Irrigation water as source of foodborne pathogens on fruit and vegetables

Sustainable fabrication of dimorphic plant derived ZnO nanoparticles and exploration of their biomedical and environmental potentialities

Although, different plant species were utilized for the fabrication of polymorphic, hexagonal, spherical, and nanoflower ZnO NPs with various diameters, few studies succeeded in synthesizing small diameter ZnO nanorods from plant extract at ambient temperature. This work sought to pioneer the ZnO NPs fabrication from the aqueous extract of a Mediterranean salt marsh plant species Limoniastrum monopetalum (L.) Boiss. and assess the role of temperature in the fabrication process. Various techniques have been used to evaluate the quality and physicochemical characteristics of ZnO NPs. Ultraviolet-visible spectroscopy (UV-VIS) was used as the primary test for formation confirmation. TEM analysis confirmed the formation of two different shapes of ZnO NPs, nano-rods and near hexagonal NPs at varying reaction temperatures. The nano-rods were about 25.3 and 297.9 nm in diameter and in length, respectively while hexagonal NPs were about 29.3 nm. The UV-VIS absorption spectra of the two forms of ZnO NPs produced were 370 and 365 nm for nano-rods and hexagonal NPs, respectively. FT-IR analysis showed Zn-O stretching at 642 cm-1 and XRD confirmed the crystalline structure of the produced ZnO NPs. Thermogravimetric analysis; TGA was also used to confirm the thermal stability of ZnO NPs. The anti-tumor activities of the two prepared ZnO NPs forms were investigated by the MTT assay, which revealed an effective dose-dependent cytotoxic effect on A-431 cell lines. Both forms displayed considerable antioxidant potential, particularly the rod-shaped ZnO NPs, with an IC50 of 148.43 µg mL-1. The rod-shaped ZnO NPs were superior candidates for destroying skin cancer, with IC50 of 93.88 ± 1 µg mL-1 ZnO NPs. Thus, rod-shaped ZnO NPs are promising, highly biocompatible candidate for biological and biomedical applications. Furthermore, both shapes of phyto-synthesized NPs demonstrated effective antimicrobial activity against various pathogens. The outcomes highlight the potential of phyto-synthesized ZnO NPs as an eco-friendly alternative for water and wastewater disinfection.

Gaseous ozone and ozonized mist in the control of Escherichia coli on 'Rama Forte' persimmon

This study aimed to evaluate the effectiveness of using two ozone applications (gaseous and mist) as a disinfection method for fresh persimmon. To test these sanitizers, in vitro and in vivo assays were performed, and the Escherichia coli was selected because it is a pathogen that causes foodborne diseases in humans. For in vitro experiments, a plate was inoculated with Escherichia coli strain ATCC 25922 and treated. For in vivo assays, persimmon fruit surface was inoculated with the bacteria and treated. For both assays, it was used 10,15,20,30,40 and 50 μL L-1 of gaseous ozone or ozonized mist for five minutes. The results demonstrated that the gas ozone application significantly reduced the growth of E. coli on the plate surface in vitro at doses of 30, 40 and 50 μL L-1 (with 0.83, 0.89 and 0.95 log CFU mL-1, respectively). The application of ozonized mist showed a significant reduction for 50 μL L-1 (with 1.28 log CFU g-1). And, for the in vivo assays, ozonized mist significantly reduced the number of bacteria on the persimmon surface, with a 1.57 log reduction, which was the largest for 40 μL L-1. Therefore, it is possible to conclude that the ozone application can contribute to the control of microorganisms present on fruit surfaces.

Unveiling the genomic landscape of Salmonella enterica serotypes Typhimurium, Newport, and Infantis in Latin American surface waters: a comparative analysis

Surface waters are considered ecological habitats where Salmonella enterica can persist and disseminate to fresh produce production systems. This study aimed to explore the genomic profiles of S. enterica serotypes Typhimurium, Newport, and Infantis from surface waters in Chile, Mexico, and Brazil collected between 2019 and 2022. We analyzed the whole genomes of 106 S. Typhimurium, 161 S. Newport, and 113 S. Infantis isolates. Our phylogenetic analysis exhibited distinct groupings of isolates by their respective countries except for a notable case involving a Chilean S. Newport isolate closely related to two Mexican isolates, showing 4 and 13 single nucleotide polymorphisms of difference, respectively. The patterns of the most frequently detected antimicrobial resistance genes varied across countries and serotypes. A strong correlation existed between integron carriage and genotypic multidrug resistance (MDR) across serotypes in Chile and Mexico (R > 0.90, P < 0.01), while integron(s) were not detected in any of the Brazilian isolates. By contrast, we did not identify any strong correlation between plasmid carriage and genotypic MDR across diverse countries and serotypes.IMPORTANCEUnveiling the genomic landscape of S. enterica in Latin American surface waters is pivotal for ensuring public health. This investigation sheds light on the intricate genomic diversity of S. enterica in surface waters across Chile, Mexico, and Brazil. Our research also addresses critical knowledge gaps, pioneering a comprehensive understanding of surface waters as a reservoir for multidrug-resistant S. enterica. By integrating our understanding of integron carriage as biomarkers into broader MDR control strategies, we can also work toward targeted interventions that mitigate the emergence and dissemination of MDR in S. enterica in surface waters. Given its potential implications for food safety, this study emphasizes the critical need for informed policies and collaborative initiatives to address the risks associated with S. enterica in surface waters.

Occurrence of parasites in waters used for crops irrigation and vegetables from the Savannah of Bogotá, Colombia

The World Health Organization (WHO) has established as a criterion of parasitological quality for irrigation water, ≤ 1 helminth egg/liter, which guarantees the safety in agricultural products. In this study, the presence of parasites in surface water used for irrigation of crops (n = 96) and vegetables (celery and lettuce) (n = 120), from the Former La Ramada irrigation district, was evaluated using conventional and molecular parasitological methods. Our findings showed contamination of irrigation systems in the study area with domestic wastewater, demonstrated by the presence of Ancylostomatidae eggs, Ascaris spp., Hymenolepis spp., Trichuris spp., Capillaria spp., Giardia spp. cysts, and oocysts of Toxoplasma gondii and Cryptosporidium spp. A prevalence of 33% and 23.3% was calculated for helminths and protozoa, respectively in vegetables, representing a possible risk to human and animal health in relation to these parasites. These findings show the need for continuous monitoring of the water quality used for crop irrigation, as well as the safety of food, taking into account the values established in national and international regulations.

Wastewater contaminants in a fractured bedrock aquifer and their potential use as enteric virus indicators

Domestic wastewater is a source of persistent organic pollutants and pathogens to the aquatic environment, including groundwater aquifers. Wastewater contaminants include a variety of personal care products, pharmaceuticals, endocrine disrupters, bacteria, and viruses. Groundwater from 22 wells completed in a semi-confined to confined, fractured Silurian dolostone aquifer in southern Wellington County, Ontario, Canada, was analyzed for 14 organic wastewater contaminants (4 artificial sweeteners, 10 pharmaceuticals) as well as E. coli, total coliforms, and 6 human enteric viruses. Enteric viruses were detected in 8.6% of 116 samples, and at least one organic wastewater contaminant was detected in 82% of the wells (in order of decreasing detection frequency: acesulfame, ibuprofen, sulfamethoxazole, triclosan, carbamazepine, and saccharin). Virus indicator metrics [positive and negative predictive values (PPV, NPV), sensitivity, specificity] were calculated at the sample and well level for the organic wastewater compounds, E. coli, and total coliforms. Fecal bacteria were not good predictors of virus presence (PPV = 0%-8%). Of the potential chemical indicators, triclosan performed the best at the sample level (PPV = 50%, NPV = 100%), and ibuprofen performed the best at the well level (PPV = 60%, NPV = 67%); however, no samples had triclosan or ibuprofen concentrations above their practical quantification limits. Therefore, none of the compounds performed sufficiently well to be considered reliable for assessing the potential threat of enteric viruses in wastewater-impacted groundwater in this bedrock aquifer. Future studies need to evaluate the indicator potential of persistent organic wastewater contaminants in different types of aquifers, especially in fractured rock where heterogeneity is strong.IMPORTANCEAssessing the potential risk that human enteric viruses pose in groundwater aquifers used for potable water supply is complicated by several factors, including: (i) labor-intensive methods for the isolation and quantification of viruses in groundwater, (ii) the temporal variability of these viruses in domestic wastewater, and (iii) their potentially rapid transport in the subsurface, especially in fractured rock aquifers. Therefore, aquifer risk assessment would benefit from the identification of suitable proxy indicators of enteric viruses that are easier to analyze and less variable in wastewater sources. Traditional fecal indicators (e.g., E. coli and coliforms) are generally poor indicators of enteric viruses in groundwater. While many studies have examined the use of pharmaceutical and personal care products as tracers of domestic wastewater and fecal pollution in the environment, there is a paucity of data on the potential use of these chemical tracers as enteric virus indicators, especially in groundwater.

A flow cytometric assay to detect viability and persistence of Salmonella enterica subsp. enterica serotypes in nuclease-free water at 4 and 25°C

Salmonella spp. is one of the most isolated microorganisms reported to be responsible for human foodborne diseases and death. Water constitutes a major reservoir where the Salmonella spp. can persist and go undetected when present in low numbers. In this study, we assessed the viability of 12 serotypes of Salmonella enterica subsp. enterica for 160 days in nuclease-free water at 4 and 25°C using flow cytometry and Tryptic Soy Agar (TSA) plate counts. The results show that all 12 serotypes remain viable after 160 days in distilled water using flow cytometry, whereas traditional plate counts failed to detect ten serotypes incubated at 25°C. Moreover, the findings demonstrate that 4°C constitutes a more favorable environment where Salmonella can remain viable for prolonged periods without nutrients. Under such conditions, however, Salmonella exhibits a higher susceptibility to all tested antibiotics and benzalkonium chloride (BZK). The pre-enrichment with Universal Pre-enrichment Broth (UP) and 1/10 × Tryptic Soy broth (1/10 × TSB) resuscitated all tested serotypes on TSA plates, nevertheless cell size decreased after 160 days. Furthermore, phenotype microarray (PM) analysis of S. Inverness and S. Enteritidis combined with principal component analysis (PCA) revealed an inter-individual variability in serotypes with their phenotype characteristics, and the impact of long-term storage at 4 and 25°C for 160 days in nuclease-free water. This study provides an insight to Salmonella spp. long-term survivability at different temperatures and highlights the need for powerful tools to detect this microorganism to reduce the risk of disease transmission of foodborne pathogens via nuclease-free water.

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

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

Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis

The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially manufactured fermented liquids live up to their claims by analyzing pathogens and beneficial bacteria using a 16S rRNA sequencing technique called metagenomic analysis. Paenibacillus, Lentibacillus, Bacillus, Enterococcus, Levilactobacillus, and Oenococcus were the most abundant bacterial genera observed as potential probiotics. Pseudomonas stutzeri, Acinetobacter, and Collimonas, which have plant-growth-promoting traits, were also detected. The fact that we encounter biocontroller bacteria that promote plant growth demonstrates that these organisms are widely used in foods and emphasizes the necessity of evaluating them in terms of public health. Their potential applications in agriculture may pose a danger to food hygiene and human health in the long term, so our data suggest that this should be evaluated.

Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producing Escherichia coli in enriched agricultural water

Culture-independent metagenomic sequencing of enriched agricultural water could expedite the detection and virulotyping of Shiga toxin-producing Escherichia coli (STEC). We previously determined the limits of a complete, closed metagenome-assembled genome (MAG) assembly and of a complete, fragmented MAG assembly for O157:H7 in enriched agricultural water using long reads (Oxford Nanopore Technologies, Oxford), which were 107 and 105 CFU/ml, respectively. However, the nanopore assemblies did not have enough accuracy to be used in Single Nucleotide Polymorphism (SNP) phylogenies and cannot be used for the precise identification of an outbreak STEC strain. The present study aimed to determine the limits of detection and assembly for STECs in enriched agricultural water by Illumina MiSeq sequencing technology alone, followed by establishing the limit of hybrid assembly with nanopore long-read sequencing using three different hybrid assemblers (SPAdes, Unicycler, and OPERA-MS). We also aimed to generate a genome with enough accuracy to be used in a SNP phylogeny. The classification of MiSeq and nanopore sequencing identified the same highly abundant species. Using the totality of the MiSeq output and a precision metagenomics approach in which the E. coli reads are binned before assembly, the limit of detection and assembly of STECs by MiSeq were determined to be 105 and 107 CFU/ml, respectively. While a complete, closed MAG could not be generated at any concentration, a complete, fragmented MAG was produced using the SPAdes assembler with an STEC concentration of at least 107 CFU/ml. At this concentration, hybrid assembled contigs aligned to the nanopore-assembled genome could be accurately placed in a neighbor-joining tree. The MiSeq limit of detection and assembly was less sensitive than nanopore sequencing, which was likely due to factors including the small starting material (50 vs. 1 μg) and the dilution of the library loaded on the cartridge. This pilot study demonstrates that MiSeq sequencing requires higher coverage in precision metagenomic samples; however, with sufficient concentration, STECs can be characterized and phylogeny can be accurately determined.

The Potential for Cover Crops to Reduce the Load of Escherichia coli in Contaminated Agricultural Soil

Cover crops are plants seeded before or after cash crops to improve soil health, reduce weed pressure, and prevent erosion. Cover crops also produce various antimicrobial secondary metabolites (i.e., glucosinolates, quercetin), yet the role of cover crops in moderating the population of human pathogens in the soil has rarely been investigated. This study aims to determine the antimicrobial capacity of three cover crop species to reduce the population of generic Escherichia coli (E. coli) in contaminated agricultural soil. Four-week-old mustard greens (Brassicajuncea), sunn hemp (Crotalaria juncea), and buckwheat (Fagopyrum esculentum) were mixed into autoclaved soil and inoculated with rifampicin-resistant generic E. coli to achieve a starting concentration of 5 log CFU/g. The surviving microbial populations on days 0, 4, 10, 15, 20, 30, and 40 were enumerated. All three cover crops significantly reduced the population of generic E. coli compared to the control (p < 0.0001), particularly between days 10 and to 30. Buckwheat resulted in the highest reduction (3.92 log CFU/g). An inhibitory effect (p < 0.0001) on microbial growth was also observed in soils containing mustard greens and sunn hemp. This study provides evidence for the bacteriostatic and bactericidal effect of particular cover crops. More research regarding the secondary metabolites produced by certain cover crops and their potential as a bio mitigation strategy to improve on-farm produce safety is warranted.

Development of two microbial source tracking markers for detection of wastewater-associated Escherichia coli isolates

Escherichia coli has been used as an indicator of fecal pollution in environmental waters. However, its presence in environmental waters does not provide information on the source of water pollution. Identifying the source of water pollution is paramount to be able to effectively reduce contamination. The present study aimed to identify E. coli microbial source tracking (MST) markers that can be used to identify domestic wastewater contamination in environmental waters. We first analyzed wastewater E. coli genomes sequenced by us (n = 50) and RefSeq animal E. coli genomes of fecal origin (n = 82), and identified 144 candidate wastewater-associated marker genes. The sensitivity and specificity of the candidate marker genes were then assessed by screening the genes in 335 RefSeq wastewater E. coli genomes and 3318 RefSeq animal E. coli genomes. We finally identified two MST markers, namely W_nqrC and W_clsA_2, which could be used for detection of wastewater-associated E. coli isolates. These two markers showed higher performance than the previously developed human wastewater-associated E. coli markers H8 and H12. When used in combination, W_nqrC and W_clsA_2 showed specificity of 98.9 % and sensitivity of 25.7 %. PCR assays to detect W_nqrC and W_clsA_2 were also developed and validated. The developed PCR assays are potentially useful for detecting E. coli isolates of wastewater origin in environmental waters, though users should keep in mind that the sensitivity of these markers is not high. Further studies are needed to assess the applicability of the developed markers to a culture-independent approach.

Microgreen Variety Impacts Leaf Surface Persistence of a Human Norovirus Surrogate

Human norovirus (HuNoV) is a pathogenic agent that is frequently associated with foodborne disease outbreaks linked to fresh produce. Within microgreen production systems, understanding of virus transmission routes and persistence is limited. To investigate virus persistence on microgreen leaf surfaces, this study mimicked virus contaminations caused during microgreen handling by farm workers or during overhead irrigation with contaminated water. Specifically, approximately 5 log PFU of Tulane virus (TV)-a HuNoV surrogate-was inoculated on sunflower (SF) and pea shoot (PS) microgreen leaves at 7-day age. The virus reduction on SF was significantly higher than PS (p < 0.05). On day 10, total TV reduction for SF and PS were 3.70 ± 0.10 and 2.52 ± 0.30 log PFU/plant, respectively. Under the environmental scanning electron microscope (ESEM) observation, the leaf surfaces of SF were visually smoother than PS, while their specific effect on virus persistence were not further characterized. Overall, this study revealed that TV persistence on microgreen leaves was plant variety dependent. In addition, this study provided a preliminary estimation on the risk of HuNoV contamination in a microgreen production system which will aim the future development of prevention and control measures.

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.

Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study

Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.

Microbial and Parasitic Contamination of Vegetables in Developing Countries and Their Food Safety Guidelines

The safety of humans is of paramount importance in the vegetable production chain. Evidence of microbial and parasitic contamination of these products poses a great threat to consumers. This is an emerging issue the world is battling, and it is still in the process of unravelling. However, one of the contributing factors responsible for the rapid spread of these pathogens to millions of people among other factors is the distribution of food in our food systems. The purpose of this study was to draw the attention of producers, retailers, consumers, and various stakeholders to the occurrence and potential hazard of these organisms, their contamination origin, and food safety protocols. Among the food system, vegetables play a major role, and their consumption has increased as they form a larger portion of daily diets. This urge for healthy diets coupled with changing dietary habits and human population explosion has therefore accelerated their production. This has resulted in parasitic and microbial contamination gaining grounds in salad vegetables, and as such, a wide range of microbes such as Escherichia coli O157: H7, Listeria monocytogenes, Salmonella spp., Shigella, and Staphylococcus, and parasites such as Giardia lamblia, Entamoeba coli, Entamoeba histolytica, Cystoisospora belli, Toxoplasma gondii, Trichuris trichiura, and Ascaris lumbricoides have been isolated from them. Therefore, major routes for salad vegetable contamination and prevention methods have been pointed out in this review article. The topic of protective countermeasures will also be covered here in this review. Notwithstanding, several control measures have been reported to be effective and efficient in removing or eliminating pathogens, including treatment of irrigation water and fertilizers, use of disinfectants like vinegar and saltwater, irradiation, ozone, and bacteriophages. Though consumption of vegetables and salads is encouraged due to their nutritional advantage, appropriate systems should be put in place to ensure their safety.

Current methodologies and future direction of Campylobacter isolation and detection from food matrices, clinical samples, and the agricultural environment

Campylobacter spp. are the leading cause of bacterial foodborne infections in both developed and developing countries. The food commodities primarily attributed to campylobacteriosis include raw milk, poultry, seafood, and fresh produce. Furthermore, insects, animal/bird fecal material, and agricultural water have been shown to be the sources of Campylobacter contamination in these commodities. Both established and emerging species of Campylobacter have been recovered from food and environmental sources. Therefore, optimal detection and isolation of Campylobacter spp., including the emerging species, is critical for improved surveillance, prevention, and traceback of Campylobacter outbreaks. This review focuses on the existing variability in Campylobacter enrichment and isolation procedures used by researchers and regulatory agencies worldwide, for various matrices. Additionally, the challenges associated with developing and validating new culture, molecular, and immunological methods for rapid and sensitive Campylobacter detection are discussed.

Listeria monocytogenes in Irrigation Water: An Assessment of Outbreaks, Sources, Prevalence, and Persistence

As more fresh fruits and vegetables are needed to meet the demands of a growing population, growers may need to start depending on more varied sources of water, including environmental, recycled, and reclaimed waters. Some of these sources might be susceptible to contamination with microbial pathogens, such as Listeria monocytogenes. Surveys have found this pathogen in water, soil, vegetation, and farm animal feces around the world. The frequency at which this pathogen is present in water sources is dependent on multiple factors, including the season, surrounding land use, presence of animals, and physicochemical water parameters. Understanding the survival duration of L. monocytogenes in specific water sources is important, but studies are limited concerning this environment and the impact of these highly variable factors. Understanding the pathogen’s ability to remain infectious is key to understanding how L. monocytogenes impacts produce outbreaks and, ultimately, consumers’ health.

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.

Factors Driving Microbial Community Dynamics and Potential Health Effects of Bacterial Pathogen on Landscape Lakes with Reclaimed Water Replenishment in Beijing, PR China

Assessing the bacteria pathogens in the lakes with reclaimed water as major influents are important for public health. This study investigated microbial communities of five landscape lakes replenished by reclaimed water, then analyzed driven factors and identified health effects of bacterial pathogens. 16S rRNA gene sequence analysis demonstrated that Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, and Verrucomicrobia were the most dominant phyla in five landscape lakes. The microbial community diversities were higher in June and July than that in other months. Temperature, total nitrogen and phosphorus were the main drivers of the dominant microbial from the Redundancy analysis (RDA) results. Various potential bacterial pathogens were identified, including Pseudomonas, GKS98_freshwater_group, Sporosarcina, Pseudochrobactrum, Streptomyces and Bacillus, etc, some of which are easily infectious to human. The microbial network analysis showed that some potential pathogens were nodes that had significant health effects. The work provides a basis for understanding the microbial community dynamics and safety issues for health effects in landscape lakes replenished by reclaimed water.

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

The Survival of Salmonella Senftenberg, Escherichia coli O157:H7, Listeria monocytogenes, Enterococcus faecalis and Clostridium sporogenes in Sandy and Clay Loam Textured Soils When Applied in Bovine Slurry or Unpasteurised Digestate and the Run-Off Rate for a Test Bacterium, Listeria innocua, When Applied to Grass in Slurry and Digestate

This study investigated the survival of Salmonella Senftenberg, Escherichia coli O157:H7, Listeria monocytogenes, Enterococcus faecalis and Clostridium sporogenes in sandy and clay loam textured soils when applied in bovine slurry or unpasteurised digestate, using laboratory based inoculation studies. The run-off rate for a test bacterium, Listeria innocua, when applied to grass in slurry and digestate, was also examined using field studies. Bovine slurry and digestate were inoculated with the target bacteria to a final concentration of 106 log10 cfu/g or spores/g, thoroughly mixed into soil samples and incubated at 4°C or 14°C. Samples were removed periodically and the surviving cells enumerated using AOAC or equivalent methods. The loss of viability/culturability phase followed first order kinetics and T90 values ranged from 11.9 to 166.7 d at 4°C and from 6.0 to 156 d at 14°C. With the exception of E. coli O157:H7 and E. faecalis in sandy loam textured soil at 14°C (T90 values were significantly (P &lt; 0.05) higher in slurry) the type of soil texture or application material (slurry or digestate) did not affect survival rates. In the field study, 12 grass covered micro-plots were prepared. L. innocua was applied in digestate and bovine slurry and rainfall was simulated at a target rate of ~11 mm per plot per h−1. Rainfall simulation (30 min) took place after 24, 48 h, 14 d and 30 d. Run-off samples were tested for the L. innocua strain using Brilliance Listeria agar supplemented with streptomycin sulphate (1,000 μg/ml) at 37°C for 48 h, as were soil samples after 30, 58, 86 and 112 d. Significantly (P &lt; 0.05) lower counts were obtained in the run-off from digestate after 1, 2 and 30 d as compared to slurry. It was concluded that the type of organic fertiliser does not affect the bacterial survival rates in sandy and clay soils, with the exception of E. coli O157:H7 and E. faecalis in sandy loam textured soil at 14°C. Furthermore, bacteria may be retained better in the soil-digestate matrices during rainfall although additional research is required to further validate and provide the scientific basis for this observation.

Estimating the Risk of Acute Gastrointestinal Disease Attributed to E. coli O157:H7 in Irrigation Water and Agricultural Soil: A Quantitative Microbial Risk Assessment

Introduction: The occurrence of E. coli O157:H7 in the agricultural environment poses a serious threat to public health. The primary aim was to estimate the probability of illness caused by E. coli O157:H7 in irrigation water and agricultural soil niches. Methods: The Quantitative Microbial Risk Assessment was used and the risks were characterized using the Monte Carlo simulation with 10,000 iterations. Results: The mean levels of E. coli O157:H7 in the irrigation water and agricultural soil samples was 1.328 × 103 CFU/100 mL (Range: 0.00 to 13.000 × 103 CFU/100 mL) and 2.482 × 103 CFU/g (Range: 0.167 × 103 to 16.333 × 103 CFU/g), respectively. The risk of infection in humans exposed to this water and soil was 100%. In addition, a high risk of acute diarrheal disease was estimated at 25.0 × 10−2 for humans exposed to contaminated water and/or soil. Summary: These results exceeded the WHO diarrheal disease risk standard of 1.0 × 10−3. These findings demonstrated a high probability of acute gastrointestinal disease among humans exposed to E. coli O157:H7 in irrigation water and agricultural soil samples collected from the study sites representing a huge public health threat.

Study Effect of nAg Particle Size on the Properties and Antibacterial Characteristics of Polysulfone Membranes

Polysulfone ultrafiltration membranes were fabricated using various sizes (20, 40, and 90-210 nm) of silver nanoparticles (nAg) blended in a dope solution. To characterize the performance and properties of the prepared membranes, scanning electron microscopy (SEM), water contact angle, protein separation, water flux, and antibacterial tests were conducted. The characterization results revealed that when nAg particles (20 nm) were blended into the base polymer PSF, the PSF/nAg blended membrane had the lowest contact angle (58.5°) and surface energy (110.7 mN/m). When experimenting with ultrafiltration using protein solutions, bare PSF and PSF/nAg-20 blended membranes gave similar values of protein rejection: 93% of bovine serum albumin (BSA) and 70% of lysozyme rejection. Furthermore, SEM studies showed that the surface pore size was reduced by adding 20 nm nAg particles in the casting solution. Most importantly, the introduction of 40 nm nAg particles reduced the growth of bacterial colonies on the membrane surface by up to 72%. These findings revealed that nAg particles are expected to be a potential modifier for the fabrication of an ultrafiltration membrane.

Modelling the Potential Risk of Infection Associated with Listeria monocytogenes in Irrigation Water and Agricultural Soil in Two District Municipalities in South Africa

Listeria monocytogenes (L. monocytogenes) is the etiologic agent of listeriosis which significantly affects immunocompromised individuals. The potential risk of infection attributed to L. monocytogenes in irrigation water and agricultural soil, which are key transmission pathways of microbial hazards to the human population, was evaluated using the quantitative microbial risk assessment modelling. A Monte Carlo simulation with 10,000 iterations was used to characterize the risks. High counts of L. monocytogenes in irrigation water (mean: 11.96 × 10² CFU/100 mL; range: 0.00 to 56.67 × 10² CFU/100 mL) and agricultural soil samples (mean: 19.64 × 10² CFU/g; range: 1.33 × 10² to 62.33 × 10² CFU/g) were documented. Consequently, a high annual infection risk of 5.50 × 10⁻² (0.00 to 48.30 × 10⁻²), 54.50 × 10⁻² (9.10 × 10⁻³ to 1.00) and 70.50 × 10⁻² (3.60 × 10⁻² to 1.00) was observed for adults exposed to contaminated irrigation water, adults exposed to contaminated agricultural soil and children exposed to agricultural soil, respectively. This study, therefore, documents a huge public health threat attributed to the high probability of infection in humans exposed to L. monocytogenes in irrigation water and agricultural soil in Amathole and Chris Hani District Municipalities in the Eastern Cape province of South Africa.

High burden of multidrug resistant bacteria detected in Little Akaki River

Spread of antimicrobial-resistant bacteria between humans and animals occurs when the environment is contaminated with animal and human wastes. A total of 30 samples were collected from the Akaki river to identify antimicrobial-resistant bacteria. Bacterial enumeration and characterization was done by spreading serially diluted water samples on MacConkey agar. Sixty four bacterial isolates were identified and susceptibility tested using VITEK 2. The most frequently identified bacteria were Providencia alcalifaciens 10 (15.6%), Kluyvera cryocrescens 9 (14.1%) and Citrobacter freundii 7(10.9%), respectively. Multiple drug resistant bacteria were identified, constituting 17 (28%) of the 64 identified isolates. Multiple antimicrobial resistance (MAR) index of the six sites laid in the range 0.13-0.27, being the highest score located downstream of all the sampling sites. Species MAR index varied from 0.12 to 0.40. Out of 64 isolates, 54 (84.4%) of them were resistant to Ampicillin. On the contrary, most of the isolates were sensitive to Amikacin and meropenem. In conclusion, our findings indicated E.coli count was above the WHO permissible levels. The predominant isolates were P. alcalifaciens, and C. freundii. The MAR index of major isolates was greater than two, implying the study sites were exposed to high-risk sources of human or animal contamination.

Fate of enteric viruses during leafy greens (romaine lettuce) production using treated municipal wastewater and AP205 bacteriophage as a surrogate

Water reuse programs are being explored to close the gap between supply and demand for irrigation in agriculture. However, these sources could contain hazardous microbial contaminants, and pose risks to public health. This study aimed to grow and irrigate romaine lettuce with inoculated wastewater effluent to track AP205 bacteriophage prevalence through cultivation and post-harvest storage. AP205 is a bacteriophage and was used as a surrogate for enteric viruses. Low and high dosages (mean ± standard deviation) of AP205 at 4.8 ± 0.4 log PFU/mL and 6.6 ± 0.2 log PFU/mL; respectively, were prepared to examine viral load influence on contamination levels. Foliage, leachate, and soil contamination levels were directly related to AP205 concentrations in the effluent. AP205 concentrations increased throughout cultivation for foliage and leachate, suggesting bacteriophage accumulation. During post-harvest storage (14 day at 4 °C), there was a significant decrease in AP205 concentration on the foliage. Results show that wastewater effluents usage for leafy greens cultivation can pose risks to humans and additional steps are required to safely apply wastewater effluents to soils and crops.

Prevalence and molecular characterization of Listeria monocytogenes isolated from wastewater of cattle slaughterhouses in Turkey

AIM

The study aimed to investigate the role of cattle slaughterhouse wastewater as a possible source for the environmental distribution of Listeria monocytogenes.

METHODS AND RESULTS

Listeria spp. isolation was performed by collecting 117 wastewater samples from four different cattle slaughterhouses in Turkey. Species-specific identification was performed biochemically, and L. monocytogenes isolates were confirmed with polymerase chain reaction (PCR). In all, 71 (62.2%) of the wastewater samples were found to be positive for Listeria spp., and 17 (14.9%) of these samples were contaminated with L. monocytogenes. Pulsed field gel electrophoresis (PFGE) analysis revealed that all L. monocytogenes isolates were of different pulsotypes and isolates belonged to seven different phylogenetic clusters. Multiplex PCR analysis for genoserotypes and lineage determination showed that the isolates were divided into genoserotypes IVb and IIc in Lineages I and II. Also, it has been investigated with SYBR-Green Real-time PCR whether the L. monocytogenes isolates harboured virulence genes (hly, sigB, plcA, plcB, inlA, inlB, inlC and inlJ), and it was found that all isolates were substantially positive. Antibiotic resistance profiles and MIC values of the isolates were determined, and all L. monocytogenes isolates were found susceptible to ampicillin. In contrast, two isolates were resistant to meropenem and erythromycin, and three isolates were resistant to trimethoprim/sulfamethoxazole.

CONCLUSION

L. monocytogenes, which pose a threat to public health and resists to antibiotics effectively used in treatments, can environmentally spread via wastewater of cattle slaughterhouses. The wastewater of the food industry, which has rich microbiota, should be treated carefully, and possible environmental contamination should be prevented.

SIGNIFICANCE AND IMPACT OF STUDY

This is the first study that investigates the molecular characterization of L. monocytogenes isolated from cattle slaughterhouse wastewater and the findings represent the importance of cattle wastewater in the epidemiology of L. monocytogenes in Turkey.

Aeromonas spp. diversity in U.S. mid-Atlantic surface and reclaimed water, seasonal dynamics, virulence gene patterns and attachment to lettuce

Aeromonas, a ubiquitous taxon in water environments, is emerging as a foodborne pathogen of concern that remains understudied and under-reported. We evaluated the distribution of 331 Aeromonas spp. isolates collected from irrigation water over one year and characterised their virulence profile, attachment and ability to persist on lettuce. Water sources included non-tidal and tidal river, farm pond and reclaimed water. Twenty Aeromonas species were identified; A. veronii, A. hydrophila and A. jandaei predominated in all water types and seasons, comprising ~63% of isolates. Species distribution was most affected by water type. The highest and lowest diversity were detected in river and pond water, respectively. A. hydrophila and A. veronii ranked highest in frequency in fresh river and reclaimed water, while A. jandaei ranked first in pond water. Only two isolates carried all five virulence genes tested, while 46% of A. hydrophila (n = 50), 54% of A. veronii (n = 61) and 50% of A. jandaei (n = 32) isolates harboured multiple enterotoxin genes. Detection of alt and ast genes was more likely in summer collections, while ast detection was less likely in tidal brackish river and pond water isolates. Season was a factor in attachment to polystyrene, being strongest in spring isolates. The gene flaA was associated with strong attachment and was more likely to be detected in non-tidal fresh river isolates. A. hydrophila and A. jandaei isolates persisted on lettuce leaves for 24 h, but populations dwindled over 120 h, while loosely and strongly attached cells of A. veronii isolates persisted for 120 h. This study provides comprehensive data on Aeromonas species distribution and environmental traits. The associations revealed among diversity, water type, season, virulence factors and phyllosphere attachment capacity can inform agricultural water standards in novel ways. Moreover, understanding Aeromonas-plant interactions is an important step in advancing food safety of fruit and vegetables.

Synergistic effect of citric acid and xenon light for inactivating foodborne pathogens on spinach leaves

The aim of this study was to evaluate the synergistic antimicrobial effect of xenon light (XL) and citric acid (CA) combination against Escherichia coli O157:H7, Salmonella Typhimurium, and Listeria monocytogenes on spinach leaves and determine the effect of XL-CA combination on quality of spinach leaves. The XL-CA combined treatment for 8 min synergistically decreased the cell counts of E. coli O157:H7 and S. Typhimurium by 5.25 and 5.05 log CFU/cm², respectively, and additively decreased the L. monocytogenes cells by 5.02 log unit on spinach. The mechanisms underlying synergistic lethal effect of the XL-CA combination were investigated. Qualitative and quantitative analyses revealed that the bacterial cell membrane damage was strongly associated with the synergistic antimicrobial effect of the XL-CA combination. Additionally, treatment with XL-CA combination for 8 min did not affect the quality attributes (color, total phenol contents, and texture) of spinach leaves. These results suggest that the XL-CA combination treatment can be effectively used to control major pathogens on fresh produce.

Contamination of fresh produce sold on the Italian market with Cyclospora cayetanensis and Echinococcus multilocularis

To investigate the presence of Cyclospora cayetanensis, Toxoplasma gondii and Echinococcus spp. in fresh produce sold in Italy, 324 locally produced 'ready-to-eat' (RTE) mixed-salad packages belonging to three brands and 324 berries packages (blueberries and blackberries imported from Peru and Mexico, respectively, and raspberries grown in Italy) were purchased at retail. Nine individual packages from each of the six types of fresh produce were collected monthly for one year, and with the same produce pooled, this resulted in a total of 72 pools for the whole year. Using microscopy (FLOTAC), a Cyclospora-like oocyst was detected in a blueberry sample and a taeniid egg was detected in a RTE-salad sample. Molecular tools confirmed these to be C. cayetanensis and Echinococcus multilocularis, respectively. Toxoplasma gondii was not detected in any of the samples. This study shows for the first time in Europe that imported berries on the Italian market may be contaminated with C. cayetanensis and RTE salads grown in Italy with E. multilocularis. The results indicate a new epidemiological scenario and highlight that current management of fresh produce, locally produced or imported, does not ensure products are free from parasite contamination.

Microbial and physicochemical assessment of irrigation water treatment methods

AIMS

The presence of foodborne pathogens in preharvest agricultural water has been identified as a potential contamination source in outbreak investigations, driving markets and auditing bodies to begin requiring water treatment for high-risk produce. Therefore, it is essential that we identify water treatment methods which are effective as well as practical in their application on farm.

METHODS AND RESULTS

In this work, we evaluated two sanitizers which are most prominent in preharvest agricultural water treatment (calcium hypochlorite (free chlorine: 3-5 ppm) and peracetic acid (PAA: 5 ppm)), an EPA registered antimicrobial device (ultraviolet light (UV)), in addition to a combination approach (chlorine + UV, PAA + UV). Treatments were evaluated for their ability to inactivate total coliforms and generic Escherichia coli and consistency in treatment efficacy over 1 h of operation. Physicochemical variables were measured along with microbial populations at 0, 5, 15, 30, 45 and 60 min of operation. Escherichia coli and coliform counts showed a significant (P < 0·05) reduction after treatment, with combination and singular treatments equally effective at inactivating E. coli and coliforms. A significant increase (P < 0·05) in oxidation-reduction potential was seen during water treatment (Chlorine; UV + Chlorine), and a significant reduction (P < 0·05) in pH was seen after PAA and PAA + UV treatments (60 min).

CONCLUSION

Overall, the results indicate that all treatments evaluated are equally efficacious for inactivating E. coli and coliforms present in surface agricultural water.

SIGNIFICANCE AND IMPACT OF THE STUDY

This information when paired with challenge studies targeting foodborne pathogens of interest can be used to support grower decisions when selecting and validating a preharvest agricultural water treatment programme.

Genomic signatures of adaptation to natural settings in non-typhoidal Salmonella enterica Serovars Saintpaul, Thompson and Weltevreden

Salmonella enterica is a pathogenic bacterium responsible for intestinal illness and systemic diseases such as typhoid and paratyphoid fevers. Among clinical manifestation classification, non-typhoidal Salmonella is mainly known as foodborne pathogen associated with the consumption of fecal contaminated food and water. Even though Salmonella hosts include humans and warm-blooded animals, it has been found in non-host environments as river water where the bacteria use different strategies to fitness the environment persisting and establishment. Now with the availability of WGS and bioinformatics tools, we can explore bacterial genomes with higher resolution to increase our understanding of specific genetic signatures among environmental and clinical isolates, being the goal of this work. Pangenome construction allowed the detection of specific environmental and clinical gene clusters related to metabolism and secretion systems as the main signature respectively. Specifically, D-galactonate degradation pathway was observed mainly in environmental genomes while T3SS and flagellum genes were detected for all clinical but not for all environmental isolates. Gene duplication and pseudogenes accumulation were detected as the main adaptation strategy for environmental isolates; thus, isolation source may play an important role in genome plasticity, conferring a selective advantage to survive and persist for environmental Salmonella isolates. Intact prophage sequences with cargo genes were observable for both isolation sources playing an important role in virulence contribution.

Understanding Biopsychosocial Health Outcomes of Syndemic Water and Food Insecurity: Applications for Global Health

Household food and water insecurity often co-occur, and both can lead to malnutrition, psycho-emotional stress, and increased risk of infectious and chronic diseases. This can occur through multiple pathways including poor diet and inadequate sanitation. In this perspective, we discuss the potential advantages of a syndemic approach to understanding the consequences of food and water insecurity, that is, one that makes possible the assessment of their mutually enhancing effects on health. Syndemic theory considers the concerted, deleterious interaction of two or more diseases or other health conditions, such as psycho-emotional stress, that result from structural inequities. We therefore call for an approach that links localized morbidity of individual- or household-level experiences of concurrent food and water insecurity to larger structural and contextual forces/risk environments. Such an approach permits the investigation of food and water insecurity as suites of risk, such that certain disease outcomes serve as signals for interlinked stressors. For example, the use of a syndemic perspective could help explain the persistence of conditions like diarrhea or stunting after food or water interventions; that is, existing approaches may be too narrow in scope to protect individuals from multiple and overlapping environmental and biopsychosocial stressors.

Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water

Shiga toxin-producing Escherichia coli (STEC) contamination of agricultural water might be an important factor to recent foodborne illness and outbreaks involving leafy greens. Closed bacterial genomes from whole genome sequencing play an important role in source tracking. We aimed to determine the limits of detection and classification of STECs by qPCR and nanopore sequencing using 24 hour enriched irrigation water artificially contaminated with E. coli O157:H7 (EDL933). We determined the limit of STEC detection by qPCR to be 30 CFU/reaction, which is equivalent to 105 CFU/ml in the enrichment. By using Oxford Nanopore's EPI2ME WIMP workflow and de novo assembly with Flye followed by taxon classification with a k-mer analysis software (Kraken2), E. coli O157:H7 could be detected at 103 CFU/ml (68 reads) and a complete fragmented E. coli O157:H7 metagenome-assembled genome (MAG) was obtained at 105-108 CFU/ml. Using a custom script to extract the E. coli reads, a completely closed MAG was obtained at 107-108 CFU/ml and a complete, fragmented MAG was obtained at 105-106 CFU/ml. In silico virulence detection for E. coli MAGs for 105-108 CFU/ml showed that the virulotype was indistinguishable from the spiked E. coli O157:H7 strain. We further identified the bacterial species in the un-spiked enrichment, including antimicrobial resistance genes, which could have important implications to food safety. We propose this workflow provides proof of concept for faster detection and complete genomic characterization of STECs from a complex microbial sample compared to current reporting protocols and could be applied to determine the limit of detection and assembly of other foodborne bacterial pathogens.

Antimicrobial Blue Light versus Pathogenic Bacteria: Mechanism, Application in the Food Industry, Hurdle Technologies and Potential Resistance

Blue light primarily exhibits antimicrobial activity through the activation of endogenous photosensitizers, which leads to the formation of reactive oxygen species that attack components of bacterial cells. Current data show that blue light is innocuous on the skin, but may inflict photo-damage to the eyes. Laboratory measurements indicate that antimicrobial blue light has minimal effects on the sensorial and nutritional properties of foods, although future research using human panels is required to ascertain these findings. Food properties also affect the efficacy of antimicrobial blue light, with attenuation or enhancement of the bactericidal activity observed in the presence of absorptive materials (for example, proteins on meats) or photosensitizers (for example, riboflavin in milk), respectively. Blue light can also be coupled with other treatments, such as polyphenols, essential oils and organic acids. While complete resistance to blue light has not been reported, isolated evidence suggests that bacterial tolerance to blue light may occur over time, especially through gene mutations, although at a slower rate than antibiotic resistance. Future studies can aim at characterizing the amount and type of intracellular photosensitizers across bacterial species and at assessing the oxygen-independent mechanism of blue light-for example, the inactivation of spoilage bacteria in vacuum-packed meats.

Persistence of Escherichia coli O157:H12 and Escherichia coli K12 as Non-pathogenic Surrogates for O157:H7 on Lettuce Cultivars Irrigated With Secondary-Treated Wastewater and Roof-Collected Rain Water in the Field

Treated wastewater (TW) and roof-collected rain water (RW) that meet the required microbial quality as per Food Safety Modernization Act (FSMA) regulation may serve as alternative irrigation water sources to decrease the pressure on the current water scarcity. Alternative water sources may have different water characteristics that influence the survival and transfer of microorganisms to the irrigated produce. Further, these water sources may contain pathogenic bacteria such as Shiga-toxigenic Escherichia coli. To evaluate the risk associated with TW and RW irrigation on the fresh produce safety, the effect of TW and RW irrigation on the transfer of two non-pathogenic E. coli strains as surrogates for E. coli O157:H7 to different lettuce cultivars grown in the field was investigated. Lettuce cultivars “Annapolis,” “Celinet,” and “Coastline” were grown in the field at the Fulton farm (Chambersburg, PA). Approximately 10 days before harvest, lettuce plants were spray-irrigated with groundwater (GW), TW, or RW containing 6 log CFU ml−1 of a mixture of nalidixic acid-resistant E. coli O157:H12 and chloramphenicol-resistant E. coli K12 in fecal slurry as non-pathogenic surrogates for E. coli O157:H7. On 0, 1, 3, 7, and 10 days post-irrigation, four replicate lettuce leaf samples (30 g per sample) from each group were collected and pummeled in 120 ml of buffered peptone water for 2 min, followed by spiral plating on MacConkey agars with antibiotics. Results showed that the recovery of E. coli O157:H12 was significantly greater than the populations of E. coli K12 recovered from the irrigated lettuce regardless of the water sources and the lettuce cultivars. The TW irrigation resulted in the lowest recovery of the E. coli surrogates on the lettuce compared to the populations of these bacteria recovered from the lettuce with RW and GW irrigation on day 0. The difference in leaf characteristics of lettuce cultivars significantly influenced the recovery of these surrogates on lettuce leaves. Populations of E. coli O157:H12 recovered from the RW-irrigated “Annapolis” lettuce were significantly lower than the recovery of this bacterium from the “Celinet” and “Coastline” lettuce (P &lt; 0.05). Overall, the recovery of specific E. coli surrogates from the RW and TW irrigated lettuce was comparable to the lettuce with the GW irrigation, where GW served as a baseline water source. E. coli O157:H12 could be a more suitable surrogate compared to E. coli K12 because it is an environmental watershed isolate. The findings of this study provide critical information in risk assessment evaluation of RW and TW irrigation on lettuce in Mid-Atlantic area.

Assessing the Food Safety Risk Posed by Birds Entering Leafy Greens Fields in the US Southwest

In the US Southwest, it is common to observe birds in leafy green fields, though the risk they contribute to foodborne outbreaks remains unclear. In this study, we investigated and recorded the relationship between birds near leafy green fields and the risk for contaminated irrigation water or leafy green plants. We monitored the presence of birds for over two years and performed cloacal swab analysis for non-pathogenic Escherichia coli, E. coli O157:H7 and Salmonellaenterica, while also monitoring the incidence of other microbial indicators. We also assessed the risks from bird feces by performing observations in a commercial field reported with Salmonella positive samples and by analyzing the survival of foodborne pathogens in bird feces. Our results showed that most of the birds near the crop fields were resident small birds. We did not observe a correlation between the number of birds in sites and the incidence of indicator bacteria (e.g., coliforms, E. coli) in irrigation canal water, with the exception of one out of four sites where water flow was low or stagnant. Using walk-in-traps, 305 birds were captured and placed in short-term captivity to determine the presence of various bacteria. None of the birds tested positive for E. coli O157:H7 or Salmonella. However, nearly 40% of the birds captured were confirmed positive for non-pathogenic E. coli. We found no correlation between age (young, adult, unknown), gender (male, female, unknown) and the incidence of E. coli positive birds, but we observed significantly higher probability of incidence during October-December. The role of relative humidity and temperature on bacterial survival appeared to play a key role in the survival of Salmonella on the leaves of spinach plants in a commercial field. This was also confirmed in laboratory conditions where Salmonella inoculated in bird feces and exposed to 15 °C and 80% RH(Relative humidity) survived beyond 133 days, while at 26 °C and 40% RH, the organism was undetectable after 63 days. Our results suggest that local birds associated with leafy green fields likely pose a minimal impact of risk for food contamination, but also points out the need for increased analysis specifically for E. coli O157:H7. Furthermore, our study suggests the need for expanding research that addresses risks associated with large migratory birds, especially in areas where stagnated water sources would be used for overhead sprinkle irrigation.

Prevalence and Antimicrobial Resistance of Salmonella spp. From Irrigation Water in Two Major Sources in Jordan

Irrigation water could be a direct source of pathogenic microorganisms that contaminates fresh produce and causes human diseases. In this study, we evaluated the prevalence of Salmonella spp. and its serotypes Typhimurium and Enteritidis, antimicrobial susceptibility and multidrug resistance (MDR) status, and seasonal variation, of Salmonella spp. in irrigation water of King Abdullah Canal (KAC) and Wadi Shueib (WS) in Jordan. The study results demonstrated that 32.2% (29/90) of irrigation water was contaminated with Salmonella spp. and the irrigation water of WS was found highly contaminated (62.1%) with Salmonella spp. compared to KAC (37.9%). In addition, higher prevalence of Salmonella were recorded in spring (33.3%) and summer (36.3%) seasons, compared to winter seasons. Among the contaminated irrigation water samples, prevalence of Salmonella Typhimurium serotype was found in (37.9%) (11/29) samples, while S. Enteritidis was absent. The most common antimicrobial resistance of Salmonella isolates was observed as tetracycline (11/29, 37.9%) and 6 (20.7%) Salmonella Typhimurium isolates were found multidrug resistance (MDR). Thus, this study results confirmed that the irrigation water was contaminated with pathogenic MDR Salmonella spp.

Food safety in Peru: A review of fresh produce production and challenges in the public health system

Peru has a commodities-based economy where agriculture plays an essential role in the nation's development. Among agricultural products, fruits and vegetables are foundational to Peruvian culture and a healthy and nutritious diet. Produce is also the primary income source for thousands of small-scale farmers and producers throughout the country. Peru has significant potential to export agricultural and value-added products. Nevertheless, the Peruvian food chain has weak food safety and quality standards, limiting access to international markets. The inherent lack of food safety surveillance and management systems negatively affects public health. In the past decade, fresh and raw produce has been associated with several foodborne outbreaks worldwide, resulting in significant health and economic losses. This alarming situation for public health officials and regulators has called for the strengthening of produce safety standards and food safety risk management for safer food and to reduce the incidence of foodborne illnesses. This review summarizes the current status of produce safety in Peru and explores opportunities (e.g., policy, university capacity development) toward a safer food system.

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).

Metabolically-active bacteria in reclaimed water and ponds revealed using bromodeoxyuridine DNA labeling coupled with 16S rRNA and shotgun sequencing

Understanding the complex microbiota of agricultural irrigation water is vital to multiple sectors of sustainable agriculture and public health. To date, microbiome characterization methods have provided comprehensive profiles of aquatic microbiotas, but have not described which taxa are likely metabolically-active. Here, we combined 5‑bromo‑2'-deoxyuridine (BrdU) labeling with 16S rRNA and shotgun sequencing to identify metabolically-active bacteria in reclaimed and agricultural pond water samples (n = 28) recovered from the Mid-Atlantic United States between March 2017 and January 2018. BrdU-treated samples were significantly less diverse (alpha diversity) compared to non-BrdU-treated samples. The most abundant taxa in the metabolically-active fraction of water samples (BrdU-treated samples) were unclassified Actinobacteria, Flavobacterium spp., Pseudomonas spp. and Aeromonas spp. Interestingly, we also observed that antimicrobial resistance and virulence gene profiles seemed to be more diverse and more abundant in non-BrdU-treated water samples compared to BrdU-treated samples. These findings raise the possibility that these genes may be associated more with relic (inactive) DNA present in the tested water types rather than viable, metabolically-active microorganisms. Our study demonstrates that the coupled use of BrdU labeling and sequencing can enhance understanding of the metabolically-active fraction of bacterial communities in alternative irrigation water sources. Agricultural pond and reclaimed waters are vital to the future of sustainable agriculture, and thus, the full understanding of the pathogenic potential of these waters is important to guide mitigation strategies that ensure appropriate water quality for intended purposes.

Longitudinal Assessment of the Dynamics of Escherichia coli, Total Coliforms, Enterococcus spp., and Aeromonas spp. in Alternative Irrigation Water Sources: a CONSERVE Study

As climate change continues to stress freshwater resources, we have a pressing need to identify alternative (nontraditional) sources of microbially safe water for irrigation of fresh produce. This study is part of the center CONSERVE, which aims to facilitate the adoption of adequate agricultural water sources. A 26-month longitudinal study was conducted at 11 sites to assess the prevalence of bacteria indicating water quality, fecal contamination, and crop contamination risk (Escherichia coli, total coliforms [TC], Enterococcus, and Aeromonas). Sites included nontidal freshwater rivers/creeks (NF), a tidal brackish river (TB), irrigation ponds (PW), and reclaimed water sites (RW). Water samples were filtered for bacterial quantification. E. coli, TC, enterococci (∼86%, 98%, and 90% positive, respectively; n = 333), and Aeromonas (∼98% positive; n = 133) were widespread in water samples tested. Highest E. coli counts were in rivers, TC counts in TB, and enterococci in rivers and ponds (P < 0.001 in all cases) compared to other water types. Aeromonas counts were consistent across sites. Seasonal dynamics were detected in NF and PW samples only. E. coli counts were higher in the vegetable crop-growing (May-October) than nongrowing (November-April) season in all water types (P < 0.05). Only one RW and both PW sites met the U.S. Food Safety Modernization Act water standards. However, implementation of recommended mitigation measures of allowing time for microbial die-off between irrigation and harvest would bring all other sites into compliance within 2 days. This study provides comprehensive microbial data on alternative irrigation water and serves as an important resource for food safety planning and policy setting.IMPORTANCE Increasing demands for fresh fruit and vegetables, a variable climate affecting agricultural water availability, and microbial food safety goals are pressing the need to identify new, safe, alternative sources of irrigation water. Our study generated microbial data collected over a 2-year period from potential sources of irrigation (rivers, ponds, and reclaimed water sites). Pond water was found to comply with Food Safety Modernization Act (FSMA) microbial standards for irrigation of fruit and vegetables. Bacterial counts in reclaimed water, a resource that is not universally allowed on fresh produce in the United States, generally met microbial standards or needed minimal mitigation. We detected the most seasonality and the highest microbial loads in river water, which emerged as the water type that would require the most mitigation to be compliant with established FSMA standards. This data set represents one of the most comprehensive, longitudinal analyses of alternative irrigation water sources in the United States.

Prevalence, Distribution, and Diversity of Salmonella Strains Isolated From a Subtropical Lake

This study investigated the prevalence, serovar distribution, antimicrobial resistance, and pulsed field gel electrophoresis (PFGE) typing of Salmonella enterica isolated from Lake Zapotlán, Jalisco, Mexico. Additionally, the association of the presence of Salmonella with physicochemical and environmental parameters was analyzed using Pearson correlation analysis and principal component analysis (PCA). Salmonella spp. were identified in 19 of 63 (30.15%) samples. The prevalence of Salmonella was positively correlated with air temperature, electrical conductivity, pH, and dissolved oxygen and negatively correlated with relative humidity, water temperature, turbidity, and precipitation. The predominant serotype identified was Agona (68.48%), followed by Weltevreden (5.26%), Typhimurium (5.26%), and serogroup B (21.05%). Overall, the highest detected antimicrobial resistance was toward colistin (73.68%), followed by sulfamethoxazole (63.15%), tetracycline (57.89%), nalidixic acid (52.63%), and trimethoprim (52.63%). All Salmonella strains were genetically diverse, with a total of 11 XbaI and four BlnI profiles on PFGE. The use of these two enzymes allowed differentiate strains of Salmonella of the same serotype. The results obtained in this study contribute to a better understanding of the Salmonella spp. ecology in an endorheic subtropical lake and provide information for decision makers to propose and implement effective strategies to control point and non-point sources of pathogen contamination.

Potential for Bacteriophage Cocktail to Complement Commercial Sanitizer Use on Produce Against Escherichia coli O157:H7

The increasing concern for food safety has created a need to evaluate novel techniques to eliminate or control pathogens, resulting in safe food. In this study, four bacteriophages of bovine origin, specific to E. coli O157:H7, were successfully isolated and characterized. A microplate reader assay demonstrated the efficacy of the bacteriophage (phage) cocktail against E. coli O157:H7 resulting in a significant reduction (p < 0.01) in the target pathogen population. The phage cocktail demonstrated significant efficacy (p < 0.05) against E. coli O157:H7 in the presence of the most utilized sanitizers in the United States, namely 100 parts per million (ppm) free chlorine and 100-ppm peroxyacetic acid. Survival in the sanitizer concentrations demonstrates the potential use of phage cocktail and sanitizer synergistically to enhance sanitation operations in the food industry.

Effect of Weather on the Die-Off of Escherichia coli and Attenuated Salmonella enterica Serovar Typhimurium on Preharvest Leafy Greens following Irrigation with Contaminated Water

The Food Safety Modernization Act (FSMA) includes a time-to-harvest interval following the application of noncompliant water to preharvest produce to allow for microbial die-off. However, additional scientific evidence is needed to support this rule. This study aimed to determine the impact of weather on the die-off rate of Escherichia coli and Salmonella on spinach and lettuce under field conditions. Standardized, replicated field trials were conducted in California, New York, and Spain over 2 years. Baby spinach and lettuce were grown and inoculated with an ∼104-CFU/ml cocktail of E. coli and attenuated Salmonella Leaf samples were collected at 7 time points (0 to 96 h) following inoculation; E. coli and Salmonella were enumerated. The associations of die-off with study design factors (location, produce type, and bacteria) and weather were assessed using log-linear and biphasic segmented log-linear regression. A segmented log-linear model best fit die-off on inoculated leaves in most cases, with a greater variation in the segment 1 die-off rate across trials (-0.46 [95% confidence interval {95% CI}, -0.52, -0.41] to -6.99 [95% CI, -7.38, -6.59] log10 die-off/day) than in the segment 2 die-off rate (0.28 [95% CI, -0.20, 0.77] to -1.00 [95% CI, -1.16, -0.85] log10 die-off/day). A lower relative humidity was associated with a faster segment 1 die-off and an earlier breakpoint (the time when segment 1 die-off rate switches to the segment 2 rate). Relative humidity was also found to be associated with whether die-off would comply with FSMA's specified die-off rate of -0.5 log10 die-off/day.IMPORTANCE The log-linear die-off rate proposed by FSMA is not always appropriate, as the die-off rates of foodborne bacterial pathogens and specified agricultural water quality indicator organisms appear to commonly follow a biphasic pattern with an initial rapid decline followed by a period of tailing. While we observed substantial variation in the net culturable population levels of Salmonella and E. coli at each time point, die-off rate and FSMA compliance (i.e., at least a 2 log10 die-off over 4 days) appear to be impacted by produce type, bacteria, and weather; die-off on lettuce tended to be faster than that on spinach, die-off of E. coli tended to be faster than that of attenuated Salmonella, and die-off tended to become faster as relative humidity decreased. Thus, the use of a single die-off rate for estimating time-to-harvest intervals across different weather conditions, produce types, and bacteria should be revised.

Effects of Weather and Environmental Factors on the Seasonal Prevalence of Foodborne Viruses in Irrigation Waters in Gyeonggi Province, Korea

This study aimed to investigate the prevalence of foodborne viruses in reservoirs (an important resource of irrigation water) and its correlation with environmental and weather factors. From May 2017 to November 2018, we visited ten reservoirs and a river in the Anseong region of South Korea and collected a total of 192 samples in accordance with the environment protection agency guidelines. We recorded the weather factors (temperature, humidity, and accumulated precipitation) and investigated the surrounding environment factors (livestock, fishing site, the catchment area of reservoirs, etc.). Our research results show that from the river and reservoirs, the detection rates of human norovirus GII, adenovirus, rotavirus, human norovirus GI, and astrovirus were 27.1, 10.4, 10.4, 4.16, and 3.1%, respectively. Their viral load ranged from -1.48 to 1.55 log₁₀ genome copies/l. However, hepatitis A virus was not detected in any irrigation water sample. Although no sampling was performed in winter, foodborne viruses and male-specific coliphages were frequently found during spring (40.78%) and autumn (39.47%). Interestingly, the significant correlation between the accumulative precipitation and the number of detected norovirus and adenovirus was confirmed by linear regression analysis. Furthermore, when the accumulative precipitation ranged from 20 to 60 mm, it significantly affected the viral load and prevalence. Among the environmental factors, recreational facilities such as fishing sites and bungalow fishing spots were identified as contamination sources by correlation analysis. Our research results confirmed the correlations between environmental contamination factors in the reservoir and weather factors with the prevalence of foodborne viruses in the reservoir. These facilitates the assessment of potential foodborne virus contamination during crop irrigation. In addition, predictive models including environmental and weather factors should be developed for monitoring and controlling the safety of irrigation waters in reservoirs.

MCR-1 Gene Encoded Colistin-Resistant Escherichia coli in Raw Chicken Meat and Bean Sprouts in Malaysia

This study was conducted to detect the presence of colistin-resistant Escherichia coli (E. coli) in raw chicken meat and bean sprouts collected from local markets and to determine the antimicrobial resistance patterns of the E. coli isolates. A total of 100 samples, comprised of 50 raw chicken meat and 50 bean sprouts, were collected and processed. Kirby-Bauer method was used to determine the antimicrobial resistance patterns, and PCR amplification was used to detect E. coli species-specific and colistin resistance (mcr-1 and mcr-2) genes. The results showed that 52.1% (12/23) of the E. coli isolated from raw chicken meat were positive for the colistin resistance encoding gene, mcr-1, whereas all the E. coli isolates from bean sprouts were negative for colistin resistance encoding genes. The findings show that chicken meat contaminated with colistin-resistant E. coli may pose public health risk to the consumers. Hence, prudent usage of antibiotics and hygienic handling of food items helps to prevent and combat the risks of spreading of colistin-resistant E. coli and the public health risks it may pose. More comprehensive and large-scale studies focusing on all the possible sources of colistin-resistant E. coli are recommended.