Microbial Indicator Profiling of Fresh Produce and Environmental Samples from Farms and Packing Facilities in Northern Mexico

Foodborne Viruses and Somatic Coliphages Occurrence in Fresh Produce at Retail from Northern Mexico

Foodborne disease outbreaks linked to consumption of vegetables have been often attributed to human enteric viruses, such as Norovirus (NoV), Hepatitis A virus (HAV), and Rotavirus (RoV). Information about the occurrence of these viruses is scarce in many fresh-producing countries. Viral contamination detection of indicators, such as somatic coliphages, could indirectly reflect the presence of viral pathogens, being a valuable tool for better viral risk assessment in food industry. This study aimed to establish the occurrence and correlation of foodborne viruses and somatic coliphages in leafy greens in northern Mexico. A total of 320 vegetable samples were collected, resulting in 80 composite rinses, 40 of lettuce and 40 of parsley. Somatic coliphages were determined using the EPA 1602 method, while foodborne viruses (HAV, RoV, NoV GI, and GII) were determined by qPCR. The occurrence of RoV was 22.5% (9/40, mean 2.11 log gc/g) in lettuce and 20% (8/40, mean 1.91 log gc/g) in parsley. NoV and HAV were not detected in any samples. Somatic coliphages were present in all lettuce and parsley samples, with mean levels of 1.85 log PFU/100 ml and 2.28 log PFU/100 ml, respectively. Spearman analysis established the correlation of somatic coliphages and genomic copies of RoV, resulting in an r2 value of - 0.026 in lettuce and 0.349 in parsley. Although NoV or HAV were undetected in the samples, the presence of RoV is a matter of concern as leafy greens are usually eaten raw, which poses a potential risk of infection.

Food Safety Risks of Harvesting Dropped and Drooping Produce: A Review

ABSTRACT

The Produce Safety Rule of the Food Safety Modernization Act (FSMA) sets forth minimum standards for fruit and vegetable production in the United States. One provision states that growers must not harvest dropped produce because damage or ground contact may contaminate produce. In an unpublished survey of 2020 food safety inspections conducted by the Northeast Center to Advance Food Safety, handling of dropped produce covered by the FSMA was a common misunderstood and noncompliance issue among growers in the Northeast. In consideration of this provision's on-farm practicality, this review was conducted to evaluate the risks associated with dropped and drooping produce, to guide growers in making informed risk management decisions, and to answer the following questions: (i) what are the risk factors that influence transferability of pathogens from touching the ground to produce and (ii) what are the risks associated with harvesting dropped or drooping produce covered under the Produce Safety Rule? A search of online databases revealed 12 relevant publications, which highlighted moisture, contact time, and crop features as affecting contamination rates from a ground surface to a crop surface. Soil and mulch posed a differential risk, with bare soil generally presenting a lower risk than plastic mulch. The effects of other mulch types are unclear. Mulches may promote pathogen persistence in soil, although they may also protect produce from contaminated soils. These studies were limited in their scope and applicability and most did not directly address dropped produce. Research is needed to clarify the various effects of dropped and drooping produce, the impact of ground surface type on pathogen survivability and transfer, soil and crop features that facilitate contamination, and postharvest risks of harvesting dropped or drooping produce. A comprehensive understanding of these issues will guide growers in implementing preventive measures and better managing risk in a way practicable to each farm's unique conditions.

HIGHLIGHTS

Detection, quantification, and characterization of Salmonella enterica in mango, tomato, and raw chicken purchased in the central region of Mexico

To estimate human exposure to Salmonella enterica, it is essential to understand the pathogen distribution and characteristics. Prevalence and concentration of S. enterica were determined in mango, tomato, and raw chicken samples purchased in three states (Aguascalientes, Querétaro, and Guadalajara) located in the central region of Mexico during two seasons. In addition, S. enterica isolates were characterized by absence/presence of 13 virulence genes (chromosomal, prophage, and plasmid) and resistance to 14 antibiotics. A total of 300 samples of mango, 272 of tomato, and 354 of raw chicken were analyzed. The mean of the prevalence (24.9%) and concentration (-0.61 Log MPN/g) of S. enterica in chicken was higher than in mango (1.3%, -1.7 Log MPN/g) and tomato (1.1%, -1.7 Log MPN). Among S. enterica isolates (284), there were 7 different virulotypes, belonging 68.7% of isolates to V2; there was high variability in the presence of mobile genetic elements. The occurrence of specific mobile elements ranged from 81.4% to 11.3% among isolates. Among the isolates, 91.5% were resistant to at least one antibiotic with ampicillin being the most frequent; 54.9% of isolates were multidrug resistant. Data from this study can be used for quantitative microbial risk assessment of S. enterica related to mango, tomato, and raw chicken consumption in the central region of Mexico. PRACTICAL APPLICATION: Data on the prevalence and concentration of Salmonella enterica obtained in this study can be used to estimate the exposure assessment for the consumption of mango, tomato, and chicken in the central region of Mexico. In addition, the characteristics of the S. enterica isolates could be used to select representative strains for future studies to evaluate the intraspecies variability.

Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment

Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this work was to characterize the bacterial communities present on cantaloupe farms. Fruit, soil, and harvester hand rinsates were collected from two Mexican cantaloupe farms, each visited three times. Microbiome analysis was performed by sequencing 16sRNA and analyzed using qiime2 software. Correlations were determined between sample type and microbial populations. The α and β diversity analysis identified 2777 sequences across all samples. The soil samples had the highest number and diversity of unique species (from 130 to 1329 OTUs); cantaloupe (from 112 to 205 OTUs), and hands (from 67 to 151 OTUs) had similar diversity. Collectively, Proteobacteria was the most abundant phyla (from 42 to 95%), followed by Firmicutes (1-47%), Actinobacteria (< 1 to 23%), and Bacteroidetes (< 1 to 4.8%). The most abundant genera were Acinetobacter (20-58%), Pseudomonas (14.5%), Erwinia (13%), and Exiguobacterium (6.3%). Genera with potential to be pathogenic included Bacillus (4%), Salmonella (0.85%), Escherichia-Shigella (0.38%), Staphylococcus (0.32%), Listeria (0.29%), Clostridium (0.28%), and Cronobacter (0.27%), which were found at lower frequencies. This study provides information on the cantaloupe production microbiome, which can inform future research into critical food safety issues such as antimicrobial resistance, virulence, and genomic epidemiology.

The Cantaloupe Farm Environment Has a Diverse Genetic Pool of Antibiotic-Resistance and Virulence Genes

Cantaloupes contaminated with pathogens have led to many high-profile outbreaks and illnesses. Since bacterial virulence genes (VGs) can act in tandem with antibiotic-resistance and mobile genetic elements, there is a need to evaluate these gene reservoirs in fresh produce, such as cantaloupes. The goal of this study was to assess the distribution of antibiotic-resistance, virulence, and mobile genetic elements genes (MGEGs) in cantaloupe farm environments. A total of 200 samples from cantaloupe melons (n = 99), farm workers' hands (n = 66), and production water (n = 35) were collected in México. Each sample was assayed for the presence of 14 antibiotic-resistance genes, 15 VGs, and 5 MGEGs by polymerase chain reaction. Our results indicated that tetracycline (tetA and tetB) (18% of cantaloupe, 45% of hand samples) and sulfonamide (sul1) (30% of cantaloupe, 71% of hand samples) resistance genes were frequently detected. The colistin resistance gene (mcr1) was detected in 10% of cantaloupe and 23% of farm workers' hands. Among VGs, Salmonella genes invA and spiA were the most abundant. There was a significantly higher likelihood of detecting antibiotic-resistance, virulence, and MGEGs on hands compared with water samples. These results demonstrate a diverse pool of antibiotic-resistance and VGs in cantaloupe production.

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.

Both Handwashing and an Alcohol-Based Hand Sanitizer Intervention Reduce Soil and Microbial Contamination on Farmworker Hands during Harvest, but Produce Type Matters

Hand hygiene interventions are critical for reducing farmworker hand contamination and preventing the spread of produce-associated illness. Hand hygiene effectiveness may be produce-commodity specific, which could influence implementation strategies. This study's goal was to determine if produce commodity influences the ability of handwashing with soap and water or two-step alcohol-based hand sanitizer (ABHS) interventions to reduce soil and bacteria on farmworker hands. Farmworkers (n = 326) harvested produce (cantaloupe, jalapeño, and tomato) for 30 to 90 minutes before engaging in handwashing, two-step ABHS (jalapeño and cantaloupe), or no hand hygiene. Hands were rinsed to measure amounts of soil (absorbance at 600 nm) and indicator bacteria (coliforms, Enterococcus sp., generic Escherichia coli, and Bacteroidales universal [AllBac] and human-specific [BFD] 16S rRNA gene markers). Without hand hygiene, bacterial concentrations (0.88 to 5.1 log₁₀ CFU/hand) on hands significantly differed by the produce commodity harvested. Moderate significant correlations (ρ = -0.41 to 0.56) between soil load and bacterial concentrations were observed. There were significant produce-commodity-specific differences in the ability of handwashing and two-step ABHS interventions to reduce soil (P < 0.0001), coliforms (P = 0.002), and Enterococcus sp. (P = 0.003), but not the Bacteroidales markers AllBac (P = 0.4) or BFD (P = 0.3). Contamination on hands of farmworkers who harvested cantaloupe was more difficult to remove. Overall, we found that a two-step ABHS intervention was similar to handwashing with soap and water at reducing bacteria on farmworker hands. In summary, produce commodity type should be considered when developing hand hygiene interventions on farms.IMPORTANCE This study demonstrated that the type of produce commodity handled influences the ability of handwashing with soap and water or a two-step alcohol-based hand sanitizer (ABHS) intervention to reduce soil and bacterial hand contamination. Handwashing with soap and water, as recommended by the FDA's Produce Safety Rule, when tested in three agricultural environments, does not always reduce bacterial loads. Consistent with past results, we found that the two-step ABHS method performed similarly to handwashing with soap and water but also does not always reduce bacterial loads in these contexts. Given the ease of use of the two-step ABHS method, which may increase compliance, the two-step ABHS method should be further evaluated and possibly considered for implementation in the agricultural environment. Taken together, these results provide important information on hand hygiene effectiveness in three agricultural contexts.

Microbiological Quality and Incidence of Salmonella on Cherry Tomatoes at Retail in Querétaro, México

Multiple outbreaks related to Salmonella in tomatoes require an evaluation of the risk associated with cherry tomatoes due to the increase in its production, consumption, and marketing in Mexico's central region. The purpose of this study was to determine the microbial quality of cherry tomatoes obtained from two retail sale points (supermarkets and local markets). Cherry tomato samples (333) were collected from four supermarkets and from four local markets, and the contents of aerobic plate count, molds and yeasts, total coliforms, and Escherichia coli were quantified; the presence of Salmonella was simultaneously determined. The median values of the microbial populations were obtained, and the data were analyzed per the sampling site by using the Wilcoxon and Kruskal-Wallis tests. The median of aerobic plate count content in tomatoes obtained from supermarkets ranged between 2.2 and 4.4 log CFU/g, and in markets from 2.9 to 4.8 log CFU/g. For molds and yeasts, the tomatoes from supermarkets (2.0 to 4.1 log CFU/g) and markets (1.5 to 4.5 log CFU/g) showed similar contents. Regardless of the sampling site, the values of total coliforms were very low, ranging from 1.0 to 1.8 log CFU/g. E. coli was detected in 5.4 and 20.1% of samples from supermarkets and markets, respectively; in both sites, the content was low (0.3 to 5.8 most probable number per g). The incidence of Salmonella was 14.1% in supermarkets and 7.8% in local markets. The results obtained from this investigation highlight the elevated risk for consumer health associated with the ingestion of cherry tomatoes.

Inactivation of Escherichia coli O157:H7 and Salmonella deposited on gloves in a liquid state and subjected to drying conditions

Gloves are worn by workers harvesting ready-to-eat produce as a deterrent for contaminating the produce with enteric pathogens that may reside on their hands. As fields are not sterile environments, the probability for gloves to become contaminated still exists and therefore it is critical to understand the conditions that affect the survival of pathogens on gloves. Both Escherichia coli O157:H7 and Salmonella deposited on glove surfaces in a liquid state survived longer when the pathogen had been suspended in lettuce sap than when suspended in water. Despite this protection, pathogens deposited on clean single-use gloves were more likely to survive during drying than pathogens deposited on dirty gloves (a film of lettuce sap had been applied to the surface prior to pathogen application and soil had been ground into the gloves). Survival of both E. coli O157:H7 and Salmonella was biphasic with the greatest losses occurring during the first hour of drying followed by much slower losses in the ensuing hours. Pathogens grown in rich media (tryptic soy broth) versus minimal media (M9) as well as those cultured on solid agar versus liquid broth were also more likely to be resistant to desiccation when deposited onto gloves. Although survival of E. coli O157:H7 on nitrile gloves was in general greater than it was on latex gloves, the relative survival of Salmonella on the two glove types was inconsistent. Due to these inconsistencies, no one glove type is considered better than another in reducing the risk for contamination with enteric pathogens. In addition, the extended survival of what are generally referred to as stress-resistant pathogens suggests that gloves either be changed frequently during the day or washed in a disinfectant to reduce the risk of glove contamination that could otherwise contaminate product handled with the contaminated gloves.

Contamination of Fresh Produce by Microbial Indicators on Farms and in Packing Facilities: Elucidation of Environmental Routes

To improve food safety on farms, it is critical to quantify the impact of environmental microbial contamination sources on fresh produce. However, studies are hampered by difficulties achieving study designs with powered sample sizes to elucidate relationships between environmental and produce contamination. Our goal was to quantify, in the agricultural production environment, the relationship between microbial contamination on hands, soil, and water and contamination on fresh produce. In 11 farms and packing facilities in northern Mexico, we applied a matched study design: composite samples (n = 636, equivalent to 11,046 units) of produce rinses were matched to water, soil, and worker hand rinses during two growing seasons. Microbial indicators (coliforms, Escherichia coli, Enterococcus spp., and somatic coliphage) were quantified from composite samples. Statistical measures of association and correlations were calculated through Spearman's correlation, linear regression, and logistic regression models. The concentrations of all microbial indicators were positively correlated between produce and hands (ρ range, 0.41 to 0.75; P < 0.01). When E. coli was present on hands, the handled produce was nine times more likely to contain E. coli (P < 0.05). Similarly, when coliphage was present on hands, the handled produce was eight times more likely to contain coliphage (P < 0.05). There were relatively low concentrations of indicators in soil and water samples, and a few sporadic significant associations were observed between contamination of soil and water and contamination of produce. This methodology provides a foundation for future field studies, and results highlight the need for interventions surrounding farmworker hygiene and sanitation to reduce microbial contamination of farmworkers' hands.IMPORTANCE This study of the relationships between microbes on produce and in the farm environment can be used to support the design of targeted interventions to prevent or reduce microbial contamination of fresh produce with associated reductions in foodborne illness.

Microbial Load of Fresh Produce and Paired Equipment Surfaces in Packing Facilities Near the U.S. and Mexico Border

Several produce-associated outbreaks have been linked to the packing facility. Equipment surfaces may be an important source of contamination. The goal was to assess whether the microbial load of packing facility surfaces is associated with the microbial load of produce. From November 2000 to December 2003, 487 matched produce (14 types) and equipment surfaces (six production steps) were sampled from eight packing facilities in the United States near the border with Mexico and enumerated for aerobic plate counts (APC), Escherichia coli , Enterococcus, and coliforms. Bivariate correlations were assessed by Spearman's ρ, and adjusted associations were assessed by multilevel mixed linear regression models. In general, the microbial load both increased and decreased on produce (0.2 to 1.0 log CFU/g) and equipment surfaces (0.5 to 3.0 log CFU/cm²) across production steps. Equipment surface and produce microbial loads were correlated, but correlations varied from none to high depending on the equipment surface. For example, significant correlations (P < 0.01) included APC (ρ = 0.386) and Enterococcus (ρ = 0.562) with the harvest bin, E. coli (ρ = 0.372) and Enterococcus (ρ = 0.355) with the merry-go-round, Enterococcus (ρ = 0.679) with rinse cycle equipment, APC (ρ = 0.542) with the conveyer belt, and for all indicators with the packing box (ρ = 0.310 to 0.657). After controlling for crop type, sample replicate group, and sample location, there were significant positive associations between the log concentration of Enterococcus on produce and the harvest bin (β = 0.259, P < 0.01) and the rinse cycle (β = 0.010, P = 0.01), and between the log concentration of all indicators on produce and the packing box (β = 0.155 to 0.500, all P < 0.01). These statistically significant associations between microbial loads on packing facility surfaces and fresh produce confirm the importance of packing facility sanitation to protect produce quality and safety.

Somatic Coliphage Profiles of Produce and Environmental Samples from Farms in Northern México

Somatic coliphages were quantified in 459 produce and environmental samples from 11 farms in Northern Mexico to compare amounts of somatic coliphages among different types of fresh produce and environmental samples across the production steps on farms. Rinsates from cantaloupe melons, jalapeño peppers, tomatoes, and the hands of workers, soil, and water were collected during 2011-2012 at four successive steps on each farm, from the field before harvest through the packing facility, and assayed by FastPhage MPN Quanti-tray method. Cantaloupe farm samples contained more coliphages than jalapeño or tomato (p range <0.01-0.03). Across production steps, jalapeños had higher coliphage percentages before harvest than during packing (p = 0.03), while tomatoes had higher coliphage concentrations at packing than all preceding production steps (p range <0.01-0.02). These findings support the use of targeted produce-specific interventions at multiple points in the process of growing and packing produce to reduce the risk of enteric virus contamination and improve food safety during fruit and vegetable production.