecal indicator bacteria, were evaluated. High levels of total coliforms (>1.78 log CFU/100 mL) were detected in all samples, and substantial numbers of Enterococcus (>2.32 log CFU/100 mL) were detected in two ponds located in a city park and in an urban garden. Escherichia coli counts ranged from undetectable to 2.76 log CFU/100 mL. Salmonella spp. was isolated from two sites, the city park and the natural pond, while L. monocytogenes was isolated from three sites: the city garden, the natural pond and the artificial pond, both in the rural area. These data show that artificial and natural ponds are a reservoir of fecal indicator bacteria and enteric and zoonotic pathogens. This may impact the potential risks of human infections by potential contaminants during recreational activities, being important for assessing the water quality for strategic management of these areas.

Thermophilic Composting of Human Feces: Development of Bacterial Community Composition and Antimicrobial Resistance Gene Pool

In times of climate change, practicing sustainable, climate-resilient, and productive agriculture is of primordial importance. Compost from different resources, now treated as wastes, could be one form of sustainable fertilizer creating a resilience of agriculture to the adverse effects of climate change. However, the safety of the produced compost regarding human pathogens, pharmaceuticals, and related resistance genes must be considered. We have assessed the effect of thermophilic composting of dry toilet contents, green cuttings, and straw, with and without biochar, on fecal indicators, the bacterial community, and antibiotic resistance genes (ARGs). Mature compost samples were analyzed regarding fecal indicator organisms, revealing low levels of Escherichia coli that are in line with German regulations for fertilizers. However, one finding of Salmonella spp. exceeded the threshold value. Cultivation of bacteria from the mature compost resulted in 200 isolates with 36.5% of biosafety level 2 (BSL-2) species. The majority is known as opportunistic pathogens that likewise occur in different environments. A quarter of the isolated BSL-2 strains exhibited multiresistance to different classes of antibiotics. Molecular analysis of total DNA before and after composting revealed changes in bacterial community composition and ARGs. 16S rRNA gene amplicon sequencing showed a decline of the two most abundant phyla Proteobacteria (start: 36-48%, end: 27-30%) and Firmicutes (start: 13-33%, end: 12-16%), whereas the abundance of Chloroflexi, Gemmatimonadetes, and Planctomycetes rose. Groups containing many human pathogens decreased during composting, like Pseudomonadales, Bacilli with Bacillus spp., or Staphylococcaceae and Enterococcaceae. Gene-specific PCR showed a decline in the number of detectable ARGs from 15 before to 8 after composting. The results reveal the importance of sufficiently high temperatures lasting for a sufficiently long period during the thermophilic phase of composting for reducing Salmonella to levels matching the criteria for fertilizers. However, most severe human pathogens that were targeted by isolation conditions were not detected. Cultivation-independent analyses also indicated a decline in bacterial orders comprising many pathogenic bacteria, as well as a decrease in ARGs. In summary, thermophilic composting could be a promising approach for producing hygienically safe organic fertilizer from ecological sanitation.

Cross-examination of engineered nanomaterials in crop production: Application and related implications

The review presents the current knowledge on the development and implementation of nanotechnology in crop production, giving particular attention to potential opportunities and challenges of the use of nano-sensors, nano-pesticides, and nano-fertilizers. Due to the size-dependent properties, e.g. high reactivity, targeted and controlled delivery of active ingredients, engineered nanomaterials (ENMs) are expected to be more efficient agrochemicals than conventional agents. Growing production and usage of ENMs result in the spread of ENMs in the environment. Because plants constitute an important component of the agri-ecosystem, they are subjected to the ENMs activity. A number of studies have confirmed the uptake and translocation of ENMs by plants as well as their positive/negative effects on plants. Here, these endpoints are briefly summarized to show the diversity of plant responses to ENMs. The review includes a detailed molecular analysis of ENMs-plant interactions. The transcriptomics, proteomics and metabolomics tools have been very recently employed to explore ENMs-induced effects in planta. The omics approach allows a comprehensive understanding of the specific machinery of ENMs occurring at the molecular level. The summary of data will be valuable in defining future studies on the ENMs-plant system, which is crucial for developing a suitable strategy for the ENMs usage.

Fate and mitigation of Salmonella contaminated in lettuce (Lactuca sativa) seeds grown in a hydroponic system

AIMS

We investigated the fate of Salmonella in lettuce seeds grown in a hydroponic system and the potentials of applying photodynamic inactivation (PDI) to enhance microbial safety of hydroponic farming systems.

METHODS AND RESULTS

Lettuce was grown from Salmonella-contaminated seeds, and rose bengal-mediated PDI was applied. Without intervention, Salmonella could persist in plants and hydroponic farming environment throughout 6 weeks of lettuce growth. Cross-contamination from Salmonella-inoculated to noninoculated seedlings was observed. PDI significantly decreased Salmonella from 3.90 ± 0.31 log colony-forming unit (CFU) per plant to 2.77 ± 0.49 log CFU per plant without extra illumination needed (p < 0.01) by week six.

CONCLUSIONS

Salmonella from contaminated seeds could survive for an extended period in lettuce and hydroponic farming environment and posed serious cross-contamination risks. Rose bengal-mediated PDI showed promise in controlling Salmonella contamination in lettuce in a hydroponic farming setting.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shed light on the serious food safety implications that Salmonella-contaminated lettuce seeds might entail in a hydroponic farming environment and demonstrated rose bengal-mediated PDI as a potential mitigation strategy. These findings contribute to the increasingly relevant field of urban farming systems and their associated food safety concerns.

Analysis of Salmonella enterica Adhesion to Leaves of Corn Salad or Lettuce

Human infections by gastrointestinal bacterial pathogens are commonly associated with the consumption of contaminated food of animal origin (e.g., chicken, fish, eggs) or contaminated water. However, further contamination sources must be considered since number of Salmonella enterica infections associated with the consumption of food of non-animal origin (e.g., vegetables, fruits, nuts) are increasing. This gives raise to interest in understanding the interaction of S. enterica with leafy produce, such as various salads. Especially adhesion as initial step of contamination of salad by S. enterica deserves further investigation. Here we introduce methods to analyse Salmonella adhesion to various salads that provide insights into bacterial factors involved in Salmonella colonization of plants.

Dual transcriptomic analysis reveals metabolic changes associated with differential persistence of human pathogenic bacteria in leaves of Arabidopsis and lettuce

Understanding the molecular determinants underlying the interaction between the leaf and human pathogenic bacteria is key to provide the foundation to develop science-based strategies to prevent or decrease the pathogen contamination of leafy greens. In this study, we conducted a dual RNA-sequencing analysis to simultaneously define changes in the transcriptomic profiles of the plant and the bacterium when they come in contact. We used an economically relevant vegetable crop, lettuce (Lactuca sativa L. cultivar Salinas), and a model plant, Arabidopsis thaliana Col-0, as well as two pathogenic bacterial strains that cause disease outbreaks associated with fresh produce, Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium 14028s (STm 14028s). We observed commonalities and specificities in the modulation of biological processes between Arabidopsis and lettuce and between O157:H7 and STm 14028s during early stages of the interaction. We detected a larger alteration of gene expression at the whole transcriptome level in lettuce and Arabidopsis at 24 h post inoculation with STm 14028s compared to that with O157:H7. In addition, bacterial transcriptomic adjustments were substantially larger in Arabidopsis than in lettuce. Bacterial transcriptome was affected at a larger extent in the first 4 h compared to the subsequent 20 h after inoculation. Overall, we gained valuable knowledge about the responses and counter-responses of both bacterial pathogen and plant host when these bacteria are residing in the leaf intercellular space. These findings and the public genomic resources generated in this study are valuable for additional data mining.

Bioaccumulation of Manure-borne antibiotic resistance genes in carrot and its exposure assessment

The effect of manure application on the distribution and accumulation of antibiotic resistance genes (ARGs) in tissue of root vegetables remains unclear, which poses a bottleneck in assessing the health risks from root vegetables due to application of manure. Towards this goal, experiments were conducted in pots to investigate the distribution and bioaccumulation of ARGs in carrot tissues due to application of pig manure. The 144 ARGs targeting nine types of antibiotics were quantified by high throughput qPCR in the soil and plant samples. The rhizosphere was a hot spot for ARGs enrichment in the manured soil. The abundance, diversity, and bioaccumulation factors of ARGs in the phyllosphere were significantly higher than those of carrot root skin and tuber. Manure application increased bioaccumulation of 12 ARGs and 2 MGEs in carrot tuber with 124 the highest factor. The application of manure increased transfer of 10 ARGs and 3 MGEs from carrot skin to inner tuber by factors of 0.1-11.8. The average gene copy number of ARGs of per gram carrot root was about 4.8 × 10⁴ and 1.1 × 10⁶ in the control and the manured treatment, respectively. Children and adults may co-ingest 2.7 × 10⁷ and 3.2 × 10⁷ of ARGs copies/d from carrots grown with pig manure, using estimated human intake values. However, peeling may reduce the intake of ARGs by 28-91% and of MGEs by 46-59%. In conclusion, the application of pig manure increased the accumulation of ARGs in the skin of carrots, whereas peeling was an effective strategy to reduce the risk.

Plant Bioactive Compounds as an Intrinsic and Sustainable Tool to Enhance the Microbial Safety of Crops

Outbreaks of produce-associated foodborne illness continue to pose a threat to human health worldwide. New approaches are necessary to improve produce safety. Plant innate immunity has potential as a host-based strategy for the deactivation of enteric pathogens. In response to various biotic and abiotic threats, plants mount defense responses that are governed by signaling pathways. Once activated, these result in the release of reactive oxygen and nitrogen species in addition to secondary metabolites that aim at tempering microbial infection and pest attack. These phytochemicals have been investigated as alternatives to chemical sanitization, as many are effective antimicrobial compounds in vitro. Their antagonistic activity toward enteric pathogens may also provide an intrinsic hurdle to their viability and multiplication in planta. Plants can detect and mount basal defenses against enteric pathogens. Evidence supports the role of plant bioactive compounds in the physiology of Salmonella enterica, Escherichia coli, and Listeria monocytogenes as well as their fitness on plants. Here, we review the current state of knowledge of the effect of phytochemicals on enteric pathogens and their colonization of plants. Further understanding of the interplay between foodborne pathogens and the chemical environment on/in host plants may have lasting impacts on crop management for enhanced microbial safety through translational applications in plant breeding, editing technologies, and defense priming.

Survival of Enterohemorrhagic Escherichia coli O104:H4 Strain C227/11Φcu in Agricultural Soils Depends on rpoS and Environmental Factors

The consumption of contaminated fresh produce caused outbreaks of enterohemorrhagic (EHEC) Escherichia coli. Agricultural soil might be a reservoir for EHEC strains and represent a contamination source for edible plants. Furthermore, the application of manure as fertilizer is an important contamination route. Thus, the German fertilizer ordinance prohibits the use of manure 12 weeks before crop harvest to avoid pathogen transmission into the food chain. In this study, the survival of E. coli O104:H4 strain C227/11Φcu in soil microenvironments with either diluvial sand or alluvial loam at two temperatures was investigated for more than 12 weeks. It was analyzed whether the addition of cattle manure extends EHEC survival in these microenvironments. The experiments were additionally performed with isogenic ΔrpoS and ΔfliC deletion mutants of C227/11Φcu. The survival of C227/11Φcu was highest at 4 °C, whereas the soil type had a minor influence. The addition of cattle manure increased the survival at 22 °C. Deletion of rpoS significantly decreased the survival period under all cultivation conditions, whereas fliC deletion did not have any influence. The results of our study demonstrate that EHEC C227/11Φcu is able to survive for more than 12 weeks in soil microenvironments and that RpoS is an important determinant for survival.

Systematic Review: Nontyphoidal Salmonella in Food from Latin America

In Latin America, nontyphoidal Salmonella (NTS) is one of the most important etiological agents of foodborne infections; it can survive in soil, water, and food even after processing. Here, we aimed to perform a systematic review by collecting data on the prevalence, serotypes, and antimicrobial resistance (AMR) of NTS isolated from different food products in Latin America, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Out of 1766 studies screened, 244 reports from 13 Latin American countries were eligible. Among these, 182 reported NTS prevalence, 87 reported NTS serotypes, and 83 reported serotypes with AMR patterns. The NTS prevalence ranged from 0.005% to 93.3%, regardless of country and food. Meat showed the highest NTS prevalence. Enteritidis, Typhimurium, and Derby were the most frequently observed serotypes in different food products. The serotypes Enteritidis, Typhimurium, and Infantis, isolated from animal products, showed the highest AMR rate. The presence of NTS in fruits and vegetables, which are generally consumed raw or as ready-to-eat food, indicates a high risk of salmonellosis from consuming these foods. Thus, the reduction of this pathogen in the food chain requires a One Health approach, involving good agricultural and manufacturing practices, low antimicrobial use, and proper waste management.

Quantitative characterization and effective inactivation of biological hazards in struvite recovered from digested poultry slurry

Struvite formed from digested poultry slurries can serve as an alternative to chemical fertilizers; however, the biological safety of such products is questionable. Therefore, quantification and inactivation of foodborne pathogens existing in struvite are important. Herein, the dynamics of foodborne pathogens' (Streptococcus faecalis, S. typhimurium, Clostridium perfringens, and Escherichia coli) living status, whether culturable and viable but non-culturable (VBNC) in struvite, were quantified for the first time. Meanwhile, inactivation technologies, namely high-humidity hot air impingement blanching (HHAIB), cold plasma, and hot air treatment, were evaluated and compared for their potential to inactivate/kill foodborne pathogens in struvite. An increase in precipitation pH from 9.0 to 11.0 decreased the culturable count of pathogens in the struvite from 75 to 86% to 7-20%, while the VBNC pathogen counts increased from 16 to 24% to 35-55%. Among the tested inactivation technologies, the HHAIB treatment at 130 °C for 120 s killed approximately 68-79% of foodborne pathogens in struvite precipitated at pH 9.0. VBNC pathogens increased from 16 to 24% to 57-68% after HHAIB treatment at 130 °C for 120 s. Struvite treatment with different inactivation technologies did not change its crystalline structure; however, it reduced functional group abundance. Therefore, further research on inactivation technologies is required to achieve better pathogen reduction efficiency in struvite to make it a biologically safe fertilizer for crop production.

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature

Salmonella enterica serovar Typhimurium strain ATCC14028s is commercially available from multiple national type culture collections, and has been widely used since 1960 for quality control of growth media and experiments on fitness (“laboratory evolution”). ATCC14028s has been implicated in multiple cross-contaminations in the laboratory, and has also caused multiple laboratory infections and one known attempt at bioterrorism. According to hierarchical clustering of 3002 core gene sequences, ATCC14028s belongs to HierCC cluster HC20_373 in which most internal branch lengths are only one to three SNPs long. Many natural Typhimurium isolates from humans, domesticated animals and the environment also belong to HC20_373, and their core genomes are almost indistinguishable from those of laboratory strains. These natural isolates have infected humans in Ireland and Taiwan for decades, and are common in the British Isles as well as the Americas. The isolation history of some of the natural isolates confirms the conclusion that they do not represent recent contamination by the laboratory strain, and 10% carry plasmids or bacteriophages which have been acquired in nature by HGT from unrelated bacteria. We propose that ATCC14028s has repeatedly escaped from the laboratory environment into nature via laboratory accidents or infections, but the escaped micro-lineages have only a limited life span. As a result, there is a genetic gap separating HC20_373 from its closest natural relatives due to a divergence between them in the late 19^th century followed by repeated extinction events of escaped HC20_373.

Clades of closely related bacteria exist in nature. Individual isolates from such clades are often distinguishable by genomic sequencing because genomic sequence differences can be acquired over a few years due to neutral drift and natural selection. The evolution of laboratory strains is often largely frozen, physically due to storage conditions and genetically due to long periods of storage. Thus, laboratory strains can normally be readily distinguished from natural isolates because they show much less diversity. However, laboratory strain ATCC14028s shows modest levels of sequence diversity because it has been shipped around the world to multiple laboratories and is routinely used for analyses of laboratory evolution. Closely related natural isolates also exist, but their genetic diversity is not dramatically greater at the core genome level. Indeed, many scientists doubt that such isolates are natural, and interpret them as undetected contamination by the laboratory strain. We present data indicating that ATCC14028s has repeatedly escaped from the laboratory through inadvertent contamination of the environment, infection of technical staff and deliberate bioterrorism. The escapees survive in nature long enough that some acquire mobile genomic elements by horizontal gene transfer, but eventually they go extinct. As a result, even extensive global databases of natural isolates lack closely related isolates whose ancestors diverged from ATCC14028s within the last 100 years.

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'.

Antibiotic Resistance Gene-Carrying Plasmid Spreads into the Plant Endophytic Bacteria using Soil Bacteria as Carriers

Applications of animal manure and treated wastewater could enrich antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the plant microbiome. However, the mechanistic studies of the transmission of ARB and ARGs from the environment to plant endophytic bacteria were few. Herein, a genetically engineered fluorescent Escherichia coli harboring a conjugative RP4 plasmid that carries three ARGs was used to trace its spread into Arabidopsis thaliana interior in a tetracycline-amended hydroponic system in the absence or presence of a simulated soil bacterial community. Confocal microscope observation demonstrated that E. coli was internalized into plant tissues and the carried RP4 plasmid was transferred into plant endophytic bacteria. More importantly, we observed that soil bacteria inhibited the internalization of E. coli but substantially promoted RP4 plasmid spread into the plant microbiome. The altered RP4-carrying bacterial community composition in the plant microbiome and the increased core-shared RP4-carrying bacteria number between plant interior and exterior in the presence of soil bacteria collectively confirmed that soil bacteria, especially Proteobacteria, might capture RP4 from E. coli and then translocate into plant microbiome, resulting in the increased RP4 plasmid spread in the plant endophytes. Overall, our findings provided important insights into the dissemination of ARB and ARGs from the environment to the plant microbiome.