Understanding and predicting food safety risks posed by wild birds

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.

1. 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. 

2. Determine the diversity of Campylobacter and Salmonella in wild bird feces and perform fine-scale tracking and source attribution using whole genome sequencing.

Key Findings: 

• The overall prevalence of culturable Salmonella and Campylobacter in wild bird feces was low, and zero, respectively. 

• There was no evidence of pathogen transmission from contaminated feces to produce on the same plant or the leaves of neighboring plants.

 • Viable Salmonella was only identified in moist fecal samples. 

• Molecular assays detected Salmonella in both moist and dry feces, with the majority found in moist samples. 

• Bird species that defecated on produce plants were associated with lower natural land use and higher animal agriculture land use. 

• Deep serotyping resulting in the identification of 13 serovars in 14 samples, including six in the CDC top 10 serovars of human concern. 

• In almost three-quarter of positive samples, Salmonella was found to exist as populations of mixed serovars, including one fecal sample containing seven different serovars. 

• Whole genome sequencing revealed a subset of isolates are related to isolates from a variety of sources including animal agriculture (chicken and turkey), humans, and the environment (surface water). 

• Microbiome analyses showed that viable Salmonella was positively associated with the Enterobacteriaceae family and negatively associated with the Enterococcaceae and Erwiniaceae families. 

Recommendations – 

• While harvesting produce, care should be taken to avoid any plants or produce with feces present. 

• Good Agricultural Practice (GAP) recommendations for no-harvest buffer zone distances around feces should be examined to better guide buffer distance recommendations. 

• If there is significant bird intrusion, growers could consider measures to reduce wild bird presence on farms, which can include scaring (decoys, lasers, or predator sounds) and physical (netting and spikes) deterrents. 

• While prevalence is low, the presence of clinically relevant Salmonella serovars suggests that all wild bird feces should be handled as if they contain viable pathogens. 

• Growers should be aware that the use of stakes, cages, and other structures in and around produce plants can provide a space for birds to forage and may result in increased fecal deposits. 

• A reduction of natural habitat may encourage bird intrusion into produce production and handling areas.