The growing season, but not the farming system, is a food safety risk determinant for leafy greens in the mid-Atlantic region of the United States

Effects of plants-associated microbiota on cultivation and quality of Chinese herbal medicines

Microbial resource influences the life activities of medicinal plants from several perspectives. Endophytes, rhizosphere microorganisms, and other environmental microorganisms play essential roles in medicinal plant growth and development, plant yield, and clinical efficacy. The microbiota can influence the biosynthesis of active compounds in medicinal plants by stimulating specific metabolic pathways. They induce host plants to improve their resistance to environmental stresses by accumulating secondary metabolites. Microorganisms can interact with their host plants to produce long-term, targeted selection results and improve their ability to adapt to the environment. Due to the interdependence and interaction between microorganisms and medicinal plants, Chinese herbal medicines (CHMs) quality is closely related to the associated microorganisms. This review summarizes the relationship between medicinal plants and their associated microorganisms, including their species, distribution, life activities, and metabolites. Microorganisms can aid in quality control, improve the efficacy of medicinal plants, and provide markers for identifying the origin and storage time of CHMs. Therefore, a comprehensive understanding of the relationship between microorganisms and medicinal plants will help to control the quality of CHMs from different perspectives.

Applied microbiology of the phyllosphere

The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.

Effects of Fumigation on the Reduction of Salmonella enterica in Soil

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

Effect of pre-harvest sanitizer treatments on Listeria survival, sensory quality and bacterial community dynamics on leafy green vegetables grown under commercial conditions

Leafy green vegetables (LGVs) have large surface areas and can be colonized by various microorganisms including pathogens. In this study, we investigated the effect of pre-harvest sanitizer treatments on the survival of inoculated proxy pathogen Listeria innocua ATCC 33090 and the natural microbial community of mizuna, rocket (arugula), red chard and spinach grown under commercial conditions. Electrolyzed water (e-water), peracetic acid (PAA), and 1-bromo-3-chloro-5-dimethylhydantoin (BCDMH) were tested against water controls. We also observed the subsequent sensorial changes of harvested, bagged LGV leaves over a period of 12 days within chill storage alongside the growth, diversity and structure of bacterial populations determined using 16S rRNA gene amplicon sequencing and total viable counts (TVC). Treatment with PAA resulted in the highest reductions of L. innocua (2.4-5.5 log units) compared to the other treatments (0.25-2.5 log units). On day 0 (24 h after sanitizer application), the TVC on sanitizer treated LGVs were significantly reduced compared to water controls, except for rocket. During storage at 4.5 (±0.5)°C sanitisers only hindered microbial growth on LGVs initially and did not influence final bacterial population levels, growth rates or changes in LGV sample colour, decay, odour and texture compared to water controls. Shelf-life was not extended nor was it reduced. The community structure on LGV types differed though a core set of bacterial amplicon sequence variants (ASV) were present across all samples. No significant differences were observed in bacterial diversity between sanitizer treatments, however sanitizer treated LGV samples had initially reduced diversity compared to water treated samples. The bacterial compositions observed at the end point of storage considerably differed from what was observed at initial point owing to the increase in abundance of specific bacterial taxa, mainly Pseudomonas spp., the abundance and growth responses differing between LGV types studied. This study provides a better understanding on the microbiology and sensory impact of pre-harvest applied sanitiser treatments on different LGVs destined for commercial food use.

Aggregative Soil Sampling Using Boot Covers Compared to Soil Grabs From Commercial Romaine Fields Shows Similar Indicator Organism and Microbial Community Recoveries

Aggregative boot cover sampling may be a more representative, practical, and powerful method for preharvest produce soil testing than grab sampling because boot covers aggregate soil from larger areas. Our study tests if boot cover sampling results reflect quality and safety indicator organisms and community diversity of grab sampling. We collected soil samples from commercial romaine lettuce fields spanning 5060 m2 using boot covers (n = 28, m = 1.1 ± 0.4 g; wearing boot covers and walking along the path), composite grabs (n = 28, m = 231 ± 24 g; consisting of 60 grabs of 3-5 g each), and high-resolution grabs (n = 72, m = 56 ± 4 g; taking one sample per stratum). Means and standard deviations of log-transformed aerobic plate counts (APCs) were 7.0 ± 0.3, 7.1 ± 0.2, and 7.3 ± 0.2 log(CFU/g) for boot covers, composite grabs, and high-resolution grabs, respectively. APCs did not show biologically meaningful differences between sample types. Boot covers recovered on average 0.6 log(CFU/g) more total coliforms than both grabs (p < 0.001) where means and standard deviations of log-transformed counts were 3.2 ± 1.0, 2.6 ± 0.6, and 2.6 ± 1.0 log(CFU/g) for boot covers, composite grabs, and high-resolution grabs, respectively. There were no generic E. coli detected in any sample by enumeration methods with LODs of 1.3-2.1 log(CFU/g) for boot covers and 0.5 log(CFU/g) for both grabs. By 16S rRNA sequencing, community species diversity (alpha diversity) was not significantly different within collection methods. While communities differed (p < 0.001) between soil sampling methods (beta diversity), variance in microbial communities was not significantly different. Of the 28 phyla and 297 genera detected, 25 phyla (89%) and 258 genera (87%) were found by all methods. Overall, aggregative boot cover sampling is similar to both grab methods for recovering quality and safety indicator organisms and representative microbiomes. This justifies future work testing aggregative soil sampling for foodborne pathogen detection.

Absence of Shiga toxin-producing Escherichia coli (STEC) in organic leafy greens from the metropolitan region of São Paulo, Brazil

Shiga toxin-producing Escherichia coli (STEC) is an important pathogen with public health implications, including its potential association with vegetables. In this study, we investigated the presence of STEC in vegetables obtained from organic producers located in São Paulo city, Brazil. As part of a routine surveillance study conducted over (years of isolation), a total of 200 samples of organic vegetables were screened using biochemical and PCR methods. Among the vegetable samples tested, 30 (15%) were positive for non-Shiga toxin-producing E. coli. While no STEC was detected in the organic vegetables in this study, the presence of non-STEC in vegetables raises concerns about the lack of proper hygiene practices during vegetable handling. This contamination represents a public health risk, particularly considering that these isolates can still be pathogenic, and vegetables are often consumed raw. To address this important issue, continuous monitoring of these farms is recommended to ensure the quality and safety of organic vegetables produced for both domestic consumption and exportation.

Salmonella and other Enterobacteriaceae in conventional and organic vegetables grown in Brazilian farms

This study aimed to assess the microbiological profile of conventional and organic vegetables grown in Brazilian farms through the detection of Salmonella and other Enterobacteriaceae. A total of 200 samples (100 conventional and 100 organic), including leafy greens, spices/herbs, and other unusual vegetables, were submitted to the enumeration of Enterobacteriaceae by plating on VRBG agar. Moreover, colonies of Enterobacteriaceae were randomly selected and submitted to identification by MALDI-TOF MS. Samples were also tested for Salmonella, using culture-based and PCR-based enrichment methods. The mean counts of Enterobacteriaceae in conventional and organic vegetables were 5.1 ± 1.5 and 5.4 ± 1.4 log CFU/g, respectively (P > 0.05). A total of 18 genera (including 38 species) of Enterobacteriaceae were identified, and the most frequent ones found in samples from both farming systems were Enterobacter (76%) and Pantoea (68%). Salmonella was identified in 17 samples (8.5%): nine (4.5%) in conventional and eight (4.0%) in organic vegetables. These results indicate that the farming system had no impact on the Enterobacteriaceae populations and rates of Salmonella and revealed unsatisfactory microbiological safety of some samples, mainly due to the presence of Salmonella. These findings highlight the need for control measures during vegetable production, regardless of the farming system, to reduce microbial contamination and the risks of foodborne illnesses.

Risk factors associated with the prevalence of Shiga-toxin-producing Escherichia coli in manured soils on certified organic farms in four regions of the USA

Introduction

Biological soil amendments of animal origin (BSAAO), including untreated amendments are often used to improve soil fertility and are particularly important in organic agriculture. However, application of untreated manure on cropland can potentially introduce foodborne pathogens into the soil and onto produce. Certified organic farms follow the USDA National Organic Program (NOP) standards that stipulate a 90- or 120-day interval between application of untreated manure and crop harvest, depending on whether the edible portion of the crop directly contacts the soil. This time-interval metric is based on environmental factors and does not consider a multitude of factors that might affect the survival of the main pathogens of concern. The objective of this study was to assess predictors for the prevalence of Shiga-toxin-producing Escherichia coli (non-O157 STEC) in soils amended with untreated manure on USDA-NOP certified farms.

Methods

A longitudinal, multi-regional study was conducted on 19 farms in four USA regions for two growing seasons (2017–2018). Untreated manure (cattle, horse, and poultry), soil, and irrigation water samples were collected and enrichment cultured for non-O157 STEC. Mixed effects logistic regression models were used to analyze the predictors of non-O157 STEC in the soil up to 180 days post-manure application.

Results and discussion

Results show that farm management practices (previous use with livestock, presence of animal feces on the field, season of manure application) and soil characteristics (presence of generic E. coli in the soil, soil moisture, sodium) increased the odds of STEC-positive soil samples. Manure application method and snowfall decreased the odds of detecting STEC in the soil. Time-variant predictors (year and sampling day) affected the presence of STEC. This study shows that a single metric, such as the time interval between application of untreated manure and crop harvest, may not be sufficient to reduce the food safety risks from untreated manure, and additional environmental and farm-management practices should also be considered. These findings are of particular importance because they provide multi-regional baseline data relating to current NOP wait-time standards. They can therefore contribute to the development of strategies to reduce pathogen persistence that may contribute to contamination of fresh produce typically eaten raw from NOP-certified farms using untreated manure.

A longitudinal study to examine the influence of farming practices and environmental factors on pathogen prevalence using structural equation modeling

The contamination of fresh produce with foodborne pathogens has been an on-going concern with outbreaks linked to these commodities. Evaluation of farm practices, such as use of manure, irrigation water source, and other factors that could influence pathogen prevalence in the farming environment could lead to improved mitigation strategies to reduce the potential for contamination events. Soil, water, manure, and compost were sampled from farms in Ohio and Georgia to identify the prevalence of Salmonella, Listeria monocytogenes (Lm), Campylobacter, and Shiga-toxin-producing Escherichia coli (STEC), as well as Arcobacter, an emerging human pathogen. This study investigated agricultural practices to determine which influenced pathogen prevalence, i.e., the percent positive samples. These efforts identified a low prevalence of Salmonella, STEC, and Campylobacter in soil and water (< 10%), preventing statistical modeling of these pathogens. However, Lm and Arcobacter were found in soil (13 and 7%, respectively), manure (49 and 32%, respectively), and water samples (18 and 39%, respectively) at a comparatively higher prevalence, suggesting different dynamics are involved in their survival in the farm environment. Lm and Arcobacter prevalence data, soil chemical characteristics, as well as farm practices and weather, were analyzed using structural equation modeling to identify which factors play a role, directly or indirectly, on the prevalence of these pathogens. These analyses identified an association between pathogen prevalence and weather, as well as biological soil amendments of animal origin. Increasing air temperature increased Arcobacter and decreased Lm. Lm prevalence was found to be inversely correlated with the use of surface water for irrigation, despite a high Lm prevalence in surface water suggesting other factors may play a role. Furthermore, Lm prevalence increased when the microbiome's Simpson's Diversity Index decreased, which occurred as soil fertility increased, leading to an indirect positive effect for soil fertility on Lm prevalence. These results suggest that pathogen, environment, and farm management practices, in addition to produce commodities, all need to be considered when developing mitigation strategies. The prevalence of Arcobacter and Lm versus the other pathogens suggests that multiple mitigation strategies may need to be employed to control these pathogens.

Meta-analysis of the prevalence of the main human pathogens in vegetables, with emphasis on lettuce

This meta-analysis aims to summarize the available information on the prevalence of the main human pathogenic microorganisms in vegetables, with emphasis on lettuce (Lactuca sativa). The database searches included scientific papers from 1980 to 2019, without language restrictions. Inclusion criteria were prevalence or incidence studies published in peer-reviewed journals reporting the total number of vegetable samples studied and the number of samples positive for the presence of the studied pathogens. The target pathogens were grouped into the following categories: bacteria, parasites and viruses. Results of different vegetable types, years of sampling, analyzed regions or species of microorganisms reported in the same article were considered as different studies. Therefore, each scientific article may contain several studies. Multilevel random-effect meta-analysis models were fitted to estimate the mean occurrence rate of pathogenic microorganisms and to compare them with different factors potentially associated with the outcome. Overall, the prevalence of bacterial, parasitic and viral pathogens in vegetables was relatively low. The mean prevalence of bacterial hazards was < 0.023, with the exception of S. aureus, whose prevalence was estimated at 0.096. The mean occurrence rates of parasites and viruses were 0.067 (95 % CI: 0.056-0.080) and 0.079 (95 % CI: 0.054-0.113), respectively. The prevalence of pathogenic E. coli and parasites increased as the year of publication of the scientific articles progressed, whereas the prevalence of the other bacterial pathogens and enteric viruses was steady. The types of vegetables evaluated did not affect pathogen prevalence. The prevalence of pathogenic microorganisms differed according to the continent of origin, except for E. coli O157:H7 and parasites. The prevalence of pathogens in vegetables is of public health importance, especially in vegetable types that are eaten raw, without thermal treatment to inactivate pathogens. This meta-analysis results show the need to apply proper sanitation methods to treat raw vegetables in order to avoid foodborne infections.

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

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

Detection of Toxoplasma gondii oocysts on organic and conventionally grown produce

Toxoplasma gondii infection can result in toxoplasmosis and potential psychological effects. Research commonly focuses on infection through contact with cat fecal matter or consumption of contaminated meat. However, T. gondii oocysts can persist in the environment for years and may be present in soils and on soil-grown produce. Rates of oocyst DNA recovery from produce were high, with 18% of vegetable samples testing positive for T. gondii via PCR test and melt curve analysis. Radishes had significantly higher oocyst counts than arugula, collard greens, kale, lettuce, and spinach. There were no significant differences in oocyst detection rates between samples taken from organic farmer's markets and conventional grocery stores. This study demonstrates that these oocysts can transfer to produce grown both conventionally and using organic techniques.

A review of chemical and microbial contamination in food: What are the threats to a circular food system?

A circular food system is one in which food waste is processed to recover plant nutrients and returned to the soil to enable the production of more food, rather than being diverted to landfill or incineration. The approach may be used to reduce energy and water use in food production and contribute to the sustainability of the system. Anaerobic digestion and composting are common food waste treatment technologies used to stabilize waste and produce residual materials that can replenish the soil, thus contributing to a circular food system. This approach can only be deemed safe and feasible, however, if food waste is uncontaminated or any contaminants are destroyed during treatment. This review brings together information on several contaminant classes at different stages of the food supply chain, their possible sources, and their fates during composting and digestion. The main aim is to identify factors that could impede the transition towards a safe, reliable and efficient circular food system. We investigated heavy metals, halogenated organic compounds, foodborne pathogens and antibiotic resistance genes (ARGs) in the food system and their fates during digestion and composting. Production and processing stages were identified as major entry points for these classes of contaminants. Heavy metals and foodborne pathogens pose less risk in a circular system than halogenated organics or antibiotic resistance. Given the diversity of properties among halogenated organic compounds, there is conflicting evidence about their fate during treatment. There are relatively few studies on the fate of ARGs during treatment, and these have produced variable results, indicating a need for more research to clarify their fate in the final products. Repeated land application of contaminated food waste residuals can increase the risk of accumulation and jeopardize the safety of a circular food system. Thus, careful management of the system and research into the fate of the contaminants during treatment is needed.

Are we overestimating risk of enteric pathogen spillover from wild birds to humans?

Enteric illnesses remain the second largest source of communicable diseases worldwide, and wild birds are suspected sources for human infection. This has led to efforts to reduce pathogen spillover through deterrence of wildlife and removal of wildlife habitat, particularly within farming systems, which can compromise conservation efforts and the ecosystem services wild birds provide. Further, Salmonella spp. are a significant cause of avian mortality, leading to additional conservation concerns. Despite numerous studies of enteric bacteria in wild birds and policies to discourage birds from food systems, we lack a comprehensive understanding of wild bird involvement in transmission of enteric bacteria to humans. Here, we propose a framework for understanding spillover of enteric pathogens from wild birds to humans, which includes pathogen acquisition, reservoir competence and bacterial shedding, contact with people and food, and pathogen survival in the environment. We place the literature into this framework to identify important knowledge gaps. Second, we conduct a meta‐analysis of prevalence data for three human enteric pathogens, Campylobacter spp., E. coli, and Salmonella spp., in 431 North American breeding bird species. Our literature review revealed that only 3% of studies addressed the complete system of pathogen transmission. In our meta‐analysis, we found a Campylobacter spp. prevalence of 27% across wild birds, while prevalence estimates of pathogenic E. coli (20%) and Salmonella spp. (6.4%) were lower. There was significant bias in which bird species have been tested, with most studies focusing on a small number of taxa that are common near people (e.g. European starlings Sturnus vulgaris and rock pigeons Columba livia) or commonly in contact with human waste (e.g. gulls). No pathogen prevalence data were available for 65% of North American breeding bird species, including many commonly in contact with humans (e.g. black‐billed magpie Pica hudsonia and great blue heron Ardea herodias), and our metadata suggest that some under‐studied species, taxonomic groups, and guilds may represent equivalent or greater risk to human infection than heavily studied species. We conclude that current data do not provide sufficient information to determine the likelihood of enteric pathogen spillover from wild birds to humans and thus preclude management solutions. The primary focus in the literature on pathogen prevalence likely overestimates the probability of enteric pathogen spillover from wild birds to humans because a pathogen must survive long enough at an infectious dose and be a strain that is able to colonize humans to cause infection. We propose that future research should focus on the large number of under‐studied species commonly in contact with people and food production and demonstrate shedding of bacterial strains pathogenic to humans into the environment where people may contact them. Finally, studies assessing the duration and intensity of bacterial shedding and survival of bacteria in the environment in bird faeces will help provide crucial missing information necessary to calculate spillover probability. Addressing these essential knowledge gaps will support policy to reduce enteric pathogen spillover to humans and enhance bird conservation efforts that are currently undermined by unsupported fears of pathogen spillover from wild birds.

Prevalence and risk factors associated with Campylobacter spp. and Salmonella enterica in livestock raised on diversified small-scale farms in California

Diversified farms are operations that raise a variety of crops and/or multiple species of livestock, with the goal of utilising the products of one for the growth of the other, thus fostering a sustainable cycle. This type of farming reflects consumers' increasing demand for sustainably produced, naturally raised or pasture-raised animal products that are commonly produced on diversified farms. The specific objectives of this study were to characterise diversified small-scale farms (DSSF) in California, estimate the prevalence of Salmonella enterica and Campylobacter spp. in livestock and poultry, and evaluate the association between farm- and sample-level risk factors and the prevalence of Campylobacter spp. on DSSF in California using a multilevel logistic model. Most participating farms were organic and raised more than one animal species. Overall Salmonella prevalence was 1.19% (95% confidence interval (CI95) 0.6-2), and overall Campylobacter spp. prevalence was 10.8% (CI95 = 9-12.9). Significant risk factors associated with Campylobacter spp. were farm size (odds ratio (OR)10-50 acres: less than 10 acres = 6, CI95 = 2.11-29.8), ownership of swine (OR = 9.3, CI95 = 3.4-38.8) and season (ORSpring: Coastal summer = 3.5, CI95 = 1.1-10.9; ORWinter: Coastal summer = 3.23, CI95 = 1.4-7.4). As the number of DSSF continues to grow, evaluating risk factors and management practices that are unique to these operations will help identify risk mitigation strategies and develop outreach materials to improve the food safety of animal and vegetable products produced on DSSF.

Salmonella spp. and Escherichia coli O157:H7 prevalence and levels on lettuce: A systematic review and meta-analysis

Lettuce (Lactuca sativa), one of the most consumed leafy vegetables in the world, is frequently implicated with foodborne disease (FBD) outbreaks, with Salmonella spp. and Escherichia coli O157:H7 being the most common bacteria to cause this illness. Estimates of prevalence and levels of these pathogens on lettuce are scarce in developed or in developing countries, which hinders risk assessment attempts. In here, we present a systematic review and meta-analysis of reported prevalence and levels of Salmonella spp. and E. coli O157:H7 on lettuce using the worldwide available data. Literature was reviewed and examined the results for inclusion of articles in the meta-analysis. Data (prevalence and/or concentration of Salmonella spp. and E. coli O157:H7 on lettuce, sample characteristic, country of origin, and Salmonella identified serovars) were extracted, and meta-analysis was performed using Open Meta-Analyst, Task Order # 2 software. Although only one work reported the presence of E coli O157:H7 on lettuce, several reports indicated the presence of other, distinct enterohemorrhagic E. coli (EHEC) strains, with a mean prevalence of 0.041 (95% CI: 0.005-0.078) and concentration varying from <3.0 MPN/g to >1100 MPN/g. Furthermore, the mean prevalence of Salmonella spp. on lettuce was 0.041 (95% CI: 0.030-0.052), with reported concentrations varying between 0.054 ± 0.058 CFU/g to 218.78 MPN/g. In addition, subgroup analysis of the presence of Salmonella spp. in lettuce revealed a mean prevalence of the bacteria of 0.028 (95% CI: 0.014-0.042) in developed nations and 0.064 (0.041-0.087) in developing nations, with reports varying from 0.001 in Japan to 0.5 in Burkina Faso. Despite a relatively low prevalence, consumption of lettuce is inherently risky because it usually is eaten raw, without thermal treatment to inactivate pathogens. This potential risk further supports performance of quantitative risk assessments to quantify the probability of FBD caused by Salmonella spp. and E. coli O157:H7 transmitted to lettuce.

Preharvest Transmission Routes of Fresh Produce Associated Bacterial Pathogens with Outbreak Potentials: A Review

Disease outbreaks caused by the ingestion of contaminated vegetables and fruits pose a significant problem to human health. The sources of contamination of these food products at the preharvest level of agricultural production, most importantly, agricultural soil and irrigation water, serve as potential reservoirs of some clinically significant foodborne pathogenic bacteria. These clinically important bacteria include: Klebsiella spp., Salmonella spp., Citrobacter spp., Shigella spp., Enterobacter spp., Listeria monocytogenes and pathogenic E. coli (and E. coli O157:H7) all of which have the potential to cause disease outbreaks. Most of these pathogens acquire antimicrobial resistance (AR) determinants due to AR selective pressure within the agroecosystem and become resistant against most available treatment options, further aggravating risks to human and environmental health, and food safety. This review critically outlines the following issues with regards to fresh produce; the global burden of fresh produce-related foodborne diseases, contamination between the continuum of farm to table, preharvest transmission routes, AR profiles, and possible interventions to minimize the preharvest contamination of fresh produce. This review reveals that the primary production niches of the agro-ecosystem play a significant role in the transmission of fresh produce associated pathogens as well as their resistant variants, thus detrimental to food safety and public health.

Microbial Contamination of Fresh Produce: What, Where, and How?

Promotion of healthier lifestyles has led to an increase in consumption of fresh produce. Such foodstuffs may expose consumers to increased risk of foodborne disease, as often they are not subjected to processing steps to ensure effective removal or inactivation of pathogenic microorganisms before consumption. Consequently, reports of ready-to-eat fruit and vegetable related disease outbreak occurrences have increased substantially in recent years, and information regarding these events is often not readily available. Identifying the nature and source of microbial contamination of these foodstuffs is critical for developing appropriate mitigation measures to be implemented by food producers. This review aimed to identify the foodstuffs most susceptible to microbial contamination and the microorganisms responsible for disease outbreaks from information available in peer-reviewed scientific publications. A total of 571 outbreaks were identified from 1980 to 2016, accounting for 72,855 infections and 173 deaths. Contaminated leafy green vegetables were responsible for 51.7% of reported outbreaks. Contaminated soft fruits caused 27.8% of infections. Pathogenic strains of Escherichia coli and Salmonella, norovirus, and hepatitis A accounted for the majority of cases. Large outbreaks resulted in particular biases such as the observation that contaminated sprouted plants caused 31.8% of deaths. Where known, contamination mainly occurred via contaminated seeds, water, and contaminated food handlers. There is a critical need for standardized datasets regarding all aspects of disease outbreaks, including how foodstuffs are contaminated with pathogenic microorganisms. Providing food business operators with this knowledge will allow them to implement better strategies to improve safety and quality of fresh produce.

Assessing the relationship between organic farming practices and microbiological characteristics of organic lettuce varieties (Lactuca sativa L.) grown in Sao Paulo, Brazil

AIMS

This study aimed to gather information on farming practices employed in organic lettuce fields in Sao Paulo, Brazil and associate these practices with the microbiological characteristics of the products.

METHODS AND RESULTS

Practices were surveyed using a questionnaire applied in ten farms, where 200 heads of lettuce were collected and submitted to enumeration of total coliforms and generic Escherichia coli and tested for Salmonella spp. using culture and molecular (qPCR) methods. Based on the responses, the farms could be clustered in two groups: group 1, comprised by six farms, where chicken manure was used as fertilizer in most of them and the composting process was not performed on site; and group 2, comprised by four farms, where other types of fertilizer were used, and the composting process was performed on site. Generic E. coli was detected in 56 (28%) samples, with an average of 1·1 ± 0·7 log MPN per g. Salmonella DNA was detected in two (1%) samples by qPCR.

CONCLUSIONS

The prevalence and bacterial loads of generic E. coli, and the occurrence of Salmonella, even at low populations undetectable by conventional culture methods, highlight the need for control measures during farming practices to reduce microbial contamination and risks of foodborne illnesses. These measures include the use of properly composted manure and appropriate washing procedures for leafy vegetables before consumption.

SIGNIFICANCE AND IMPACT OF THE STUDY

The obtained data contribute to a better understanding of the farming practices of organically grown lettuces in Sao Paulo, Brazil.

Meeting Report: Key Outcomes from a Collaborative Summit on Agricultural Water Standards for Fresh Produce

On February 27 to 28, 2018, the Produce Safety Alliance convened a national water summit in Covington, KY to discuss the requirements of the United States Food and Drug Administration's (FDA) Food Safety Modernization Act Standards for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption (Produce Safety Rule [PSR]). The goals of the meeting were to better understand the challenges growers face in implementing the requirements in Subpart E-Agricultural Water and work collaboratively to develop practical solutions to meet fruit and vegetable production needs while protecting public health. To meet these goals, the summit engaged a diverse group of stakeholders including growers, researchers, extension educators, produce industry members, and regulatory personnel. Key outcomes included defining implementation barriers due to diversity in water sources, distribution systems, commodity types, climates, farm size, and production activities. There was an articulated need for science-based solutions, such as the use of agricultural water system assessments and sharing of federal, state, and regional water quality data, to ensure qualitative and quantitative standards reduce microbial risks. These identified challenges and needs resulted in significant debate about whether reopening the PSR-Subpart E for modification or attempting to address concerns through guidance would provide the best mechanism for alleviating concerns. In addition, training, outreach, and technical assistance were identified as vital priorities once the concerns are formally addressed by FDA. The water summit highlighted the critical need for transparency of FDA's progress on reevaluating the Subpart E requirements to help guide growers' decisions regarding the use of agricultural water.

Insect exclusion limits variation in bacterial microbiomes of tomato flowers and fruit

AIMS

The effect of insect exclusion via netting on bacterial microbiota associated with field-grown tomato fruit and flowers was evaluated.

METHODS AND RESULTS

Amplicon-based bacterial community profiling from insect-exposed plants and plants wrapped in nylon mosquito netting was conducted on total DNA extracted from tomato flower and mature unripe fruit washes. The V1-V3 region of the 16S rRNA gene was sequenced using Illumina MiSeq and analysed using qiime ver. 1.8. The carposphere supported significantly more phylogenetic diversity (PD) compared to the anthosphere, as measured by operational taxonomic unit richness (P = 0·001) and Faith's PD (P = 0·004). Flowers and fruit hosted distinct bacterial community structures (R2 = 0·27, P = 0·001), with specific taxonomic differences in taxa that included the Xanthomonadaceae (higher in flowers), and the Pseudomonadaceae, Methylobacteriaceae and Rhizobiales (higher in fruit) (FDR-P < 0·05). Bacterial community profiles of netted plants were overall statistically similar to non-netted plants for both flowers and fruit (P > 0·10). However, less variation between samples was observed among flowers (~50% less, P = 0·004) and green fruit (~10% less, P = 0·038) collected from netted than non-netted plants.

CONCLUSION

Insects may introduce or augment variability in bacterial diversity associated with tomato flowers and potentially green fruit surfaces.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work contributes to knowledge on microbiome dynamics of the tomato holobiont. Deciphering drivers of bacterial diversity and community structure of fruit crops could reveal processes important to agricultural management, such as competitive exclusion of pathogens and priming of plant defense mechanisms.

Organic food and the impact on human health

In the last decade, the production and consumption of organic food have increased steadily worldwide, despite the lower productivity of organic crops. Indeed, the population attributes healthier properties to organic food. Although scientific evidence is still scarce, organic agriculture seems to contribute to maintaining an optimal health status and decreases the risk of developing chronic diseases. This may be due to the higher content of bioactive compounds and lower content of unhealthy substances such as cadmium and synthetic fertilizers and pesticides in organic foods of plant origin compared to conventional agricultural products. Thus, large long-term intervention studies are needed to determine whether an organic diet is healthier than a diet including conventionally grown food products. This review provides an update of the present knowledge of the impact of an organic versus a conventional food diet on health.

Identifying and modeling meteorological risk factors associated with pre-harvest contamination of Listeria species in a mixed produce and dairy farm

This study sought to investigate the prevalence of Listeria species (including L. monocytogenes) in a mixed produce and dairy farm and to identify specific meteorological factors affecting Listeria spp. presence. Environmental samples were collected monthly from locations within the mixed farm over 14months and were analyzed for Listeria spp. Meteorological factors were evaluated for their association with the presence of Listeria spp. by using logistic regression (LR) and random forest (RF). The developed LR model identified wind speed and precipitation as significant risk factors (P<0.05), indicating higher wind speed at day 2 prior to sampling and higher average precipitation over the previous 25days before sampling increased the probability of isolation of Listeria spp. from the mixed farm. Results from RF revealed that average wind speed at day 2 prior to sampling and average precipitation in the previous 25days before sampling were the most important factors influencing the presence of Listeria spp., which supported the findings from LR. These findings indicate that the occurrence of Listeria spp. was influenced by wind speed and precipitation, suggesting run-off and wind-driven dust might be possible routes of pathogen transmission in mixed farms. The developed LR and RF models, with robust predictive performances as measured by the area under the receiver operating characteristic curves, can be used to predict Listeria spp. contamination risk in a mixed farm under different weather conditions and can help with the evaluation of farm management practices and the development of control strategies aimed at reducing pre-harvest microbial contamination in a mixed farming system.

Susceptibility of Salmonella enterica Isolates from Tomato Farm Environments to Fatty Acids Naturally Found on Tomato Fruit

Salmonella enterica subsp. enterica can colonize tomato fruit as it interacts with fruit surface compounds. The exometabolome of tomato fruit contains a mixture of compounds, including fatty acids, which could affect Salmonella fitness. Fatty acids detected in fruit exudates were investigated for Salmonella inhibition. Pelargonic, lauric, myristic, palmitic, margaric, stearic, and oleic acids were suspended in water dissolved in dimethyl sulfoxide (DMSO) or emulsified in water and quillaja saponin to assess how bioavailability impacted Salmonella growth. The minimum inhibitory concentrations of fatty acids were determined using a resazurin assay. Quillaja saponin emulsion and DMSO solution of pelargonic acid were inhibitory to Salmonella at 31.25 mM. Lauric and myristic acid emulsions inhibited growth at 1 M concentrations in quillaja emulsions and 62.5 mM in DMSO. Lauric and myristic acids significantly affected growth of Salmonella Newport, Javiana, and Typhimurium (p ≤ 0.05). Growth curve analysis using the Baranyi model revealed reduced maxima populations for all treatments (p ≤ 0.001) and shorter lag phase durations for Salmonella Newport with lauric acid (p < 0.01) and Salmonella Javiana with lauric (p < 0.001) and myristic (p < 0.001) acids. Salmonella Newport and Javiana exhibited an accelerated growth rate with lauric acid (p < 0.001) as a result of early stationary phase transition (shorter log phase). In myristic acid-amended media, Salmonella Javiana also displayed a faster growth rate (p < 0.001). Pelargonic acid (31.25 mM) treatment of Salmonella cells resulted in a drop in culturable cells to below detection in an hour. Microscopic analysis with Cyto-dye and propidium iodide of bacterial cells treated with pelargonic acid indicated a mixture of live and dead cells, with cell lysis of some cells. A subset of cells exhibited elongation-possibly indicating filament formation, a known antibiotic stress response. The results suggest that fatty acids present in tomato fruit surface exudates may exert a restrictive effect on Salmonella growth on fruit.

Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers

Due to the intimate association between plants and their microbial symbionts, an examination of the influence of agricultural practices on phytobiome structure and diversity could foster a more comprehensive understanding of plant health and produce safety. Indeed, the impact of upstream crop producti006Fn practices cannot be overstated in their role in assuring an abundant and safe food supply. To assess whether fertilizer type impacted rhizosphere and phyllosphere bacterial communities associating with tomato plants, the bacterial microbiome of tomato cv. 'BHN602' grown in soils amended with fresh poultry litter, commercially available sterilized poultry litter pellets, vermicompost or synthetic fertilizer was described. Culture independent DNA was extracted from bulk and rhizosphere soils, and washes of tomato blossoms and ripe fruit. PCR amplicons of hypervariable regions of the 16S rRNA gene were sequenced and profiled using the QIIME pipeline. Bulk and rhizosphere soil, and blossom and fruit surfaces all supported distinct bacterial communities according to principal coordinate analysis and ANOSIM (R=0.87, p=0.001 in year 1; R=0.93, p=0.001 in year 2). Use of microbiologically diverse organic fertilizers generally did not influence bacterial diversity, community structure or relative abundance of specific taxa on any plant organ surface. However, statistically significant differences in sand and silt contents of soil (p<0.05) across the field and corresponding shifts in water activity were positively (R²=0.52, p=0.005) and negatively (R²=0.48, p=0.009) correlated with changes in bacterial community structure in the rhizosphere, respectively. Over two harvest seasons, this study demonstrated that the application of raw poultry manure, poultry litter pellets and vermicompost had little effect on the tomato microbiome in the rhizosphere and phyllosphere, when compared to synthetically fertilized plants. Plant anatomy, and other factors related to field location, possibly associated with edaphic and air characteristics, were more influential drivers of different tomato organ microbiomes than were diverse soil amendment applications.

Salmonella Surveillance Among Great-Tailed Grackles (Quiscalus mexicanus) and Other Urban Bird Species in Eastern Texas

Wild birds may play an important role in maintaining and transmitting Salmonella. Their ability to travel large distances and their proximity to human habitations could make them a vehicle for bridging Salmonella from wild and domestic animals to humans. To determine the potential public health risk presented by urban birds, we investigated the prevalence of Salmonella among great-tailed grackles (Quiscalus mexicanus) and other cohabiting urban bird species. Fecal samples were collected from 114 birds communally roosting in parking lots of retail locations in Brazos County, Texas, from February through July of 2015. Great-tailed grackles and European starlings (Sturnus vulgaris) were the predominant species sampled. Standard bacteriologic culture methods were used to isolate Salmonella from samples, and isolates were characterized by serotyping and antimicrobial susceptibility testing. Overall, 1.8% (2/114) of samples were confirmed positive for Salmonella. Both positive birds were great-tailed grackles sampled in June, yielding a 2.6% (2/76) apparent prevalence among this species. Isolates were serotyped as Salmonella Typhimurium and found to be pan-susceptible based on the National Antimicrobial Resistance Monitoring System (NARMS) panel of antimicrobial agents. The occurrence of Salmonella in great-tailed grackles represents a potential threat to public health, particularly considering their population size and tendency to congregate near human establishments such as grocery stores.

Microbiology of organic and conventionally grown fresh produce

Fresh produce is a generalized term for a group of farm-produced crops, including fruits and vegetables. Organic agriculture has been on the rise and attracting the attention of the food production sector, since it uses eco-agricultural principles that are ostensibly environmentally-friendly and provides products potentially free from the residues of agrochemicals. Organic farming practices such as the use of animal manure can however increase the risk of contamination by enteric pathogenic microorganisms and may consequently pose health risks. A number of scientific studies conducted in different countries have compared the microbiological quality of produce samples from organic and conventional production and results are contradictory. While some have reported greater microbial counts in fresh produce from organic production, other studies do not. This manuscript provides a brief review of the current knowledge and summarizes data on the occurrence of pathogenic microorganisms in vegetables from organic production.

Using a Control to Better Understand Phyllosphere Microbiota

An important data gap in our understanding of the phyllosphere surrounds the origin of the many microbes described as phyllosphere communities. Most sampling in phyllosphere research has focused on the collection of microbiota without the use of a control, so the opportunity to determine which taxa are actually driven by the biology and physiology of plants as opposed to introduced by environmental forces has yet to be fully realized. To address this data gap, we used plastic plants as inanimate controls adjacent to live tomato plants (phyllosphere) in the field with the hope of distinguishing between bacterial microbiota that may be endemic to plants as opposed to introduced by environmental forces. Using 16S rRNA gene amplicons to study bacterial membership at four time points, we found that the vast majority of all species-level operational taxonomic units were shared at all time-points. Very few taxa were unique to phyllosphere samples. A higher taxonomic diversity was consistently observed in the control samples. The high level of shared taxonomy suggests that environmental forces likely play a very important role in the introduction of microbes to plant surfaces. The observation that very few taxa were unique to the plants compared to the number that were unique to controls was surprising and further suggests that a subset of environmentally introduced taxa thrive on plants. This finding has important implications for improving our approach to the description of core phytobiomes as well as potentially helping us better understand how foodborne pathogens may become associated with plant surfaces.

Drip Line Flushing with Chlorine May Not Be Effective in Reducing Bacterial Loads in Irrigation Water Distribution Systems

Irrigation water distribution systems are used to supply water to produce crops, but the system may also provide a protected environment for the growth of human pathogens present in irrigation water. In this study, the effects of drip tape installation depth and sanitization on the microbial quality of irrigation groundwater were evaluated. Drip tape lines were installed on the soil surface or 5 or 10 cm below the soil surface. Water samples were collected from the irrigation source and the end of each drip line every 2 weeks over an 11-week period, and the levels of Escherichia coli, total coliforms, aerobic mesophilic bacteria, and enterococci were quantified. Half of the lines installed at each depth were flushed with sodium hypochlorite for 1 h during week 6 to achieve a residual of 10 ppm at the end of the line. There was a statistically significant (P = 0.01) effect of drip tape installation depth and sanitizer application on the recovery of E. coli, with increased levels measured at the 5-cm depth and in nonsanitized lines, although the levels were at the limit of detection, potentially confounding the results. There was no significant effect of drip tape depth on total coliforms, aerobic mesophiles, or enterococci. In contrast, a statistically significant increase (P < 0.01) in the recovery of total coliforms was recorded from the ends of lines that received chlorine. This may be indicative of shedding of cells owing to degradation of biofilms that formed on the inner walls of the lines. These findings emphasize the need to better understand conditions that may lead to corrosion and increases in bacterial loads inside drip lines during flushing. Recommendations to growers should suggest collecting groundwater samples for testing at the end of drip lines rather than at the source. Guidelines on flushing drip lines with chlorine may need to include water pH monitoring, a parameter that influences the corrosive properties of chlorine.

Microbial Survey of Pennsylvania Surface Water Used for Irrigating Produce Crops

Recent produce-associated foodborne illness outbreaks have been attributed to contaminated irrigation water. This study examined microbial levels in Pennsylvania surface waters used for irrigation, relationships between microbial indicator organisms and water physicochemical characteristics, and the potential use of indicators for predicting the presence of human pathogens. A total of 153 samples taken from surface water sources used for irrigation in southeastern Pennsylvania were collected from 39 farms over a 2-year period. Samples were analyzed for six microbial indicator organisms (aerobic plate count, Enterobacteriaceae, coliform, fecal coliforms, Escherichia coli, and enterococci), two human pathogens (Salmonella and E. coli O157), and seven physical and environmental characteristics (pH, conductivity, turbidity, air and water temperature, and sampling day and 3-day-accumulated precipitation levels). Indicator populations were highly variable and not predicted by water and environmental characteristics. Only five samples were confirmed positive for Salmonella, and no E. coli O157 was detected in any samples. Predictive relationships between microbial indicators and the occurrence of pathogens could therefore not be determined.

Impact of mulches and growing season on indicator bacteria survival during lettuce cultivation

In fresh produce production, the use of mulches as ground cover to retain moisture and control weeds is a common agricultural practice, but the influence that various mulches have on enteric pathogen survival and dispersal is unknown. The goal of this study was to assess the impact of different mulching methods on the survival of soil and epiphytic fecal indicator bacteria on organically grown lettuce during different growing seasons. Organically managed lettuce, cultivated with various ground covers--polyethylene plastic, corn-based biodegradable plastic, paper and straw mulch--and bare ground as a no-mulch control, was overhead inoculated with manure-contaminated water containing known levels of generic Escherichia coli and Enterococcus spp. Leaves and soil samples were collected at intervals over a two week period on days 0, 1, 3, 5, 7, 10 and 14, and quantitatively assessed for E. coli, fecal coliforms and Enterococcus spp. Data were analyzed using mixed models with repeated measures and an exponential decline with asymptote survival model. Indicator bacterial concentrations in the lettuce phyllosphere decreased over time under all treatments, with more rapid E. coli declines in the fall than in the spring (p<0.01). Persistence of E. coli in spring was correlated with higher maximum and minimum temperatures in this season, and more regular rainfall. The survival model gave very good fits for the progression of E. coli concentrations in the phyllosphere over time (R(2)=0.88 ± 0.12). In the spring season, decline rates of E. coli counts were faster (2013 p=0.18; 2014 p<0.005) for the bare ground-cultivated lettuce compared to mulches. In fall 2014, the E. coli decline rate on paper mulch-grown lettuce was higher (p<0.005). Bacteria fluctuated more, and persisted longer, in soil compared to lettuce phyllosphere, and mulch type was a factor for fecal coliform levels (p<0.05), with higher counts retrieved under plastic mulches in all trials, and higher enterococci levels under straw in fall 2014 (p<0.05). This study demonstrates that mulches used in lettuce production may impact the fate of enteric bacteria in soil or on lettuce, most likely in relation to soil moisture retention, and other weather-related factors, such as temperature and rainfall. The data suggest that the time between exposure to a source of enteric bacteria and harvesting of the crop is season dependent, which has implications for determining best harvest times.