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Safeguarding the Food Supply

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The ARS food safety research program ensures a safe food supply that meets foreign and domestic regulatory requirements. Emerging research areas focus on metagenomics, climate change and mycotoxin contamination, food adulteration and fraud, reduction of foodborne pathogens during animal and produce production and food processing, and contamination of ready-to-eat foods. The following accomplishments highlight ARS advances in food safety research in FY 2019. Hyperlinked accomplishment titles point to active parent research projects.

E. coli transmission by cattle pest flies in leafy greens. Leafy greens are a leading source of E. coli O157:H7 bacteria that cause human foodborne illness. Pest flies can carry this pathogen and may transmit it to leafy greens and other fresh produce. ARS scientists in Clay Center, Nebraska, determined the occurrence of E. coli O157:H7-positive flies in leafy greens planted up to 600 feet from a cattle feedlot, and assessed their potential risk for transmitting this pathogen to leafy greens. E. coli O157:H7 carriage rates of house, face, flesh, and blow flies were similar to each other and were greater than the carriage rate of stable flies. E. coli O157:H7 carriage rates were not different in flies found at different distances from the feedlot, ranging from 0 to 600 feet. Genetic subtyping showed that the majority of the E. coli O157:H7 found in the flies were of the same predominant subtypes found in the feedlot pen surface manure and the leafy greens, indicating the potential role for flies to transmit E. coli O157:H7 to the leafy greens. Due in part to this work and previous research, the produce industry has revised its guidelines for growers to increase the set-back distance between leafy greens fields and concentrated animal feeding operations. This information is critical for understanding the food safety risks associated with growing leafy greens in close proximity to cattle production, for determining safe distances between cattle feedlots and fresh produce that will reduce preharvest contamination and protect public health, and as potential guidance under the Produce Safety Rule as part of the Food and Drug Administration’s Food Safety Modernization Act.

Imagery from drones for microbial water quality assessment in irrigation ponds. The microbial quality of water used for irrigation must be assessed to prevent the spread of microbes that can cause disease in humans. Microbial quality of irrigation water is evaluated based on concentrations of the indicator bacterium Escherichia coli. No recommendations have existed so far on where pond water samples should be taken for microbial analysis. ARS scientists from Beltsville, Maryland, proposed and tested a method of using drone-based imagery and artificial intelligence to obtain representative water samples for E. coli enumeration across irrigation ponds. Reflectance in different parts of the spectra are combined to characterize E. coli habitat in water. Results of this work provide the knowledge base for efficient microbial water quality sampling and indicate a new direction for monitoring microbial water quality, thus contributing to the improvements in food safety.

New metagenomics pipeline for pathogen detection. Rapid and accurate detection of pathogens from food samples is critically needed by the food industry, and the cost of whole genome sequencing from bacterial samples continues to decrease. ARS scientists in Albany, California, in collaboration with scientists at the Georgia Institute of Technology, developed a technique called imGLAD (in-silico-metagenomics for genome low-abundance detection) to detect human foodborne pathogens in samples of mixed DNA extracted from environmental samples. imGLAD was validated by detecting pathogenic Escherichia coli O157:H7 cells inoculated into field-grown, organic baby spinach leaves where the limit of detection was 100 cells/100 grams of spinach leaves. Metagenomics-based detection of pathogens is much faster than current culture-based methods and provides additional information that can be used for source-tracking foodborne outbreaks, which is essential information for public health investigations. This cutting-edge method is of interest to industries developing detection methods, growers, and public health agencies.

Global and regional contributors to mycotoxin contamination of wheat and barley. Fusarium head blight (FHB) is a destructive disease of cereals crops worldwide and a major food safety concern because FHB pathogens can contaminate grain with vomitoxin and other fungal toxins (mycotoxins). FHB is caused by a diverse set of fungal species that make different mycotoxins. Understanding which FHB species and toxin types are present in an area is key to disease and mycotoxin control programs. ARS scientists in Peoria, Illinois, worked in collaboration with scientists in Uruguay and Brazil to identify and characterize FHB pathogens from their countries. The most common FHB pathogen of wheat and barley in Uruguay and Brazil, as well as the United States, is Fusarium graminearum, which can make a form of vomitoxin. However, a new species, F. subtropicale, was found in Brazil that produces a related mycotoxin with greater toxicity for humans and animals. Analyses of genetic diversity revealed that wheat and barley share a common FHB pathogen population that moves back and forth between these two hosts. The FHB pathogens in this study exhibited different levels of aggressiveness toward barley and different levels of resistance to two commonly used fungicides. These results provide new information on FHB pathogen and mycotoxin prevalence, host distributions, aggressiveness, and fungicide sensitivity that can be used to develop globally applicable and regionally targeted disease and mycotoxin control programs that improve crop production and food safety.

Factors affecting pathogen survival in manure-amended soils. The Produce Safety Rule, part of the Food and Drug Administration’s Food Safety Modernization Act, states that untreated manure must be applied 90 or 120 days prior to the harvest of edible produce crops to minimize contamination from pathogens that may be present in untreated manure. However, this interval was not scientifically validated. Over 12 separate field trials conducted in mid-Atlantic States over 4 years, ARS researchers in Beltsville, Maryland, and university collaborator showed that spatiotemporal factors (site, year, and season) affect survival durations of Escherichia coli in manure-amended soils more than agricultural factors (manure type, organic or conventional management of soils, and depth of application) or weather effects. The results provide critical information to growers on the potential risk of produce contamination with specific raw animal manure application. The Food and Drug Administration will use these data to develop food safety standards for controlling bacterial contamination of fresh produce from soil.

Systems biology tool for the analysis of agriculturally important bacteria. Systems biology is the computational modeling of genes, their interactions, and the influence of the environment on the system. Until now, microbiologists and other researchers working on bacteria-related problems in animal disease, food safety, bioengineering, and other agricultural domains were not able to efficiently create realistic systems biology models. Through an ARS Scientific/High Performance Computing collaborative research initiative (SCINet) including ARS researchers in Clay Center, Nebraska, and collaborators with industry and at Iowa State University, the Pathway Tools systems biology analytical platform was customized to run on Amazon Web Services to host systems biology models of bacterial field isolates sequenced and assembled by USDA. The primary beneficiaries of this resource are researchers and others wishing to use, create, and publish systems biology models that relate bacterial genes to key bacterial functions or physical traits. These models will assist in generating evidence-based strategies to combat the effects of bacterial infection, improve food safety protocols, and promote solutions to bacteria-related problems in agriculture.