Co-existence of fresh produce with animal agriculture has come under increased scrutiny, given multiple recent outbreaks where pathogen strains on produce have been linked to livestock. An important consideration in this co-existence is understanding how pathogens are vectored from animals and their environments to fresh produce. This proposal centers on understanding the risks posed by wild birds and how their fecal pathogen content is influenced by nearby animal agriculture. Previous studies examining wild birds have been focused in the western US, where ‘cattle is king’ in terms of animal agriculture. The southeast has a $4 billion fresh produce and nut industry and, while also having beef and dairy cattle, in this region, ‘poultry is king.’ Campylobacter and Salmonella are the top bacterial causes of foodborne illness in the US, are frequently isolated from food animals, and have been linked to outbreaks in fresh produce. This study will examine the role of poultry and cattle in influencing the pathogens deposited onto fresh produce by wild birds. Mapping and modeling technologies will be implemented to develop risk profiles resulting from links between integrated/proximal animal agriculture and wild bird feces containing viable pathogens that are deposited on produce foliage. High-resolution molecular tools will be used to generate pathogen population profiles and, alongside genomic analyses, will be used to attribute pathogen source to zoonotic reservoirs associated with animal agriculture.
There is abundant evidence that wildlife often carries potential foodborne pathogenic bacteria. Indeed, wildlife sources have been associated with several outbreaks, leading to calls to remove natural habitats from farms to discourage wildlife visits. Thus, it was surprising that a recent study found that the likelihood of produce contamination actually increased, rather than decreased, in leafy greens fields where natural habitats had been removed (31). Consistent with this, we found that wild bird feces collected from broccoli were more likely to carry Campylobacter when those fields were surrounded by intensified livestock and crop production, rather than more-natural habitats (52). Pathogens were associated with invasive starlings and house sparrows, known to frequent feedlots and other high-density livestock areas, but also with many native birds (e.g., American robins) that also are associated with pastures and cropping fields. Altogether, work to-date suggests three interacting links between wild bird-associated food safety problems: (i) intensive livestock production that provides a pathogen reservoir, (ii) heavily farmed landscapes that support large numbers of invasive birds, and (iii) simple on-farm habitats that draw livestock-associated birds to a particular field. However, thus far these links have been drawn from circumstantial, rather than direct, evidence of pathogen movement. This limits the ability of fresh produce growers to definitively assess food safety risks associated based on local and regional land-use patterns, or to manipulate on-farm habitats to mediate these risks.
Fortunately, recent advances in pathogen tracking, using fine-scale genetic differences in pathogen genomes, is providing a means to directly separate different animal agriculture, wildlife, and environmental pathogen sources. For example, Salmonella Typhimurium isolates have been attributed to different zoonotic sources based on their genome sequences (59). PI Shariat has been a leader in using next-generation sequencing approaches to assess pathogen populations, having developed CRISPR-SeroSeq as a tool to produce high-resolution population profiles of Salmonella serotypes. Here, we propose to definitively establish links between livestock/poultry pathogen reservoirs and pathogens in bird feces on produce foliage growing in the field. We will also examine how likely pathogens in bird feces are to move from deposition points to surrounding produce and plants. We propose two primary research objectives focusing on bird fecal samples collected directly from the fields of our cooperating growers: In Obj. 1 we will assess the risk posed by wild bird feces on fresh produce plants and the influence of proximal animal agriculture on pathogen presence in wild bird feces. In Obj. 2, we will determine the diversity, not just the dominant species or serotype, of Campylobacter and Salmonella in bird feces and perform fine-scale tracking and source attribution using whole genome sequencing. Both of these research objectives will be directly paired with outreach products/strategies that move our findings directly to the hands of growers, processors, and others in the industry that critically need this information. Altogether, we seek to provide produce growers with the science-based knowledge and tools to assess the risk that wild birds pose to food safety on their farms, based on farm-specific local and landscape farming practices.