Evaluation of physiochemical, heavy metals, and bacteriological parameters of celery and its irrigation water within Sulaymaniyah city of Iraq

This study rigorously assesses the physicochemical, heavy metal concentrations, and bacteriological parameters of celery and its irrigation water across three rural areas of Sulaymaniyah city, Iraq. The investigation revealed that irrigation water's pH ranged significantly from 6.9 to 8.9. Notably, phosphate concentrations (PO43-) exceeded permissible levels in Tanjaro and Kanaswra across all seasons, with the highest recorded concentration being 10.4 mg L-1 during autumn in Kanaswra. Conversely, sulfate (SO42-) and sodium (Na+) concentrations remained within standard limits, with SO42- peaking at 115.1 mg L-1 in Tanjaro during summer. Celery samples reflected high Na+ concentrations in some seasons, with values exceeding 570 mg·kg in Kanaswra during summer. Heavy metal analysis indicated remarkably low levels in irrigation water, yet celery samples from Tanjaro and Aziz Awa exhibited Pb concentrations above the safety threshold of 0.3 mg·kg in all seasons. Furthermore, bacterial contamination, including total aerobic count and coliform in both water and celery, surpassed standard limits, highlighting significant health risks. This study underscores the imperative need for stringent water treatment processes to mitigate contamination and safeguard agricultural productivity and human health.

Effect of Type of Mulch on Microbial Food Safety Risk on Cucumbers Irrigated with Contaminated Water

Mulches are used to block light and retain soil moisture which may affect the survival of bacterial pathogens on soil. This study examined the effectiveness of different types of mulches to minimize microbial risk from contaminated water used for irrigation of cucumbers. A production bed of 120 ft2 with 18 beds (30 ft long) covered with five different types of mulch (paper, paper with fertilizer incorporated (PF), maize-based mulch, biodegradable plastic covering, and conventional plastic) including three beds with no cover was planted with Dasher 2 Variety cucumber. Soil samples from each bed were collected for the first five weeks to examine natural E. coli and coliforms. Well water contaminated with or without nalidixic acid-resistant mutant of E. coli (8 Log CFU/mL) was used for drip irrigation for 7 days before harvesting. Prior to irrigation with contaminated water, naturally present E. coli and coliform in the soil samples with or without mulch were in the range of 3.45-3.78 Log CFU/g and 4.18-5.31 Log CFU/g, respectively. E. coli levels on cucumbers harvested from mulched beds and irrigated with contaminated irrigation water had significantly higher (P < 0.05) levels of E. coli as compared with samples from similar beds irrigated with noncontaminated water. However, Cucumber, harvested within each irrigation water quality were not significantly different regardless of the type of mulch with E. coli levels from 1.72 to 3.30 Log CFU/cm2 (contaminated water) and 0.28-1.86 Log CFU/cm2 (noncontaminated water). A significant die-off of inoculated E. coli was observed on cucumber within 3 days (>1.17 Log CFU/cm2) and >1.38 Log CFU/cm2 after 4 days. Beds with maize mulch were effective on minimizing E. coli contamination on cucumber from contaminated irrigation water.

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.

Risk factors of Shiga toxin-producing Escherichia coli in livestock raised on diversified small-scale farms in California

The increasing number of diversified small-scale farms (DSSF) that raise outdoor-based livestock in the USA reflects growing consumer demand for sustainably produced food. Diversified farms are small scale and raise a combination of multiple livestock species and numerous produce varieties. This 2015–2016 cross-sectional study aimed to describe the unique characteristics of DSSF in California, estimate the prevalence of Shiga toxin-producing Escherichia coli (STEC) in livestock and evaluate the association between risk factors and the presence of STEC in livestock, using generalised linear mixed models. STEC prevalence was 13.62% (76/558). Significant variables in the mixed-effect logistic regression model included daily maximum temperature (OR 0.95; CI_95% 0.91–0.98), livestock sample source (cattle (OR 4.61; CI_95% 1.64–12.96) and sheep (OR 5.29; CI_95% 1.80–15.51)), multiple species sharing the same barn (OR 6.23; CI_95% 1.84–21.15) and livestock having contact with wild areas (OR 3.63; CI_95% 1.37–9.62). Identification of STEC serogroups of public health concern (e.g. O157:H7, O26, O103) in this study indicated the need for mitigation strategies to ensure food safety by evaluating risk factors and management practices that contribute to the spread and prevalence of foodborne pathogens in a pre-harvest environment on DSSF.

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.

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

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

Transmission of antimicrobial resistant non-O157 Escherichia coli at the interface of animal-fresh produce in sustainable farming environments

The interaction of typical host adapted enteric bacterial pathogens with fresh produce grown in fields is complex. These interactions can be more pronounced in co-managed or sustainable farms where animal operations are, by design, close to fresh produce, and growers frequently move between the two production environments. The primary objectives of this study were to 1) determine the transmission of STEC or enteric pathogens from small and large animal herds or operations to fresh produce on sustainable farms in TN and NC, 2) identify the possible sources that impact transmission of AMR E. coli, specifically STEC on these systems, and 3) WGS to characterize recovered E. coli from these sources. Samples were collected from raw and composted manure, environment, and produce sources. The serotype, virulence, and genotypic resistance profile were determined using the assembled genome sequences sequenced by Illumina technology. Broth microdilution was used to determine the antimicrobial susceptibility of each isolate against a panel of fourteen antimicrobials. The prevalence of E. coli increased during the summer season for all sources tested. ParSNP trees generated demonstrated that the transmission of AMR E. coli is occurring between animal feeding operations and fresh produce. Ten isolates were identified as serotype O45, a serotype that is associated with the "Big Six" group that is frequently linked with foodborne outbreaks caused by non-O157 E. coli. However, these isolates did not possess the stx gene. The highest frequency of resistance was detected against streptomycin (n = 225), ampicillin (n = 190) and sulfisoxazole FIS (n = 140). A total of 35 (13.7%) isolates from two TN farms were positive for the blaCMY (n = 5) and blaTEM (n = 32) genes. The results of this study show the potential of AMR E. coli transmission between animal feeding operations and fresh produce, and more studies are recommended to study this interaction and prevent dissemination in sustainable farming systems.

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.

Microbial Safety of Dairy Manure Fertilizer Application in Raspberry Production

Dairy manure, a by-product in the dairy industry, is also a potential source of nutrients for crops. However, improper application of biological soil amendments of animal origin can be a source of contamination with enteric foodborne pathogens. A 2-year field study was conducted to evaluate impacts of dairy manure fertilizer application on the microbial safety of red raspberry (Rubus idaeus L) production. Fertilizers, including a standard synthetic fertilizer (CON), straight lagoon raw manure (SL), anaerobically digested liquid effluent (DLE), compost (COM) and dairy manure-derived refined fertilizers including ammonium sulfate (AS) and phosphorous solid (PS), were randomly applied in quadruplicate to raspberry plots. Soil, fertilizer, foliar, and raspberry fruit samples were collected during the cropping season for the quantification of indicator microorganisms (total coliform and generic Escherichia coli) and detection of important foodborne pathogens (Shiga toxin-producing E. coli (STEC), Salmonella, and Listeria monocytogenes). Counts of total coliforms in soil were stable over the 2017 cropping season and were not impacted by fertilizer application. In 2018, total coliforms increased with season and soils treated with COM had a significantly higher coliform number than those treated with CON. Both total coliform and generic E. coli in raspberry fruit samples were below the detectable level (3 most probable number/g) regardless of fertilizer types. In both years, no STEC or L. monocytogenes was detected from any of the collected samples regardless of fertilizer treatments. However, Salmonella were detected in some of the fertilizers, including PS (2017), DLE (2018), and SL (2018), which were transferred to soil samples taken directly after application of these fertilizers. Salmonella were not detected in soil samples 2 or 4 months post fertilizer application, foliar, or raspberry fruit samples regardless of fertilizer applications. In summary, one-time application of raw dairy manure or dairy manure-derived fertilizers more than 4 months prior to harvest has no major impact on food safety of red raspberry (6 ft. tall) production in Lynden sandy loam under good agricultural practices.