Microbial Hazards in Irrigation Water: Standards, Norms, and Testing to Manage Use of Water in Fresh Produce Primary Production

Development of oriented microbial consortium-based compound enzyme strengthens food waste hydrolysis and antibiotic resistance genes removal: Deciphering of performance, metabolic pathways and microbial communities

Enzymatic hydrolysis has been considered as an eco-friendly pretreatment method for enhancing bioconversion process of food waste (FW). However, existing commercial enzymes and microbial monomer-based compound enzymes (MME) have the issues of uneven distribution of enzymatic activity and low matching degree with the components of FW, leading to low efficiency with enzymatic hydrolysis and removal of antibiotic resistance genes (ARGs). This study used FW as the substrate, under the co-culture system, produced a microbial consortium-based compound enzymes (MCE) with oriented and well-matching degree for FW hydrolysis and ARGs removal, of which the performance, metabolic pathways and microbial communities were also investigated in depth. Results showed that the best performance for ARGs was achieved by the MCE prepared by mixing 1:5 of Aspergillus oryzae and Aspergillus niger after 12 days fermentation. The highest soluble chemical oxygen demand (SCOD) concentration and ARGs removal could respectively reach 83.90 ± 1.67 g/L and 45.95% after MCE pretreatment. The analysis of metabolic pathways revealed that 1:5 MCE pretreatment strengthened the catalytic activity of carbohydrate-active enzymes, increased the abundances of genes involved in cellulose and starch degradation, polysaccharide synthesis, ATP binding cassette (ABC) transporters and global regulation, while decreased the abundances of genes involved in mating pair formation system, two-component regulatory systems and quorum sensing, thereby enhanced FW hydrolysis and restrained ARGs dissemination. Microbial community analysis further indicated that the 1:5 MCE pretreatment promoted growth, metabolism and richness of functional microbes, while inhibited the host microbes of ARGs. It is expected that this study can provide useful insights into understanding the fate of ARGs in food waste during MCE pretreatment process.

Towards a risk-based food safety management system in the fresh produce supply chain in Da Nang, Viet Nam

Food safety has emerged as a paramount concern for both Vietnamese consumers and the government. However, limited data are available on food safety management systems in Viet Nam. This study identified significant gaps in good agricultural and hygienic practices along the fresh produce chain (farmers and traditional wholesalers/market sellers) in the region of Da Nang, Viet Nam. This was achieved through a survey on good agricultural and hygienic practices for farmers (n = 100) and sellers (n = 100), which researchers further supplemented by microbiological analysis for E. coli, Salmonella spp., and Listeria monocytogenes on leafy greens, water in contact with produce and contact surfaces (hands). The results indicated that 86.0 % of farmers and 54.0 % of sellers received food safety training in the last 3 years; and women dominated both vegetable cultivation but also trading. Farm-level deficiencies included inadequate handwashing practices, lack of documentation for manure application schedules, improper washing and drying of harvest tools, failure to keep containers elevated off the ground, improper storage of vegetables, and inadequate covering of containers, with respectively 34.0 %, 30.3 %, 12.1 %, 41.7 % and 7.9 % of farmers executing the practice as prescribed by the WHO/FAO '5 keys of growing safer fruits and vegetables'. As for sellers, the most dominant gaps (<50.0 % compliance) were the way of handwashing and the practice of keeping containers elevated off the ground before, during, and after harvesting. The microbiological analysis confirmed that, in a total of 36 fresh produce samples including mustard greens, cucumber, lettuce, and crown daisy, the number of samples positive for E. coli, Salmonella spp., and L. monocytogenes were 12, 2, and 10 respectively. Samples of hands and the irrigation water showed high contamination with E. coli. Based on identified gaps, risk communication tools were developed and distributed amongst farmers, sellers, and Da Nang food safety management authority (governmental organisation performing inspections in the traditional food markets). As intervention, two farmers and two sellers were trained in safe agricultural practices for the cultivation of fresh vegetables (managerial intervention) and instructed to use tap water as irrigation water instead of uncontrolled surface water (technological intervention). A post-assessment was conducted, including redoing the survey on good practices and microbiological analysis. The outcome of these interventions showed positive results in terms of good agricultural and hygienic practices resulting in improved hygiene levels and safety of the fresh produce. The findings from this research have the potential to provide a model for the development of a science-based risk management strategy in alternative food chains or geographic areas in emerging countries.

The potential contribution of aquatic wildlife to antibiotic resistance dissemination in freshwater ecosystems: A review

Antibiotic resistance (AR) is one of the major health threats of our time. The presence of antibiotics in the environment and their continuous release from sewage treatment plants, chemical manufacturing plants and animal husbandry, agriculture and aquaculture, result in constant selection pressure on microbial organisms. This presence leads to the emergence, mobilization, horizontal gene transfer and a selection of antibiotic resistance genes, resistant bacteria and mobile genetic elements. Under these circumstances, aquatic wildlife is impacted in all compartments, including freshwater organisms with partially impermeable microbiota. In this narrative review, recent advancements in terms of occurrence of antibiotics and antibiotic resistance genes in sewage treatment plant effluents source compared to freshwater have been examined, occurrence of antibiotic resistance in wildlife, as well as experiments on antibiotic exposure. Based on this current state of knowledge, we propose the hypothesis that freshwater aquatic wildlife may play a crucial role in the dissemination of antibiotic resistance within the environment. Specifically, we suggest that organisms with high bacterial density tissues, which are partially isolated from the external environment, such as fishes and amphibians, could potentially be reservoirs and amplifiers of antibiotic resistance in the environment, potentially favoring the increase of the abundance of antibiotic resistance genes and resistant bacteria. Potential avenues for further research (trophic transfer, innovative exposure experiment) and action (biodiversity eco-engineering) are finally proposed.

Hydroponic Nutrient Solution Temperature Impacts Tulane Virus Persistence over Time

Controlled environment agriculture (CEA), or indoor agriculture, encompasses non-traditional farming methods that occur inside climate-controlled structures (e.g., greenhouses, warehouses, high tunnels) allowing for year-round production of fresh produce such as leaf lettuce. However, recent outbreaks and recalls associated with hydroponically grown lettuce contaminated with human pathogens have raised concerns. Few studies exist on the food safety risks during hydroponic cultivation of leaf lettuce; thus, it is important to identify contributing risk factors and potential mitigation strategies to prevent foodborne transmission via hydroponically grown produce. In this study, the concentration of infectious Tulane virus (TV), a human norovirus surrogate, in hydroponic nutrient solution at 15 °C, 25 °C, 30 °C, and 37 °C was determined over a duration of 21 days to mimic the time from seedling to mature lettuce. The mean log PFU reduction for TV was 0.86, 1.80, 2.87, and ≥ 3.77 log10 at 15 °C, 25 °C, 30 °C, and 37 °C, respectively, at the end of the 21-day period. Similarly, average decimal reduction values (D-values) of TV at 15 °C, 25 °C, 30 °C, and 37 °C were 48.0, 11.3, 8.57, and 7.02 days, respectively. This study aids in the (i) identification of possible food safety risks associated with hydroponic systems specifically related to nutrient solution temperature and (ii) generation of data to perform risk assessments within CEA leaf lettuce operations to inform risk management strategies for the reduction of foodborne outbreaks, fresh produce recalls, and economic losses.

Meta-analysis of the prevalence of norovirus and hepatitis a virus in berries

Norovirus (NoV) and hepatitis A virus (HAV) stand as the predominant agents associated with viral foodborne infections. Outbreaks have been documented to be caused by various types of food items, including fresh and/or frozen berries. Comprehensive data concerning crucial viral pathogens in berries remain limited and are not currently available in aggregate form. Consequently, the present study aimed to compile the existing information regarding the prevalence of NoV and HAV in this matrix. Records of foodborne viruses were systematically extracted from database repositories up to December 2022, adhering to PRISMA standards and were subjected to a multilevel random effect meta-analysis model to determine the mean occurrence rate of NoV and HAV. A high heterogeneity across studies was observed (I2 = 82 %), reflecting variations in the prevalence of sampling locations, years, berry types, and sample conditions, among other potential contributing factors. The prevalence of NoV and HAV in berries was calculated at 2.12 % (95 % CI 1.74-2.59 %), and no statistically differences were observed among the viral types or genogroup categories. However, it is important to clarify that this estimate should be taken with caution given the high heterogeneity. There was no discernible correlation between viral prevalence and any particular berry type. However, there was a temporal correlation observed with the year of sampling, revealing a significantly decreasing trend throughout the study period. A significant influence of the sample condition (fresh or frozen) was observed in relation to the prevalence of NoV GII and HAV. Overall higher viral prevalences were identified in berries originating from African countries as compared to those sourced from other continents. It was also noted that the prevalence of NoV GI was significantly higher in samples collected directly from farms compared to those obtained from retailers. The outcomes of this comprehensive meta-analysis propose that while viral contamination of berries is diminishing in more recent times, the prevalence remains substantial in certain African countries, having a significant risk for foodborne infections. It is imperative to implement intervention strategies in these regions to enhance product safety.

Assessment of irrigation water quality for vegetable farming in peri-urban Kumasi

Polluted water contains a variety of toxic compounds that tend to affect human health. Farmers have recently looked at runoff wastewater as a source of irrigation water because it comes at no cost and is a more efficient alternative to potable water due to the high demand but limited supply. This present study assesses the quality and suitability of water sources used for irrigation at the Kwame Nkrumah University of Science and Technology vegetable farmlands. The study specifically investigated the quality of water used for irrigation with the following parameters: pH, turbidity, total dissolved solids, total suspended solids, chloride, chemical oxygen demand, biological oxygen demand, oil and grease, fluoride, nitrate, nitrite, sulphate, sodium, calcium, magnesium, sodium adsorption potential, alkalinity, conductivity, phosphate, Escherichia coli, fecal and total coliforms. The results revealed that the water contained moderate levels of chloride and could be good for plant growth. The total coliform counts range from 2.1 × 106 to 4.15 × 107 MPN/100 mL, suggesting a relatively high microbial load in the irrigation water. The results also suggested that the sodium absorption ratio was very low and may not affect the quality of water for irrigation purposes. Fe levels far exceed the 5 mg/L maximum acceptable limits recommended by the WHO and FAO for the irrigation of vegetables. The high Fe concentration could discolor the leaves of some plants, especially foliage leaves. However, the levels of Cd were within the WHO maximum permissible limit of 0.01 mg/L.

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

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

Disinfection efficiency of chlorine dioxide and peracetic acid against MNV-1 and HAV in simulated soil-rich wash water

Wash water from fresh vegetables and root vegetables is an important vehicle for foodborne virus transmission. However, there is lack of assessing rapid viral inactivation strategies in wash water characterized by a high soil content at the post-harvest stage. Considering the significance of food safety during the washing stage for fresh and root vegetable produce prior to marketing, we assessed the inactivation efficacy by using chlorine dioxide (ClO2) and peracetic acid (PAA) against a surrogate of human norovirus (murine norovirus 1, MNV-1) and hepatitis A virus (HAV), in wash water containing black soil and clay loam. The results indicated that MNV-1 and HAV were reduced to the process limit of detection (PLOD), with reductions ranging from 4.89 to 6.35 log10 PFU, and 4.63 to 4.96 log10 PFU when treated with ClO2 at 2.5 ppm for 10 mins. Comparatively, when treated with 500 ppm of PAA for 10 mins, MNV-1 and HAV were maximum reduced to 1.75 ± 0.23 log10 PFU (4.50 log10 PFU reduction) and 2.13 ± 0.12 log10 PFU (2.72 log10 PFU reduction). This demonstrated the efficacy of ClO2 in eliminating foodborne viruses in soil-rich wash water. When we validated the recovery of the virus from two types of wash water, the pH (9.24 ± 0.33 and 5.95 ± 0.05) had no impact on the recovery of MNV-1, while the recovery of HAV was less than 1 %. By adjusting the pH to a neutral level, recovery of HAV and its RNA levels was increased to 15.94 and 3.89 %. Thus, this study emphasized the critical role of pH in the recovery of HAV from the complex soil-rich aqueous environment, and the efficacy of ClO2 serving as a pivotal reference for the development of control strategies against foodborne viruses in the supply chain of fresh and root vegetables.

Scale of analysis drives the observed ratio of spatial to non-spatial variance in microbial water quality: insights from two decades of citizen science data

AIMS

While fecal indicator bacteria (FIB) testing is used to monitor surface water for potential health hazards, observed variation in FIB levels may depend on the scale of analysis (SOA). Two decades of citizen science data, coupled with random effects models, were used to quantify the variance in FIB levels attributable to spatial versus temporal factors.

METHODS AND RESULTS

Separately, Bayesian models were used to quantify the ratio of spatial to non-spatial variance in FIB levels and identify associations between environmental factors and FIB levels. Separate analyses were performed for three SOA: waterway, watershed, and statewide. As SOA increased (from waterway to watershed to statewide models), variance attributable to spatial sources generally increased and variance attributable to temporal sources generally decreased. While relationships between FIB levels and environmental factors, such as flow conditions (base versus stormflow), were constant across SOA, the effect of land cover was highly dependent on SOA and consistently smaller than the effect of stormwater infrastructure (e.g. outfalls).

CONCLUSIONS

This study demonstrates the importance of SOA when developing water quality monitoring programs or designing future studies to inform water management.

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.

Fecal Contamination in the Wastewater Irrigation System and its Health Threat to Wastewater-Based Farming Households in Addis Ababa, Ethiopia

Due to rapidly growing demand, the production of vegetables is increasing along the Akaki Rivers. The objective of this study was to examine the degree of fecal contamination and levels of fecal contamination and dissemination throughout the wastewater irrigation system. Irrigation water, irrigated soil, and leafy vegetables were collected twice during 2 vegetable growing seasons, at the maturity period of the growing season, from 19 sampling points along the 2 Akaki Rivers. Composite samples were taken from all sampling points and E.coli was enumerated. The mean E.coli load in wastewater and non-wastewater sources were 1.1⁶±5.5³ CFU/100 ml and 2.23²±1.29² CFU/100 ml respectively. All counts of E. coli in the wastewater exceeded the WHO's standards indicating that the irrigation water quality was unacceptable. In the wastewater-irrigated and non-wastewater-irrigated soil, the mean E.coli were 3.6² ±1.58² CFU/g and 1.32²±87.1 CFU/g respectively. Meanwhile, the mean E.coli counts on the lettuce and Swiss chard were 78 ± 2 CFU/g and 44 ±3CFU/g respectively. The E.coli count on the leafy vegetables was found to be associated with the E.coli in the wastewater and soil. The production of leafy vegetables using wastewater with unacceptably high levels of E.coli and high occupational exposure introduces high levels of risk to the farming communities and to the consumers. Leafy, low-growing raw edible vegetables need careful treatment during food production and harvesting procedures or activities.

Effect of storage temperature and produce type on the survival or growth of Listeria monocytogenes on peeled rinds and fresh-cut produce

Whole and fresh-cut produce are minimally processed and susceptible to microbial contamination. This study evaluated the survival or growth of L. monocytogenes on peeled rinds, and fresh-cut produce at different storage temperatures. Fresh-cut fruits and vegetables, including cantaloupe, watermelon, pear, papaya, pineapple, broccoli, cauliflower, lettuce, bell pepper, and kale (25 g pieces) were spot inoculated with 4 log CFU/g of L. monocytogenes and stored at 4 or 13°C for 6  days. Cantaloupe and bell pepper rind disks (20 cm²), mimicking whole produce were inoculated with low inoculum level (4 log CFU/mL) and high inoculum level (6 log CFU/mL) and stored at 24°C up to 8  days and 4°C up to 14  days, respectively. L. monocytogenes counts on fresh-cut pear samples stored at 4°C increased significantly by 0.27 log CFU/g. However, Listeria levels on kale (day 4), cauliflower (day 6), and broccoli (day 2) were significantly reduced by 0.73, 1.18, and 0.80 log CFU/g, respectively, at 4°C. At 13°C, the bacterial counts increased significantly after a day of storage on fresh-cut watermelons (increasing by 1.10 log CFU/g) and cantaloupes (increasing by 1.52 log CFU/g). Similar increases were observed on pears (1.00 log CFU/g), papayas (1.65 log CFU/g), and green bell peppers (1.72 log CFU/g). Pineapple samples did not support the growth of L. monocytogenes at 13°C with a significant reduction of 1.80 log CFU/g by day 6. L. monocytogenes levels significantly increased in fresh-cut lettuce at 13°C but remained stable on kale, cauliflower, and broccoli after 6  days of storage. Stable population was observed also on cantaloupe rinds up to 8  days at 24°C. While on the outer surface of bell peppers, the population level decreased below the detectable limit of the test (10 CFU/20 cm²) after 14  days of storage at 4°C. The results demonstrated variable survival behavior of L. monocytogenes on fresh-cut produce with produce type and storage temperature.

Brassica rapa subsp. Chinensis juice enhances Bacillus subtilis selectively in leafy green production

Bacillus subtilis (BS) is a well-known beneficial microorganism for plants but is not competitive in the plant rhizosphere microbiome. We report the selective support of Brassica rapa subsp. Chinensis (Xiao Bai Cai) juice (XBCJ) on BS both in hydroponic nutrient solution and the plant rhizosphere of lettuce. After 2 weeks of being inoculated in the lettuce rhizosphere, the Bacillus population was enumerated at 3.30 ± 0.07 log CFU/unit in the BS group and at 5.20 ± 0.39 log CFU/unit in the BS + XBCJ group (p < 0.05). Accordingly, lettuce crops from the BS + XBCJ group were significantly higher than the control group for all of the tested biomass-related parameters (p < 0.05). The treatment did not significantly affect the texture, colour, moisture contents, total phenolic contents, or antioxidant activities of the lettuce crops (p > 0.05). Non-target ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) suggested that phenolic compounds could be the key class of phytochemicals being responsible for the selectivity. High-throughput RNA-based 16S rRNA gene sequencing and analysis were performed to depict the influence of BS and XBCJ over the global microbiome compositions of plant rhizosphere.

Reduction of pathogenic bacteria from irrigation water through a copper-loaded porous ceramic emitter

The increasing pathogenic bacteria threat in irrigation water has become a worldwide concern, prompting efforts to discover a new cost-effective method for pathogenic bacteria eradication, different than those currently in use. In this study, a novel copper-loaded porous ceramic emitter (CPCE) was developed via molded sintering method to kill bacteria from irrigation water. The material performance and hydraulic properties of CPCE are discussed herein, and the antibacterial effect against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) was evaluated. The incremental copper content in CPCE improved flexural strength and pore size, which was conducive to enhancing CPCE discharge. Moreover, antibacterial tests showed that CPCE displayed efficient antimicrobial activity, killing 99.99% and more than 70% of S. aureus and E. coli, respectively. The results reveal that CPCE, with both irrigation and sterilization functions, can provide a low-cost and effective solution for bacterial removal from irrigation water.

Microbiological quality of irrigation water for cultivation of fruits and vegetables: An overview of available guidelines, water testing strategies and some factors that influence compliance

Contaminated irrigation water is among many potential vehicles of human pathogens to food plants, constituting significant public health risks especially for the fresh produce category. This review discusses some available guidelines or regulations for microbiological safety of irrigation water, and provides a summary of some common methods used for characterizing microbial contamination. The goal of such exploration is to understand some of the considerations that influence formulation of water testing guidelines, describe priority microbial parameters particularly with respect to food safety risks, and attempt to determine what methods are most suitable for their screening. Furthermore, the review discusses factors that influence the potential for microbiologically polluted irrigation water to pose substantial risks of pathogenic contamination to produce items. Some of these factors include type of water source exploited, irrigation methods, other agro ecosystem features/practices, as well as pathogen traits such as die-off rates. Additionally, the review examines factors such as food safety knowledge, other farmer attitudes or inclinations, level of social exposure and financial circumstances that influence adherence to water testing guidelines and other safe water application practices. A thorough understanding of relevant risk metrics for the application and management of irrigation water is necessary for the development of water testing criteria. To determine sampling and analytical approach for water testing, factors such as agricultural practices (which differ among farms and regionally), as well as environmental factors that modulate how water quality may affect the microbiological safety of produce should be considered. Research and technological advancements that can improve testing approach and the determination of target levels for hazard characterization or description for the many different pollution contexts as well as farmer adherence to testing requirements, are desirable.

Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms

Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and storage tank water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3-V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phylum in the stream source and associated water samples from wetland taro fields. Cyanobacteria was also a dominant phylum in samples from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. In contrast, Oxford Nanopore MinION was a better choice for microbe classification at the genus and species levels as indicated by samples sequenced for full length 16S rRNA. No reliable taxonomic classification results were obtained while using shotgun metagenome data. In functional analyzes, only 12% of the genes were shared by two consortia and 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Full descriptions of microbial communities and their functions are essential for the development of better water management strategies aimed to produce safer fresh produce and to protect plant, animal, human and environmental health. Quantitative comparisons illustrated the importance of selecting the appropriate analytical method depending on the level of taxonomic delineation sought in each microbiome.

Development of A Rapid, Low-Cost Portable Detection Assay for Enterococci in Wastewater and Environmental Waters

Waterborne diseases are known as a leading cause of illness and death in both developing and developed countries. Several pathogens can be present in contaminated water, particularly waters containing faecal material; however, routine monitoring of all pathogens is not currently possible. Enterococcus faecalis, which is present in the microflora of human and animals has been used as a faecal indicator in water due to its abundance in surface water and soil. Accurate and fast detection methods are critical for the effective monitoring of E. faecalis in the environment. Although conventional and current molecular detection techniques provide sufficient sensitivity, specificity and throughput, their use is hampered by the long waiting period (1-6 days) to obtain results, the need for expensive laboratory equipment, skilled personnel, and cold-chain storage. Therefore, this study aimed to develop a detection system for E. faecalis that would be simple, rapid, and low-cost, using an isothermal DNA amplification assay called recombinase polymerase amplification (RPA), integrated with a lateral flow assay (LFA). The assay was found to be 100% selective for E. faecalis and capable of detecting rates as low as 2.8 × 103 cells per 100 mL from water and wastewater, and 2.8 × 104 cells per 100 mL from saline water. The assay was completed in approximately 30 min using one constant temperature (38 °C). In addition, this study demonstrated the quantitation of E. faecalis using a lateral flow strip reader for the first time, enhancing the potential use of RPA assay for the enumeration of E. faecalis in wastewater and heavily contaminated environmental waters, surface water, and wastewater. However, the sensitivity of the RPA-LFA assay for the detection of E. faecalis in tap water, saline water and in wastewater was 10-1000 times lower than that of the Enterolert-E test, depending on the water quality. Nevertheless, with further improvements, this low-cost RPA-LFA may be suitable to be used at the point-of-need (PON) if conjugated with a rapid field-deployable DNA extraction method.

Comparing the Efficacy of MALDI-TOF MS and Sequencing-Based Identification Techniques (Sanger and NGS) to Monitor the Microbial Community of Irrigation Water

In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world's rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water.

Presence of Listeria at primary production and processing of food of non-animal origin (FNAO) in Bavaria, Germany

Several foodborne outbreaks associated with food of non-animal origin (FNAO) were reported within the last years. In recent years, Listeriamonocytogenes has been associated with such outbreaks. For this reason, different producers of FNAO at the primary production and processing level in Bavaria, Germany, were inspected from July 2020 to June 2021. Environmental and food sampling as well as the sampling of irrigation and processing water was performed to investigate the prevalence of Listeriaspp., including L.monocytogenes at facilities that produce ready-to-eat FNAO. Altogether, 39 producers of soft fruit, vegetables, ready-to-eat raw fruits, and vegetables/fresh cut were inspected. In addition to the on-spot inspections, 407 samples were taken in total, among them, 229 were swab samples from food contact material and the environment, 59 food samples (including soft fruit, vegetables and ready-to-eat vegetables), and 119 samples of irrigation and processing water. Samples were analyzed using methods according to ISO11290-1:2017. Furthermore, the samples of irrigation and processing water were also quantitatively tested for the number of Escherichiacoli (ISO9308-2:2014-06), enterococci (ISO7899-2:2000-11), and Pseudomonasaeruginosa (ISO16266:2008-05). No contamination with E.coli, enterococci, and P.aeruginosa could be detected in most of the samples. Overall, in 12.53% of the samples, Listeriaspp. were detected. L.monocytogenes was identified in 1.72% of the environmental and processing water samples, whereas L.monocytogenes was not detected in food samples. In addition to water sources and quality, this study demonstrates that irrigation regime, cultivation, hygienic handling, and maintenance protocols are highly important to reduce the potential contamination of ready-to-eat soft fruits and vegetables with Listeriaspp.

Irrigation Ponds as Sources of Antimicrobial-Resistant Bacteria in Agricultural Areas with Intensive Use of Poultry Litter

Poultry litter is widely used worldwide as an organic fertilizer in agriculture. However, poultry litter may contain high concentrations of antibiotics and/or antimicrobial-resistant bacteria (ARB), which can be mobilized through soil erosion to water bodies, contributing to the spread of antimicrobial resistance genes (ARGs) in the environment. To better comprehend this kind of mobilization, the bacterial communities of four ponds used for irrigation in agricultural and poultry production areas were determined in two periods of the year: at the beginning (low volume of rainfall) and at the end of the rainy season (high volume of rainfall). 16S rRNA gene sequencing revealed not only significantly different bacterial community structures and compositions among the four ponds but also between the samplings. When the DNA obtained from the water samples was PCR amplified using primers for ARGs, those encoding integrases (intI1) and resistance to sulfonamides (sul1 and sul2) and β-lactams (blaGES, blaTEM and blaSHV) were detected in three ponds. Moreover, bacterial strains were isolated from CHROMagar plates supplemented with sulfamethoxazole, ceftriaxone or ciprofloxacin and identified as belonging to clinically important Enterobacteriaceae. The results presented here indicate a potential risk of spreading ARB through water resources in agricultural areas with extensive fertilization with poultry litter.

Lettuce Contamination and Survival of Salmonella Typhimurium and Listeria monocytogenes in Hydroponic Nutrient Film Technique Systems

Hydroponic vegetable production is increasing globally, but there is a lack of science-based recommendations to ensure their food safety. Specifically, there is limited evidence for establishing water management strategies. The purpose of this study was to determine the survival of Salmonella Typhimurium and Listeria monocytogenes in commercial nutrient flow technology (NFT) systems during the lifecycle of lettuce exposed to sporadic or extreme contamination. NFT systems were inoculated with Salmonella Typhimurium or Listeria monocytogenes, and nutrient solution, rockwool, roots, and lettuce leaves were collected over the lettuce production cycle for pathogen enumeration and detection. Both human pathogens persisted in the lettuce NFT growing system throughout the growth cycle of lettuce. Salmonella Typhimurium and L. monocytogenes accumulated in rockwool medium and on lettuce roots and were transferred to the leaves at quantifiable levels from the contaminated nutrient solution. In the nutrient solution, Salmonella concentration under sporadic and extreme conditions declined significantly 24 h after inoculation and again 7 days post-inoculation (p < 0.0001). Under extreme conditions, the concentration did not change significantly after 7 days, while under sporadic conditions, the concentration declined again 14 days post-inoculation in the nutrient solution collected from the reservoirs. L. monocytogenes populations in the nutrient solution fluctuated significantly over the 28-day growth cycle (p < 0.0001). Under extreme conditions, L. monocytogenes concentrations in the nutrient solution declined, while under sporadic conditions, the populations increased. The findings of this study, for the first time, describe human pathogen survival in commerical NFT systems and highlight the urgent need for novel approaches to mitigating the risks from nutrient solution contaminaiton in hydroponics.

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.

Insights into the diversity of cow milk production systems on the fringes of coastal cities in West Africa: A case study from Benin

In sub-Saharan Africa, rapid population growth, urbanization, increasing incomes, and changing dietary preferences are the main drivers of the rising demand for livestock products, especially fresh milk and derived products. To meet this demand, there is an increasing number of dairy cattle farms in the densely populated coastal zone of Benin, where the country's largest city and commercial capital Cotonou is located. To identify and characterize the peri-urban dairy production systems in this region, 190 cattle keepers were surveyed, using the snowball sampling method, in four municipalities neighboring Cotonou. Information on their socio-economic characteristics, cattle herd sizes, and herd management practices were collected through questionnaire-based face-to-face interviews. Factor analysis of mixed data followed by hierarchical clustering on principal components, implemented in R statistical software, were applied to classify the surveyed farms into homogeneous groups. Results revealed six types of peri-urban dairy cattle farms differing mainly in their cows' breeds, herd sizes, and daily amount of milk produced. Most herds (88%) were owned by urban dwellers, mainly civil servants and traders, who entrusted the management of their cattle to hired professional herders. Irrespective of farm type, cows were of local taurine (65%) or Sahelian zebu (35%) breeds and were exclusively fed on communal natural pasture. Mineral supplementation was provided to the animals on 42% of farms, with significant variation across farm types. About 45% of the farms integrated cattle production with other agricultural activities, including coconut plantations (22%), where cow manure was used as fertilizer. The herd structure was similar across farm types, with average proportions of cows and heifers ranging from 37.6 to 47.5% and from 13.1 to 19.7%, respectively. With significant differences across farm types, the produced milk was either transformed into traditional cheese (32% of farms) or sold raw (85%). Milk and cheese sales represented 84% of the total farm income for three out of the six farm types. In the current context of rapid urbanization, communal grazing lands alone cannot provide sufficient feed to support increased milk production. In addition to improved feeding strategies, herd structure should be balanced in terms of the ratio between milk-producing and non-producing animals.

Extended Spectrum β-Lactamase Activity and Cephalosporin Resistance in Escherichia coli from U.S. Mid-Atlantic Surface and Reclaimed Water

Phylogenetic distribution and extended spectrum β-lactamase (ESBL) activity of Escherichia coli recovered from surface and reclaimed water in the mid-Atlantic U.S. were evaluated. Among 488 isolates, phylogroups B1 and A were the most and least prevalent, respectively. Water type, but not season, affected phylogroup distribution. The likelihood of detecting group A isolates was higher in reclaimed than pond (P < 0.01), freshwater river (P < 0.01) or brackish river (P < 0.05) water. Homogeneity in group distribution was lowest in pond water, where group B1 comprised 50% of isolates. Only 16 (3.3%) isolates exhibited phenotypic resistance to one or more cephalosporins tested and only four had ESBL activity, representing groups B1, B2 isolates, and D. Phylogroup was a factor in antimicrobial resistance (P < 0.05), with group A (8.7%) and D (1.6%) exhibiting the highest and lowest rates. Resistance to cefoxitin was the most prevalent. Multi- versus single drug resistance was affected by phylogroup (P < 0.05) and more likely in groups D and B1 than A which carried resistance to cefoxitin only. The most detected β-lactam resistance genes were bla_CMY-2 and bla_TEM. Water type was a factor for bla_CTX-M gene detection (P < 0.05). Phenotypic resistance to cefotaxime, ceftriaxone, cefuroxime and ceftazidime, and genetic determinants for ESBL-mediated resistance were found predominantly in B2 and D isolates from rivers and reclaimed water. Overall, ESBL activity and cephalosporin resistance in reclaimed and surface water isolates were low. Integrating data on ESBL activity and β-lactam resistance among E. coli populations can inform decisions on safety of irrigation water sources and One Health. IMPORTANCE Extended spectrum β-lactamase (ESBL) producing bacteria, that are resistant to a broad range of antimicrobial agents, are spreading in the environment but data remain scarce. ESBL-producing Escherichia coli infections in the community are on the rise. This work was conducted to assess presence of ESBL-producing E. coli in water that could be used for irrigation of fresh produce. The study provides the most extensive evaluation of ESBL-producing E. coli in surface and reclaimed water in the mid-Atlantic United States. The prevalence of ESBL producers was low and phenotypic resistance to cephalosporins (types of β-lactam antibiotics) was affected by season but not water type. Data on antimicrobial resistance among E. coli populations in water can inform decisions on safety of irrigation water sources and One Health.

Phylogroup typing and carbapenem resistance of Escherichia coli from agricultural samples in Metro Manila, Philippines

Primary production environment is considered as reservoir of Escherichia coli contamination of produce. E. coli is classified into eight phylogroups which differ in ecological niches, evolutionary history, and phenotypic properties. To understand the population genetic structure and composition of E. coli in primary production environments in Metro Manila, Philippines, a total of 80 E. coli recovered from irrigation water, soil, vegetables, and feces of cat, carabao, chicken, dog, and goat were allocated into distinct phylogroups based on the presence and absence of genetic markers. Results showed that the most prevalent phylogroup was B1 (71.3%), followed by A (18.6%), D (6.3%), B2 (1.3%), E (1.3%), and an unknown phylogroup (1.3%). The most prevalent genetic marker was arpA, followed by TspE4.C2, yjaA, and chuA. The carbapenem resistance of 24 E. coli isolates representing different phylogroups was also evaluated. Intriguingly, all isolates exhibited uniform susceptibility. This is the first report to provide insights into the phylogroup structure and composition, as well as carbapenem resistance of E. coli from primary production in the Philippines, which highlights possible source of and solution for gastrointestinal and enteric diseases.

Antibiotic resistance in the environment

Antibiotic resistance is a global health challenge, involving the transfer of bacteria and genes between humans, animals and the environment. Although multiple barriers restrict the flow of both bacteria and genes, pathogens recurrently acquire new resistance factors from other species, thereby reducing our ability to prevent and treat bacterial infections. Evolutionary events that lead to the emergence of new resistance factors in pathogens are rare and challenging to predict, but may be associated with vast ramifications. Transmission events of already widespread resistant strains are, on the other hand, common, quantifiable and more predictable, but the consequences of each event are limited. Quantifying the pathways and identifying the drivers of and bottlenecks for environmental evolution and transmission of antibiotic resistance are key components to understand and manage the resistance crisis as a whole. In this Review, we present our current understanding of the roles of the environment, including antibiotic pollution, in resistance evolution, in transmission and as a mere reflection of the regional antibiotic resistance situation in the clinic. We provide a perspective on current evidence, describe risk scenarios, discuss methods for surveillance and the assessment of potential drivers, and finally identify some actions to mitigate risks.

Treated wastewater suitability for reuse in comparison to groundwater and surface water in a peri-urban area: Implications for water quality management

The climate change and population growth led to a severe water shortage that limits fresh water availability in some areas of Togo. Thus, the farmers of Adjougba District have no other choice than using treated wastewater as an alternative for irrigated agriculture. The purpose of this study is to compare the suitability of three types of water for uses with identification of the reliable parameters in the assessment of water suitability for irrigation and domestic purposes. The raw water quality parameters, water quality indices (WQIs) and water suitability indicators for irrigation purpose (WSI-IPs) were applied for the comparison while statistical analysis and, with some experts' consensus were used to identify reliable parameters. The results suggested that the treated wastewater is more suitable than groundwater for irrigation purpose. Treated wastewater constitutes a viable fertilizer supply and is placed like surface water from permissible to excellent classes according to WSI-IPs values. The sodium absorption ratio (SAR), electrical conductivity (EC), residual sodium carbonate (RSC), Cl^- and faecal coliforms (FC) are the most reliable parameters in the detection of water suitability for irrigation purpose. EC, DO, pH, turbidity or TSS, COD or COD_Mn, hardness, FC, NO₃^-, national sanitation foundation's water quality index (NSFWQI), and overall index of pollution (OPI) are the most reliable in the detection of water suitability for domestic use. The reliable parameters identified in this study are potential candidates for the development of a single water quality index for both irrigation and domestic uses in Adjougba District. However further study will be necessary for the identification of reliable parameters and the development of a water quality index at the country scale.

Salmonella Enteritidis survival in different temperatures and nutrient solution pH levels in hydroponically grown lettuce

Due to climate change, with contaminated and less fertile soils, and intense weather phenomena, a turn towards hydroponic vegetable production has been made. Hydroponic cultivation of vegetables is considered to be a clean, safe and environmentally friendly growing technique; however, incidence of microbial contamination i.e. foodborne pathogens, might occur, endangering human health. The aim of this study was to investigate the effects of different plant growth stages, pH (values 5, 6, 7, 8) and bacterial inoculum levels (3 and 6 log cfu/mL) on hydroponically cultivated lettuce spiked with Salmonella Enteritidis. The results revealed that the pH and inoculum levels affected the internalization and survival of the pathogen in the hydroponic environment and plant tissue. Younger plants were found to be more susceptible to pathogen internalization compared to older ones. Under the current growing conditions (hydroponics, pH and inoculum levels), no leaf internalization was observed at all lettuce growth stages, despite the bacterium presence in the hydroponic solution. Noticeably, bacteria load at the nutrient solution was lower in low pH levels. These results showed that bacterium presence initiates plant response as indicated by the increased phenols, antioxidants and damage index markers (H2O2, MDA) in order for the plant to resist contamination by the invader. Nutrient solution management can result in Taylor-made recipes for plant growth and possible controlling the survival and growth of S. Enteritidis by pH levels.

Agricultural practices in Brazilian organic farms and microbiological characteristics of samples collected along the production chain

AIMS

To gather data on agricultural practices in organic farms in Sao Paulo, Brazil, and evaluate their relationship with the microbiological characteristics of samples collected along the production chain.

METHODS AND RESULTS

Practices data were based on field observations and interviews with farmers in 10 selected organic lettuce producing farms. Counts of Enterobacteriaceae and surveys for Salmonella were performed in samples of lettuce (before and after washing), fertilizers, irrigation and washing water, all collected in the same farm. Water samples were also tested for total coliforms and generic Escherichia coli. Isolated Enterobacteriaceae were identified by MALDI-TOF MS. Contamination of lettuce was influenced by some agricultural practices: chicken manure-based fertilization resulted in higher Enterobacteriaceae counts in lettuce when compared to other types of manure, whereas pre-washed lettuces presented lower microbial counts than non-pre-washed samples. Salmonella was detected in one lettuce sample by qPCR. Escherichia coli was detected in all irrigation water samples. All sample types contained Enterobacteriaceae species commonly reported as opportunistic human pathogens.

CONCLUSIONS

The data highlight the need for improvement in the good agricultural practices in the studied farms.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides information on agricultural practices and microbiological characteristics of organic lettuce, contributing to the development of more accurate risk assessments.

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

AIMS

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

METHODS AND RESULTS

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

CONCLUSIONS

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

SIGNIFICANCE AND IMPACT OF THE STUDY

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

Microbiological safety of spinach throughout commercial supply chains in Gauteng Province, South Africa and characterization of isolated multidrug-resistant Escherichia coli

AIM

To investigate the microbiological quality, potential foodborne pathogen presence, and to phenotypically (antimicrobial resistance [AMR] profiles) and genotypically (DNA fingerprints and diarrhoeagenic genes) characterize Escherichia coli isolated throughout spinach production systems from farm-to-sale.

METHODS AND RESULTS

Samples (n = 288) were collected from two commercial supply chains using either river or borehole irrigation water. E. coli was enumerated throughout the chain where river water was directly used for overhead irrigation at levels between 0.00 and 3.22 log colony forming unit (CFU) g^-1 . Following enrichment, isolation and matrix-assisted laser desorption ionization time-of-flight mass spectrometry identification, E. coli was isolated from 22.57% (n = 65/288) of all samples. Salmonella spp. were isolated from 3% (n = 9/288) of river and irrigation water samples on one farm, and no Listeria monocytogenes was detected throughout the study. Of the 80 characterized E. coli isolates, one harboured the stx2 virulence gene, while 43.75% (n = 35) were multidrug resistant. Overall, 26.30% of the multidrug-resistant E. coli isolates were from production scenario one that used river irrigation water, and 17.50% from the second production scenario that used borehole irrigation water. A greater percentage of resistance phenotypes were from water E. coli isolates (52.50%), than isolates from spinach (37.50%). E. coli isolates from spinach and irrigation water clustered together at high similarity values (>90%) using enterobacterial repetitive intergenic consensus-polymerase chan reaction analysis.

CONCLUSIONS

This study reported the presence of multidrug-resistant environmental E. coli throughout spinach production from farm, during processing and up to retail. Furthermore, the similarity of multi-drug resistant E. coli isolates suggests transfer from irrigation water to spinach in both scenarios, reiterating that irrigation water for vegetables consumed raw, should comply with standardized microbiological safety guidelines.

SIGNIFICANCE AND IMPACT OF STUDY

Multidrug-resistant E. coli presence throughout spinach production emphasizes the necessity of increased surveillance of AMR in fresh produce and the production environment within a One Health paradigm to develop AMR mitigation strategies.

Disinfection/ammonia removal from aquaculture wastewater and disinfection of irrigation water using electrochemical flow cells: A case study in Hawaii

This field case study reports findings on disinfection/ammonia removal from aquaculture wastewater and disinfection of irrigation water carried out at an aquaculture farm and two irrigation locations in Hawaii. We used a flow cell incorporating PtRu/graphite anode and graphite cathode for the disinfection/ammonia removal from aquaculture wastewater, and a flow cell assembled with graphite plates as both anode and cathode for the disinfection of irrigation water. The removal of ammonia followed the indirect oxidation mechanism mediated by free chlorine electro-generated at the PtRu/graphite anode. Ammonia removal rate increased with the increase in NaCl concentration, applied current density, or flow rate. The disinfection of aquaculture wastewater can be readily achieved due to the presence of highly germicidal free chlorine species. The disinfection of irrigation water was realized without the addition of chemicals. The disinfection mechanism was attributed to the formation of free chlorine from the anodic oxidation of chloride ions naturally occurring in the water sources. The disinfection efficiency decreased with increasing organic matter concentration. In addition to the flow cell approach, we also successfully demonstrated the disinfection of irrigation water by adding electrolyzed NaCl solution or purging with a mixture of air and chlorine gas, both of which were generated on-site. PRACTITIONER POINTS: Field case study on disinfection/ammonia removal from aquaculture wastewater and disinfection of irrigation water was carried out in Hawaii. Electrochemical flow cell assembled with PtRu/graphite anode and graphite cathode effectively removes ammonia from aquaculture wastewater. Ammonia removal proceeds via the indirect oxidation mechanism mediated by free chlorine electro-generated at the PtRu/graphite anode. Electrochemical flow cell assembled with commercial graphite electrodes enables fast disinfection of coliform bacteria and E. coli. The primary disinfection mechanism is through chlorine species electro-generated from chloride oxidation at the graphite anode.

Tracing Antibiotic Resistance Genes along the Irrigation Water Chain to Chive: Does Tap or Surface Water Make a Difference?

Irrigation water is well known as potential source of pathogens in fresh produce. However, its role in transferring antibiotic resistance determinants is less well investigated. Therefore, we analyzed the contribution of surface and tap water to the resistome of overhead-irrigated chive plants. Field-grown chive was irrigated with either surface water (R-system) or tap water (D-system), from planting to harvest. Water along the two irrigation chains as well as the respective plants were repeatedly sampled and screened for 264 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), using high-capacity qPCR. Differentially abundant (DA) ARGs were determined by comparing the two systems. On R-chive, β-lactam ARGs, multidrug-resistance (MDR) determinants, and MGEs were most abundant, while D-chive featured DA ARGs from the vancomycin class. Diversity and number of DA ARGs was the highest on young chives, strongly diminished at harvest, and increased again at the end of shelf life. Most ARGs highly enriched on R- compared to D-chive were also enriched in R- compared to D-sprinkler water, indicating that water played a major role in ARG enrichment. Of note, blaKPC was detected at high levels in surface water and chive. We conclude that water quality significantly affects the resistome of the irrigated produce.

Survival of Escherichia coli and Listeria innocua on Lettuce after Irrigation with Contaminated Water in a Temperate Climate

Microbial disease outbreaks related to fresh produce consumption, including leafy green vegetables, have increased in recent years. Where contamination occurs, pathogen persistence may represent a risk for consumers' health. This study analysed the survival of E. coli and L. innocua on lettuce plants watered with contaminated irrigation water via a single irrigation event and within stored irrigation water. Separate lettuce plants (Lactuca sativa var. capitata) were irrigated with water spiked with Log₁₀ 7 cfu/mL of each of the two strains and survival assessed via direct enumeration, enrichment and qPCR. In parallel, individual 20 L water microcosms were spiked with Log₁₀ 7 cfu/mL of the individual strains and sampled at similar time points. Both strains were observed to survive on lettuce plants up to 28 days after inoculation. Direct quantification by culture methods showed a Log₁₀ 4 decrease in the concentration of E. coli 14 days after inoculation, and a Log₁₀ 3 decrease in the concentration of L. innocua 10 days after inoculation. E. coli was detected in water samples up to 7 days after inoculation and L. innocua was detected up to 28 days by direct enumeration. Both strains were recovered from enriched samples up to 28 days after inoculation. These results demonstrate that E. coli and L. innocua strains are able to persist on lettuce after a single contamination event up until the plants reach a harvestable state. Furthermore, the persistence of E. coli and L. innocua in water for up to 28 days after inoculation illustrates the potential for multiple plant contamination events from stored irrigation water, emphasising the importance of ensuring that irrigation water is of a high quality.

Foodborne Illness Outbreak Investigation for One Health Postsecondary Education

One Health concepts were incorporated in a foodborne disease outbreak investigation with game features of data presented as visual and manipulative clues. Postsecondary pre-veterinary medicine and animal biosciences students and food science students (n = 319) enrolled in an introductory animal and food sciences course over a 3-year period received a brief introduction to foodborne illness, an outbreak scenario, and investigative tasks to complete individually or in groups. Tasks addressed epidemiology, laboratory, environment, traceback, recall, and prevention concepts. Gamification of the exercise involved generation of a numerical code to unlock a combination lock as an indication of successful organization, compilation, and interpretation of data. Students presented investigation findings and responses to critical thought questions on their roles. Student surveys on engagement and self-perceived change in conceptual understanding indicated that nearly all expressed increased understanding of outbreak investigations, safe food production, and environmental water as a transmission vehicle. Volunteered learned concepts indicated enhanced appreciation for the complexity of food safety and interdisciplinary connections. Students enjoyed the exercise (92%) and cited the clues and group interaction among the most enjoyable features. Objective assessment of student conceptual learning with the subset of students who conducted the investigation individually (n = 58) demonstrated significant increase in correct test responses (49% pretest; 76% posttest) after completion of the investigation for all questions combined and across all learning objectives. These data demonstrate the value of a foodborne disease investigation with escape room gamification features for engaging students in One Health concepts and exercising problem-solving, critical thinking, and skills for independent and collaborative work.

Nationwide Assessment of Water Quality in Rivers across Lebanon by Quantifying Fecal Indicators Densities and Profiling Antibiotic Resistance of Escherichia coli

The use of contaminated water has been associated with severe disease outbreaks. Due to widespread pollution with untreated sewage, concerns have been raised over water quality in Lebanon, a country with well-documented challenges in infrastructure. Here, we evaluated the water quality of major rivers in Lebanon by quantifying the densities of fecal indicator bacteria (fecal coliforms and Escherichia coli). Additionally, we assessed the dissemination of antibiotic-resistant E. coli in river water. Composite water samples (n = 132) were collected from fourteen rivers, and 378 E. coli were isolated and analyzed. Fecal coliforms and E. coli were detected in 96.29% and 95.5% of the samples, respectively. Additionally, 73.48–61.3% and 31.81% of the samples exceeded the microbiological acceptability standards for irrigation and the fecal coliform limit for recreational activities, respectively. The E. coli exhibited resistance to ampicillin (40% of isolates), amoxicillin + clavulanic acid (42%), cefepime (4%), cefotaxime (14%), cefalexin (46%), cefixime (17%), doripenem (0.3%), imipenem (0.5%), gentamicin (6%), kanamycin (9%), streptomycin (35%), tetracycline (35%), ciprofloxacin (10%), norfloxacin (7%), trimethoprim-sulfamethoxazole (32%), and chloramphenicol (13%). Notably, 45.8% of the isolates were classified as multidrug resistant (MDR). Our results highlight the need to urgently address fecal pollution and the dissemination of antibiotic resistance in Lebanese rivers.

Pathogen and Surrogate Survival in Relation to Fecal Indicator Bacteria in Freshwater Mesocosms

The microbial quality of agricultural water for fresh produce production is determined by the presence of the fecal indicator bacterium (FIB) Escherichia coli, despite poor correlations with pathogen presence. Additional FIB, such as enterococci, have been utilized for assessing water quality. The study objective was to determine the survival times (first time to detect zero or censored) of FIB (E. coli and enterococci), surrogates (Listeria innocua, Listeria seeligeri, Salmonella enterica serovar Typhimurium, and PRD1), and pathogens (four strains each of pathogenic E. coli and Listeria monocytogenes and five Salmonella serovars) simultaneously inoculated in freshwater mesocosms exposed to diel and seasonal variations. Six separate mesocosm experiments were conducted for ≤28 days each season, with samples (sediment/water) collected each day for the first 7 days and weekly thereafter. Microorganisms survived significantly longer in sediment than in water (hazard ratio [HR] for water/sediment is 2.2; 95% confidence interval [CI], 1.79 to 2.71). Also, FIB E. coli survived significantly longer than FIB enterococcus (HR for enterococci/E. coli is 12.9 [95% CI, 8.18 to 20.37]) after adjusting for the sediment/water and lake/river effects. Differences in the area under the curve (calculated from log CFU or PFU over time) were used to assess pathogen and surrogate survival in relation to FIB. Despite sample type (sediment/water) and seasonal influences, survival rates of pathogenic Salmonella serovars were similar to those of FIB E. coli, and survival rates of L. monocytogenes and pathogenic E. coli were similar to those of FIB enterococci. Further investigation of microbial survival in water and sediment is needed to determine which surrogates are best suited to assess pathogen survival in agricultural water used in irrigation water for fresh produce. IMPORTANCE Contamination of fresh produce via agricultural water is well established. This research demonstrates that survival of fecal indicator bacteria, pathogenic microorganisms, and other bacterial and viral surrogates in freshwater differs by sample type (sediment/water) and season. Our work highlights potential risks associated with pathogen accumulation and survival in sediment and the possibility for resuspension and contamination of agricultural water used in fresh produce production. Specifically, a greater microbial persistence in sediments than in water over time was observed, along with differences in survival among microorganisms in relation to the fecal indicator bacteria E. coli and enterococci. Previous studies compared data among microbial groups in different environments. Conversely, fecal indicator bacteria, surrogates, and pathogenic microorganisms were assessed within the same water and sediment mesocosms in the present study during four seasons, better representing the agricultural aquatic environment. These data should be considered when agricultural microbial water quality criteria in fresh produce operations are being determined.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Treated Wastewater Irrigation—A Review

As the most important resource for life, water has been a central issue on the international agenda for several decades. Yet, the world’s supply of clean freshwater is steadily decreasing due to extensive agricultural demand for irrigated lands. Therefore, water resources should be used with greater efficiency, and the use of non-traditional water resources, such as Treated Wastewater (TW), should be increased. Reusing TW could be an alternative option to increase water resources. Thus, many countries have decided to turn wastewater into an irrigation resource to help meet urban demand and address water shortages. However, because of the nature of that water, there are potential problems associated with its use in irrigation. Some of the major concerns are health hazards, salinity build-up, and toxicity hazards. The objectives of this comprehensive literature review are to illuminate the importance of using TW in irrigation as an alternative freshwater source and to assess the effects of its use on soil fertility and other soil properties, plants, and public health. The literature review reveals that TW reuse has become part of the extension program for boosting water resource utilization. However, the uncontrolled application of such waters has many unfavorable effects on both soils and plants, especially in the long-term. To reduce these unfavorable effects when using TW in irrigation, proper guidelines for wastewater reuse and management should be followed to limit negative effects significantly.

Assessment of microbial risk during Australian industrial practices for Escherichia coli O157:H7 in fresh cut-cos lettuce: A stochastic quantitative approach

Escherichia coli O157:H7 risk associated with the consumption of fresh cut-cos lettuce during Australian industrial practices was assessed. A probabilistic risk assessment model was developed and implemented in the @Risk software by using the Monte Carlo simulation technique with 1,000,000 iterations. Australian preharvest practices yielded predicted annual mean E. coli O157:H7 levels from 0.2 to -3.4 log CFU/g and prevalence values ranged from 2 to 6.4%. While exclusion of solar radiation from the baseline model yielded a significant increase in concentration of E. coli O157:H7 (-5.2 -log fold), drip irrigation usage, exclusion of manure amended soil and rainfall reduced E. coli O157:H7 levels by 7.4, 6.5, and 4.3-log fold, respectively. The microbial quality of irrigation water and irrigation type both had a significant effect on E. coli O157:H7 concentrations at harvest (p < 0.05). The probability of illness due to consumption of E. coli O157:H7 contaminated fresh cut-cos lettuce when water washing interventions were introduced into the processing module, was reduced by 1.4-2.7-log fold (p < 0.05). This study provides a robust basis for assessment of risk associated with E. coli O157:H7 contamination on fresh cut-cos lettuce for industrial practices and will assist the leafy green industry and food safety authorities in Australia to identify potential risk management strategies.

Expiration Date of Ready-to-Eat Salads: Effects on Microbial Load and Biochemical Attributes

When minimally processed vegetables reach their expiration date, expose an increased microbial load. This includes mainly spoilage microorganisms but also foodborne pathogens, thus affecting the quality and safety of highly consumed ready-to-eat salads. A total of 144 ready-to-eat salads from the Cypriot market were analyzed in an attempt to determine the effects of the expiration date on the microbial load and plant metabolic variables of the salads. Possible correlations between them were also investigated for the first time. Furthermore, the impacts of the season (winter, summer), salad producing companies and type of salad and/or their interactions with the tested parameters were investigated. Results revealed that the microbial load (mainly spoilage microorganisms, such as Pseudomonas spp., yeasts and molds) increased towards the end of the shelf life. The microbial load was differentiated among the five salad producers and/or the salad types, highlighting the importance of a common and safe sanitation-processing chain in the preparation of ready-to-eat salads. Summer was the season in which Escherichia coli counts were found to be higher for plain lettuce, while Staphylococcus spp. was increased numbers for the lettuce+endive/radicchio, lettuce+rocket and lettuce+chives type of salads. Additionally, an increased Staphylococcus spp. was observed for plain rocket salads in winter. All samples examined were found negative for Salmonella enterica and Listeria monocytogenes. Moreover, carbon dioxide production and damage indexes (hydrogen peroxide and lipid peroxidation) increased on expiration date on both winter and summer seasons, indicating plant tissue stress at the end of shelf life. These findings indicate that the expiration date and relevant shelf life of processed vegetables are important parameters to be considered when postharvest management is applied to these products, ensuring safety and quality.

Shiga Toxin-Producing Escherichia coli in the Long-Term Survival Phase Exhibit Higher Chlorine Tolerance and Less Sublethal Injury Following Chlorine Treatment of Romaine Lettuce

The extent of chlorine inactivation and sublethal injury of stationary-phase (STAT) and long-term survival-phase (LTS) cells of Shiga toxin-producing Escherichia coli (STEC) in vitro and in a lettuce postharvest wash model was investigated. Four STEC strains were cultured in tryptic soy broth supplemented with 0.6% (w/v) yeast extract (TSBYE; 35°C) for 24 h and 21 d to obtain STAT and LTS cells, respectively. Minimum bactericidal concentration (MBC) and dose-response assays were performed to determine chlorine's antibacterial efficacy against STAT and LTS cells. Chlorine solutions (pH 6.5) and romaine lettuce were each inoculated with STAT and LTS cells to obtain initial populations of ∼7.8 log colony-forming units (CFU)/mL. Survivors in chlorine solutions were determined after 30 s. Inoculated lettuce samples were held at 22°C ± 1°C for 2 h or 20 h and then exposed to chlorine (10-40 ppm) for 60 s. Survivors were enumerated on nonselective and selective agar media following incubation (35°C, 48 h). The MBC for STAT and LTS cells was 0.04 and 0.08 ppm, respectively. Following exposure (30 s) to chlorine at 2.5, 5.0, and 10 ppm, STAT cells were reduced to <1.0 log CFU/mL, whereas LTS survivors were at 5.10 (2.5 ppm), 3.71 (5.0 ppm), and 2.55 (10 ppm) log CFU/mL. At 20 and 40 ppm chlorine, greater log CFU reductions of STAT cells (1.64 and 1.85) were observed compared with LTS cells (0.94 and 0.83) after 2 h of cell contact with lettuce (p < 0.05), but not after 20 h. Sublethal injury in STEC after chlorine (40 ppm) treatment was lower in LTS compared with STAT survivors (p < 0.05). Compared with STAT cells, LTS cells of STEC seem to have higher chlorine tolerance as planktonic cells and as attached cells depending on cell contact time on lettuce. In addition, a higher percentage of LTS cells, compared with STAT cells, survive in a noninjured state after chlorine (40 ppm) treatment of lettuce.