Growth and Extended Survival of Escherichia coli O157:H7 in Soil Organic Matter

Agricultural Mitigation Strategies to Reduce the Impact of Romaine Lettuce Contamination

BACKGROUND

Leafy greens, particularly romaine lettuce, are often associated with outbreaks due to their susceptibility to contamination from various environmental sources. This study aimed to evaluate the presence of E. coli, Salmonella, copper, nickel, zinc, and manganese in irrigation water, lettuce leaves, and agricultural soil in the Litani River Basin (LRB), Lebanon.

METHOD

Samples were collected from five demonstration plots employing different agricultural practices. Heavy metal concentrations were determined using atomic absorption spectrometry, while E. coli and Salmonella testing were conducted through conventional culturing techniques. The impact of E. coli contamination on seed germination and the interaction effects between E. coli and heavy metals were also examined. The study also compared the effectiveness of various irrigation systems in reducing bacterial contamination.

RESULTS

The results demonstrated that contamination levels varied significantly across the plots and irrigation types. This variation underscores the necessity of site-specific mitigation strategies to enhance food safety. Our findings highlight the importance of selecting appropriate irrigation methods and implementing tailored agricultural practices to minimize the risk of contamination.

CONCLUSION

This research provides valuable insights for optimizing agricultural practices in the LRB to ensure food safety and environmental sustainability.

Significant Factors for Modelling Survival of Escherichia coli in Lake Sediments

Currently available numerical models that describe the fecal contamination of aquatic environments using Escherichia coli as an indicator bacterium did not consider its survival in sediments. We conducted a series of comparative experiments to reveal the independent and interactive effects of sediment factors, including temperature, pH, water-extractable total dissolved solids (TDSs), coexisting microbes, and sampling sites, in lake environments on E. coli survival. In experiments, E. coli survival was observed by controlling any two factors at a time. Consequently, the decrease in pH and presence of coexisting microbes enhanced E. coli die-off, whereas the addition of water-extractable TDSs promoted its growth. To select factors to be considered for modelling E. coli survival in sediments, the independent effects of each factor and the interaction effect of the two factors were statistically compared based on their effect sizes (η2). As a result, pH (η2 = 59.5-89.0%) affected E. coli survival most significantly, followed by coexisting microbes (1.7-48.4%). Among the interactions affecting E. coli survival, including pH or coexisting microbes-which had larger independent effects-relatively larger statistically significant interactions were observed between pH and coexisting microbes (31.1%), coexisting microbes and water-extractable TDSs (85.4%), and coexisting microbes and temperature (26.4%).

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.

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.

Escherichia coli Strains Display Varying Susceptibility to Grazing by the Soil Amoeba Dictyostelium discoideum

Recent studies have shown that Escherichia coli can survive in different environments, including soils, and they can maintain populations in sterile soil for a long period of time. This indicates that growth-supporting nutrients are available; however, when grown in non-sterile soils, populations decline, suggesting that other biological factors play a role in controlling E. coli populations in soil. Free-living protozoa can affect the bacterial population by grazing. We hypothesized that E. coli strains capable of surviving in non-sterile soil possess mechanisms to protect themselves from amoeba predation. We determined the grazing rate of E. coli pasture isolates by using Dictyostelium discoideum. Bacterial suspensions applied to lactose agar as lines were allowed to grow for 24 h, when 4 μL of D. discoideum culture was inoculated in the center of each bacterial line. Grazing distances were measured after 4 days. The genomes of five grazing-susceptible and five grazing-resistant isolates were sequenced and compared. Grazing distance varied among isolates, which indicated that some E. coli are more susceptible to grazing by protozoa than others. When presented with a choice between grazing-susceptible and grazing-resistant isolates, D. discoideum grazed only on the susceptible strain. Grazing susceptibility phenotype did not align with the phylogroup, with both B1 and E strains found in both grazing groups. They also did not align by core genome phylogeny. Whole genome comparisons revealed that the five most highly grazed strains had 389 shared genes not found in the five least grazed strains. Conversely, the five least grazed strains shared 130 unique genes. The results indicate that long-term persistence of E. coli in soil is due at least in part to resistance to grazing by soil amoeba.

Survival behavior of six enterotoxigenic Escherichia coli strains in soil and biochar-amended soils

Some Escherichia coli serotypes are important human pathogens causing diarrhea or in some cases, life threatening diseases. E. coli is also a typical indicator microorganism, routinely used for assessing the microbiological quality of water especially to indicate fecal contamination. The soil is a sink and route of transmission to water and food resources and it is thus important to understand the survival of enterotoxigenic E. coli strains in soil. This study monitored the survival of six E. coli strains in sandy and loam soil. Furthermore, since biochar is a commonly used soil conditioner, the study investigated the impact of biochar amendment (15%) on the survival of the E. coli strains in (biochar-amended) sandy and loam soils. Addition of biochar affected the physicochemical properties of both soils, altering potassium levels, calcium, magnesium, sodium as well as levels of other metal ions. It increased the organic matter of loam soil from 44 g/dm³ to 52 g/dm³, and increased the pH of both sandy and loam soils. Survival and persistence of the E. coli strains generally varied according to soil type, with strains generally surviving better (P ≤ 0.05) in loam soil compared to in sandy soil. In loam soil and biochar amended loam soils, E. coli strains remained culturable until the 150th day with counts ranging between 3.00 and 5.94 ± 0.04 log CFU/g. The effects of biochar on the physicochemical properties of soil and the response of the E. coli strains to biochar amendment was variable depending on soil type.

Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes

This study investigates migration phenotypes of 265 Escherichia coli soil isolates from the Buffalo River basin in Minnesota, USA. Migration rates on semisolid tryptone swim plates ranged from nonmotile to 190% of the migration rate of a highly motile E. coli K-12 strain. The nonmotile isolate, LGE0550, had mutations in flagellar and chemotaxis genes, including two IS3 elements in the flagellin-encoding gene fliC. A genome-wide association study (GWAS), associating the migration rates with genetic variants in specific genes, yielded two metabolic variants (rygD-serA and metR-metE) with previous implications in chemotaxis. As a novel way of confirming GWAS results, we used minimal medium swim plates to confirm the associations. Other variants in metabolic genes and genes that are associated with biofilm were positively or negatively associated with migration rates. A determination of growth phenotypes on Biolog EcoPlates yielded differential growth for the 10 tested isolates on d-malic acid, putrescine, and d-xylose, all of which are important in the soil environment. IMPORTANCE E. coli is a Gram-negative, facultative anaerobic bacterium whose life cycle includes extra host environments in addition to human, animal, and plant hosts. The bacterium has the genomic capability of being motile. In this context, the significance of this study is severalfold: (i) the great diversity of migration phenotypes that we observed within our isolate collection supports previous (G. NandaKafle, A. A. Christie, S. Vilain, and V. S. Brözel, Front Microbiol 9:762, 2018, https://doi.org/10.3389/fmicb.2018.00762; Y. Somorin, F. Abram, F. Brennan, and C. O'Byrne, Appl Environ Microbiol 82:4628-4640, 2016, https://doi.org/10.1128/AEM.01175-16) ideas of soil promoting phenotypic heterogeneity, (ii) such heterogeneity may facilitate bacterial growth in the many different soil niches, and (iii) such heterogeneity may enable the bacteria to interact with human, animal, and plant hosts.

Identifying more targeted antimicrobials active against select bacterial phytopathogens

AIMS

Phytopathogens are a global threat to the world's food supply. Use of broad-spectrum bactericides and antibiotics to limit or eliminate bacterial infections is becoming less effective as levels of resistance increase, while concurrently becoming less desirable from an ecological perspective due to their collateral damage to beneficial members of plant and soil microbiomes. Bacteria produce numerous antimicrobials in addition to antibiotics, such as bacteriocins with their relatively narrow activity spectra, and inhibitory metabolic by-products, such as organic acids. There is interest in developing these naturally occurring antimicrobials for use as alternatives or supplements to antibiotics.

METHODS AND RESULTS

In this study, we investigate the inhibitory potential of 217 plant associated bacterial isolates from 44 species including plant pathogens, plant growth promoting rhizobacteria, and plant commensals. Over half of the isolates were found to produce antimicrobial substances, of which 68% were active against phytopathogens. Even more intriguing, 98% of phytopathogenic strains were sensitive to the compounds produced specifically by plant growth promoting rhizobacteria.

CONCLUSION

These data argue that plant-associated bacteria produce a broad range of antimicrobial substances, and that the substances produced preferentially target phytopathogenic bacteria.

SIGNIFICANCE AND IMPACT OF STUDY

There is a need for novel antimicrobials for use in agriculture. The methods presented here reveal the potential for simple phenotypic screening methods to provide a broad range of potential drug candidates.

Hotspots of root-exuded amino acids are created within a rhizosphere-on-a-chip

The rhizosphere is a challenging ecosystem to study from a systems biology perspective due to its diverse chemical, physical, and biological characteristics. In the past decade, microfluidic platforms (e.g. plant-on-a-chip) have created an alternative way to study whole rhizosphere organisms, like plants and microorganisms, under reduced-complexity conditions. However, in reducing the complexity of the environment, it is possible to inadvertently alter organism phenotype, which biases laboratory data compared to in situ experiments. To build back some of the complexity of the rhizosphere in a fully-defined, parameterized approach we have developed a rhizosphere-on-a-chip platform that mimics the physical structure of soil. We demonstrate, through computational simulation, how this synthetic soil structure can influence the emergence of molecular "hotspots" and "hotmoments" that arise naturally from the plant's exudation of labile carbon compounds. We establish the amenability of the rhizosphere-on-a-chip for long-term culture of Brachypodium distachyon, and experimentally validate the presence of exudate hotspots within the rhizosphere-on-a-chip pore spaces using liquid microjunction surface sampling probe mass spectrometry.

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.

The Diversity of a Polyclonal FluCell-SELEX Library Outperforms Individual Aptamers as Emerging Diagnostic Tools for the Identification of Carbapenem Resistant Pseudomonas aeruginosa

Textbook procedures require the use of individual aptamers enriched in SELEX libraries which are subsequently chemically synthesized after their biochemical characterization. Here we show that this reduction of the available sequence space of large libraries and thus the diversity of binding molecules reduces the labelling efficiency and fidelity of selected single aptamers towards different strains of the human pathogen Pseudomonas aeruginosa compared to a polyclonal aptamer library enriched by a whole-cell-SELEX involving fluorescent aptamers. The library outperformed single aptamers in reliable and specific targeting of different clinically relevant strains, allowed to inhibit virulence associated cellular functions and identification of bound cell surface targets by aptamer based affinity purification and mass spectrometry. The stunning ease of this FluCell-SELEX and the convincing performance of the P. aeruginosa specific library may pave the way towards generally new and efficient diagnostic techniques based on polyclonal aptamer libraries not only in clinical microbiology.

Assessment of gaseous ozone treatment on Salmonella Typhimurium and Escherichia coli O157:H7 reductions in poultry litter

Poultry litter is used as soil amendment or organic fertilizer. While poultry litter is enriched with organic matter suitable for land, the presence of pathogens such as Salmonella in poultry litter is a concern. To investigate the effect of gaseous ozone on pathogen reductions in poultry litter, this study conducted a series of experiments that involved understanding of Salmonella Typhimurium and Escherichia coli O157:H7 inactivation at various doses of Ozone (O₃) in wet and dry poultry litter conditions. Previously, ozone treatment has been shown to disinfect the surface of foods and plant materials including fruits, juices, and wastewater, however, additional research are needed to better understand the impacts of ozone on treatment of soil amendments. Sanitizing methods capable of eliminating pathogens of soil amendments are crucial to mitigate disease outbreaks related with litter/manure-based fertilizers. In this study, a bench scale continuous ozone treatment system was designed to produce O₃ gas, with a range O₃ concentrations (7.15-132.46 mg·L^-1), monitor ozone concentrations continuously, and control the ozone exposure time (15 to 90 mins) to understand the effectiveness of O₃ in eliminating S. Typhimurium and E. coli O157:H7 in poultry litter. Results showed that 7.15 mg·L^-1 did not reduce the counts of S. Typhimurium until exposure to O₃ for 90 min. The O₃ concentrations of 43.26 ~ 132.46 mg·L^-1 exposure reduced the bacterial counts. Furthermore, the moisture content of poultry litter was found to be an influencing factor for pathogen reduction. The pathogen reduction rates were reduced when the moisture content was increased. At higher moisture content, high concentrations of O₃ (132.46 mg·L^-1) were needed for pathogen reductions. The moisture content of 30% or lower was found to be more effective for controlling pathogen levels in poultry litter. Our study demonstrates that gaseous O₃ treatment could be used as an additional decontamination technique to ensure the certain degree of microbiological safety of poultry litter based soil amendment.

Predictive Models May Complement or Provide an Alternative to Existing Strategies for Assessing the Enteric Pathogen Contamination Status of Northeastern Streams Used to Provide Water for Produce Production

While the Food Safety Modernization Act established standards for the use of surface water for produce production, water quality is known to vary over space and time. Targeted approaches for identifying hazards in water that account for this variation may improve growers’ ability to address pre-harvest food safety risks. Models that utilize publicly-available data (e.g., land-use, real-time weather) may be useful for developing these approaches. The objective of this study was to use pre-existing datasets collected in 2017 (N = 181 samples) and 2018 (N = 191 samples) to train and test models that predict the likelihood of detecting Salmonella and pathogenic E. coli markers (eaeA, stx) in agricultural water. Four types of features were used to train the models: microbial, physicochemical, spatial and weather. “Full models” were built using all four features types, while “nested models” were built using between one and three types. Twenty learners were used to develop separate full models for each pathogen. Separately, to assess information gain associated with using different feature types, six learners were randomly selected and used to develop nine, nested models each. Performance measures for each model were then calculated and compared against baseline models where E. coli concentration was the sole covariate. In the methods, we outline the advantages and disadvantages of each learner. Overall, full models built using ensemble (e.g., Node Harvest) and “black-box” (e.g., SVMs) learners out-performed full models built using more interpretable learners (e.g., tree- and rule-based learners) for both outcomes. However, nested eaeA-stx models built using interpretable learners and microbial data performed almost as well as these full models. While none of the nested Salmonella models performed as well as the full models, nested models built using spatial data consistently out-performed models that excluded spatial data. These findings demonstrate that machine learning approaches can be used to predict when and where pathogens are likely to be present in agricultural water. This study serves as a proof-of-concept that can be built upon once larger datasets become available and provides guidance on the learner-data combinations that should be the foci of future efforts (e.g., tree-based microbial models for pathogenic E. coli).

Diversity of bacterial endophyte in Eucalyptus clones and their implications in water stress tolerance

The genus Eucalyptus with over 747 species occurs in wide ecological range and is preferred for bioenergy plantations due to their short rotation, rapid growth and superior wood properties. They are planted in 22 million ha area and India is third largest planter of Eucalyptus. In the present study, the bacterial endophyte community in leaves of six Eucalyptus clones belonging to E. tereticornis and E. camaldulensis was assessed by sequencing the V3-V4 region of the bacterial 16S rRNA gene. The clones were selected based on their response to progressive water stress. A total of 4947 operational taxonomic units (OTUs) were obtained and the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes. Escherichia coli was enriched in all samples at species level. Comparison of endophyte diversity was conducted between the two species and across the water stress tolerant and susceptible clones. The alpha-diversity analysis revealed that species richness and diversity was high in E. camaldulensis and water stress susceptible clones. LefSe analysis predicted 69 and 54 significantly enriched taxonomic biomarkers between species and stress response groups respectively. A maximum of 49 taxonomic biomarkers were recorded in susceptible group and the significantly enriched species were Bacteroides thetaiotaomicron and Turicibacter sanguinis, while the tolerant group documented 5 biomarkers including oscillibacter sp. The presence of functional biomarkers was also assessed in both the groups. The findings of the present study provides an insight into the diversity of bacterial endophyte in Eucalyptus leaves and to our knowledge this is the first report on documenting the endophyte abundance in water stress responsive Eucalyptus clones.

Escherichia coli O157 survival in liquid culture and artificial soil microcosms with variable pH, humic acid and clay content

AIMS

This research was performed to investigate the influence of clay and humic acid on Escherichia coli O157 survival in model soils. Additionally, the influence of pH and humic acid on E. coli O157 in liquid culture was investigated.

METHODS AND RESULTS

Artificial soil microcosms were prepared with sand, kaolinite, bentonite and humic acid. Artificial soil microcosms pH was adjusted (6·0-7·0) with aluminium sulphate before E. coli O157 inoculation. After 56 days of incubation at 30°C, significant differences in E. coli O157 log CFU per gram were observed between 0 and 1000 ppm (P < 0·0001) and 0 and 5000 ppm (P < 0·0001) humic acid in 1·5% clay soils, but not in 7·5 or 15% clay soils. Significant differences (P < 0·05) in E. coli O157 log CFU per ml were observed in liquid culture influenced by humic acid concentrations after 8 h at 37°C.

CONCLUSIONS

The developed model soils support E. coli O157 populations over 28 days, and higher clay soils may aid in E. coli O157 survival.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results provide insights into physicochemical properties of soil that may influence E. coli O157 in the environment and help explain E. coli O157 survival in various soils and geographical regions.

Interaction between Fungal Communities, Soil Properties, and the Survival of Invading E. coli O157:H7 in Soils

Pathogens that invade into the soil cancontaminate food and water, andinfect animals and human beings. It is well documented that individual bacterial phyla are well correlated with the survival of E. coliO157 (EcO157), while the interaction betweenthe fungal communities and EcO157 survival remains largely unknown. In this study, soil samples from Tongliao, Siping, and Yanji in northeast China were collected and characterized. Total DNA was extracted for fungal and bacterial community characterization. EcO157 cells were spiked into the soils, and their survival behavior was investigated. Results showed that both fungal and bacterial communities were significantly correlated (p < 0.01) with the survival of EcO157 in soils, and the relative abundances of fungal groups (Dothideomycetes and Sordariomycetes) and some bacterial phyla (Acidobacteria, Firmicutes, gamma- and delta-Proteobacteria)weresignificantly correlated with ttds (p < 0.01). Soil pH, EC (electric conductance) salinity, and water-soluble nitrate nitrogen were significantly correlated with survival time (time to reach the detection limit, ttd) (p < 0.05). The structural equation model indicated that fungal communities could directly influence ttds, and soil properties could indirectly influence the ttds through fungal communities. The first log reduction time (δ) was mainly correlated with soil properties, while the shape parameter (p) was largely correlated with fungal communities. Our data indicated that both fungal and bacterial communities were closely correlated (p < 0.05)with the survival of EcO157 in soils, and different fungal and bacterial groups might play different roles. Fungal communities and bacterial communities explained 5.87% and 17.32% of the overall variation of survival parameters, respectively. Soil properties explained about one-third of the overall variation of survival parameters. These findings expand our current understanding of the environmental behavior of human pathogens in soils.

Complex Interactions Between Weather, and Microbial and Physicochemical Water Quality Impact the Likelihood of Detecting Foodborne Pathogens in Agricultural Water

Agricultural water is an important source of foodborne pathogens on produce farms. Managing water-associated risks does not lend itself to one-size-fits-all approaches due to the heterogeneous nature of freshwater environments. To improve our ability to develop location-specific risk management practices, a study was conducted in two produce-growing regions to (i) characterize the relationship between Escherichia coli levels and pathogen presence in agricultural water, and (ii) identify environmental factors associated with pathogen detection. Three AZ and six NY waterways were sampled longitudinally using 10-L grab samples (GS) and 24-h Moore swabs (MS). Regression showed that the likelihood of Salmonella detection (Odds Ratio [OR] = 2.18), and eaeA-stx codetection (OR = 6.49) was significantly greater for MS compared to GS, while the likelihood of detecting L. monocytogenes was not. Regression also showed that eaeA-stx codetection in AZ (OR = 50.2) and NY (OR = 18.4), and Salmonella detection in AZ (OR = 4.4) were significantly associated with E. coli levels, while Salmonella detection in NY was not. Random forest analysis indicated that interactions between environmental factors (e.g., rainfall, temperature, turbidity) (i) were associated with likelihood of pathogen detection and (ii) mediated the relationship between E. coli levels and likelihood of pathogen detection. Our findings suggest that (i) environmental heterogeneity, including interactions between factors, affects microbial water quality, and (ii) E. coli levels alone may not be a suitable indicator of food safety risks. Instead, targeted methods that utilize environmental and microbial data (e.g., models that use turbidity and E. coli levels to predict when there is a high or low risk of surface water being contaminated by pathogens) are needed to assess and mitigate the food safety risks associated with preharvest water use. By identifying environmental factors associated with an increased likelihood of detecting pathogens in agricultural water, this study provides information that (i) can be used to assess when pathogen contamination of agricultural water is likely to occur, and (ii) facilitate development of targeted interventions for individual water sources, providing an alternative to existing one-size-fits-all approaches.

Landscape, Water Quality, and Weather Factors Associated With an Increased Likelihood of Foodborne Pathogen Contamination of New York Streams Used to Source Water for Produce Production

There is a need for science-based tools to (i) help manage microbial produce safety hazards associated with preharvest surface water use, and (ii) facilitate comanagement of agroecosystems for competing stakeholder aims. To develop these tools an improved understanding of foodborne pathogen ecology in freshwater systems is needed. The purpose of this study was to identify (i) sources of potential food safety hazards, and (ii) combinations of factors associated with an increased likelihood of pathogen contamination of agricultural water Sixty-eight streams were sampled between April and October 2018 (196 samples). At each sampling event separate 10-L grab samples (GS) were collected and tested for Listeria, Salmonella, and the stx and eaeA genes. A 1-L GS was also collected and used for Escherichia coli enumeration and detection of four host-associated fecal source-tracking markers (FST). Regression analysis was used to identify individual factors that were significantly associated with pathogen detection. We found that eaeA-stx codetection [Odds Ratio (OR) = 4.2; 95% Confidence Interval (CI) = 1.3, 13.4] and Salmonella isolation (OR = 1.8; CI = 0.9, 3.5) were strongly associated with detection of ruminant and human FST markers, respectively, while Listeria spp. (excluding Listeria monocytogenes) was negatively associated with log10 E. coli levels (OR = 0.50; CI = 0.26, 0.96). L. monocytogenes isolation was not associated with the detection of any fecal indicators. This observation supports the current understanding that, unlike enteric pathogens, Listeria is not fecally-associated and instead originates from other environmental sources. Separately, conditional inference trees were used to identify scenarios associated with an elevated or reduced risk of pathogen contamination. Interestingly, while the likelihood of isolating L. monocytogenes appears to be driven by complex interactions between environmental factors, the likelihood of Salmonella isolation and eaeA-stx codetection were driven by physicochemical water quality (e.g., dissolved oxygen) and temperature, respectively. Overall, these models identify environmental conditions associated with an enhanced risk of pathogen presence in agricultural water (e.g., rain events were associated with L. monocytogenes isolation from samples collected downstream of dairy farms; P = 0.002). The information presented here will enable growers to comanage their operations to mitigate the produce safety risks associated with preharvest surface water use.

Nanoscale Phenotypic Textures of Yersinia pestis Across Environmentally-Relevant Matrices

The persistence of bacterial pathogens within environmental matrices plays an important role in the epidemiology of diseases, as well as impacts biosurveillance strategies. However, the adaptation potentials, mechanisms for survival, and ecological interactions of pathogenic bacteria such as Yersinia pestis are largely uncharacterized owing to the difficulty of profiling their phenotypic signatures. In this report, we describe studies on Y. pestis organisms cultured within soil matrices, which are among the most important reservoirs for their propagation. Morphological (nanoscale) and phenotypic analysis are presented at the single cell level conducted using Atomic Force Microscopy (AFM), coupled with biochemical profiles of bulk populations using Fatty Acid Methyl Ester Profiling (FAME). These studies are facilitated by a novel, customizable, 3D printed diffusion chamber that allows for control of the external environment and easy harvesting of cells. The results show that incubation within soil matrices lead to reduction of cell size and an increase in surface hydrophobicity. FAME profiles indicate shifts in unsaturated fatty acid compositions, while other fatty acid components of the phospholipid membrane or surface lipids remained consistent across culturing conditions, suggesting that phenotypic shifts may be driven by non-lipid components of Y. pestis.

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

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

Attachment and colonization of Salmonella on 'Rayada', 'Golden Delicious', and 'Red Delicious' apples

BACKGROUND

Fruits and vegetables have been associated with outbreaks of disease in different countries. The apple (Malus domestica Borkh) and its products have been reported as vehicles for illness outbreaks. To create strategies to prevent pathogen survival it is necessary to understand how pathogens persist on fruit. This paper assessed the ability of Salmonella to attach to, and to colonize, the surface of three apple cultivars: 'Rayada', 'Golden Delicious' and 'Red Delicious'.

RESULTS

Salmonella was able to colonize and generate biofilms on the surface of apples with a soil suspension as the only source of nutrients. Significant differences in Salmonella attachment were seen among the three cultivars of apple studied. Using SEM, attached cells and the formation of exopolysaccharides and biofilms on the three apple cultivars were demonstrated. In all cultivars, the development of Salmonella was only seen in apples stored at 15 and 22 °C, with average increases in the population of 1.4 and 2.3 Log CFU/apple, respectively. At 5 °C, Salmonella growth was inhibited.

CONCLUSION

Salmonella can colonize apple surfaces under environmental conditions (relative humidity, temperature and nutrients) occurring in primary apple production. © 2018 Society of Chemical Industry.