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Population Dynamics of Escherichia Coli on New York Cattle Farms: Towards Ecological Models for Control of a Pathogen

Buckley, Daniel
Cornell University
Start date
End date
The proposed work will identify spatial trends in the distribution of E. coli on New York cattle farms. Spatial statistics will identify potential barriers to pathogen flow on the farm and in watercourses. Through genetic analysis, the proposed work will also determine the capacity for environmental E. coli populations to act as a genetic reservoir for exchange of genes between fecal pathogens in the environment. Results from this research can potentially be used to identify best practices for pathogen control and possibly to inform new strategies of runoff management from farms.

This project will inform watershed and farm management practices in the Lake Champlain Basin, one of the most valuable natural resources in New York State. The project will address the following research and extension priorities: 1) Sustainable agricultural systems that minimize environmental impact and maintain dynamic farm profitability, and 2) improving watershed and water resource protection and management in agricultural rural and developed systems.

The project has the following objectives:

  1. Over two years in the same landscapes, identify the capacity of environmental E. coli reservoirs to support adapted E. coli populations on time scales from months to years.
  2. Use landscape genetic methods to determine the potential for migration between environmental reservoirs of E. coli on cattle farms.
  3. Using population genetics data, analyze the population structure over the farm landscape to model corridors and/or barriers to E. coli migration on farms.
  4. Using recombination analysis on population genetic data, determine the extent of gene flow between subpopulations in various environmental reservoirs during residence of E. coli contaminants.
Outcome of research activities will be communicated through publication in scientific journals and to stakeholders through appropriate program work teams.
More information
Non-Technical Summary: Escherichia coli is a bacterium carried in the digestive tracts of all mammals and birds. Some strains of E. coli are of special public health concern, because they can contaminate food and water, resulting in more than 70,000 illnesses and costing the public more than $400 million per year. Outbreaks result from contamination of meat and vegetable products either on the farm or during processing, but investigations of outbreaks are rarely able to conclusively identify how contamination occurred. Cattle and sheep are the predominant source of E. coli disease, with up to 30% of cows shedding deadly strains of E. coli. The Centers for Disease Control has specified farm-based practices as key to controlling the spread of E. coli. Surveys for control of E. coli are accomplished through microbial source tracking, i.e. the practice of linking food or water contamination with the source of bacteria. For example, the E. coli in a water sample can be compared to E. coli in local cow, horse, deer, goose, and human feces to determine their origin. However, these studies often ignore the fact that fecal E. coli can persist in the environment for months. It is also well-known to microbiologists that bacteria exchange genes at great frequency. Thus, there is unknown potential for E. coli from multiple sources to interact with each other and change genetically during transport from feces to a water or food source. We propose to improve the arsenal of knowledge available to farmers, policymakers and businesses for control of a disease that continues to plague the first- and developing worlds. To understand the best practices for control of transport across the landscape, we will conduct an ecological survey of E. coli in soils and watercourses. By sampling E. coli repeatedly in a spatially defined manner, we can: i) determine the fastest routes of E. coli transport around a farm landscape, ii) determine what effective barriers to E. coli transport might exist, iii) add to existing knowledge about the environmental reservoirs of E. coli, and iv) explore the potential of environmental E. coli populations to exchange genes with fecal E. coli. This biological perspective moves beyond examination of water flow paths and identifies migration corridors and biological reservoirs that control E. coli dispersal on the farm. This proposal stands on the strength of recent progress in biogeography and landscape genetics, two complementary fields of biology which seek to discover the laws behind the spatial distribution of organisms and genes. Through the application of genetic fingerprinting methods and gene sequencing, we can map the genetic relationships of E. coli isolates across the landscape. We plan to use this information to identify control points for transmission within farms and watersheds. This information will also help us to understand the biology of other problem organisms, such as Salmonella, that have environmental reservoirs on the farm. Through this work, we can improve food quality, watershed quality, and public health by developing better methods of predicting the behavior of E. coli during transport across the landscape.

Approach: Several cattle farms within a single watershed in the Champlain Valley will be sampled. Spatially discrete sampling of soil and hydrological environmental reservoirs will be performed. A randomized grid sampling scheme will enable us to account for patchiness of E. coli distribution in soils. At each location in a grid, samples will consist of soil cores from 0-5 cm depth. The samples will be diluted in EC-MUG enrichment broth to detect E. coli. Standard microbiological procedures will be used to identify E. coli. Up to 20 E. coli isolates will be obtained from each grid location. Our random sampling design on farm landscapes provides the best balance between coverage of the landscape and resources expended in the study. Genomic profiling of E. coli isolates will be used to assess population structure with respect to landscape characteristics. Genomes will be characterized by BOX-PCR, providing a genome fingerprint for use in population genetic analyses. Select isolates of each genome type will be analyzed by multilocus sequence typing (MLST). Application of analytical methods from landscape genetics will determine the geographic distribution of E. coli subpopulations and will estimate potential for migration and recombination between subpopulations on the farm. Spatial statistical techniques can then be used to model routes and barriers for migration. Rates of population turnover and the role of recombination within environmental reservoirs will be examined by sampling at multiple points in time in the same landscapes. The rigorous methods for analysis of E. coli populations in the field will permit the identification of natural limits to E. coli transport on the landscape, and inform future work on how policies and management practices can control that transport. Engagement with extension and academic faculty in CALS will contribute to project design and provide avenues for the dissemination of our findings about E. coli population dynamics and control. Such interactions will improve strategies to manage farms and watersheds by improving our knowledge of interactions between landscape, management decisions, and pathogen biology. External stakeholders will be NY farmers, policymakers, and food and water protection personnel. Contact with stakeholders will be established during year one and maintained. Communication of results to program work teams within CUAES will facilitate information transmission to stakeholders on outcomes of the research. Stakeholder concerns about farm and watershed management for control of pathogens will be solicited.

Funding Source
Nat'l. Inst. of Food and Agriculture
Project source
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Policy and Planning
Escherichia coli
Meat, Poultry, Game