Investigation of Foodborne Pathogen Ecology throughout the Pastured Poultry Farm-to-Fork Continuum using a Microbiome Approach

Authors: Rothrock, Michael

Submitted to: International Association for Food Protection
Publication Type: Abstract Only
Publication Acceptance Date: 3/21/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary: There has been an increased demand for non-conventional raised poultry in the US, with these types of “alternative” poultry products accounting for upwards a 20% of all poultry products sold in the US. While this consumer-driven shift has resulted in this increase of alternative production, there is limited scientific data regarding any potential food safety-related issues within these systems. Therefore, the goal of this study was to look at major foodborne bacterial pathogens throughout the farm-to-fork continuum to see how different management or environmental/physiochemical variables effect the ecology of these bacteria. To achieve this, live production (feces, pasture soil), processing (ceca, whole carcass rinses) and final product (whole carcass rinses) samples were collected from 42 flocks from 11 pastured poultry farms from 2014 – 2017. With the advent of new sequencing technologies and platforms, entire microbiomes are more easily characterized than ever before, while initially used more as a surveying tool to determine what microbial taxa (and their relative abundance) comprise various microbiomes, using microbiome data in a more applied manner is essential to make it more applicable to the poultry industry. For this symposium talk, I will review the applied microbiome studies that we have been performed on the different environments of the conventional poultry production system (hatchery, live production, processing plant), and then present similar data from pastured poultry flock management systems. While general trends and taxa comparisons will be discussed, applying these microbiome tools to address food safety issues will be highlighted. Also to be stressed will be the need to link this data to other important metadata (e.g. management data, physiochemistry, cultural data) to truly unlock the potential of these datasets to address the complex issues facing our increasingly diverse poultry industry.

Technical Abstract: There has been an increased demand for non-conventional raised poultry in the US, with these types of “alternative” poultry products accounting for upwards a 20% of all poultry products sold in the US. While this consumer-driven shift has resulted in this increase of alternative production, there is limited scientific data regarding any potential food safety-related issues within these systems. Therefore, the goal of this study was to look at major foodborne bacterial pathogens throughout the farm-to-fork continuum to see how different management or environmental/physiochemical variables effect the ecology of these bacteria. To achieve this, live production (feces, pasture soil), processing (ceca, whole carcass rinses) and final product (whole carcass rinses) samples were collected from 42 flocks from 11 pastured poultry farms from 2014 – 2017. With the advent of new sequencing technologies and platforms, entire microbiomes are more easily characterized than ever before, while initially used more as a surveying tool to determine what microbial taxa (and their relative abundance) comprise various microbiomes, using microbiome data in a more applied manner is essential to make it more applicable to the poultry industry. For this symposium talk, I will review the applied microbiome studies that we have been performed on the different environments of the conventional poultry production system (hatchery, live production, processing plant), and then present similar data from pastured poultry flock management systems. While general trends and taxa comparisons will be discussed, applying these microbiome tools to address food safety issues will be highlighted. Also to be stressed will be the need to link this data to other important metadata (e.g. management data, physiochemistry, cultural data) to truly unlock the potential of these datasets to address the complex issues facing our increasingly diverse poultry industry.