Research

Johnson Lab research has the primary goal of protecting and sustaining our food supply. To that end, we strive to enhance poultry health through a better understanding of the microbiota of the bird, the biology of antimicrobial resistance, the efficacy of antimicrobial alternatives, and pathogen ecology. More specifically, we have funded research programs addressing the following:

Identify mitigation strategies for antimicrobial resistance in poultry. In this USDA-funded project, we are exploring three different mitigation strategies. First, we are using CRISPR/Cas technology to eliminate multidrug resistance-encoding bacterial plasmids from poultry production environments. Second, we are assessing the effects of vaccination on overall bacterial pathogen ecology in live production settings. Third, we are developing probiotic-based approaches by which to enhance feed conversion and weight gain in commercial turkey production.

Understanding the changing ecology of Escherichia coliOrnithobacterium rhinotrachealeGallibacterium anatis, and Pasteurella multocida through comparative bacterial genomics. This work is being performed to develop a platform by which we can model and predict ecological changes in response to vaccination in poultry. This tool will allow poultry producers to identify appropriate vaccine strains, and to predict the timing and appropriate strain combinations for vaccine changes.

Understand the biology of plasmid success in E. coli and Salmonella. We are using a combination of genomics-based approaches and benchtop experiments to further understand how plasmids evolve and adapt in the poultry production environment. We are particularly interested in the role of plasmid persistence versus plasmid decay in different conditions mimicking presence within a host or a host’s environment.

Understand the role of vertical transmission in bacterial poultry pathogen ecology. We are following matched breeder and broiler flocks over time, and assessing clonal relatedness of avian pathogenic E. coli from multiple flocks and sources within a vertically integrated turkey company. The goal of this work is to determine the extent by which vertical transmission of E. coli from breeders to commercial turkeys plays in its dissemination.

Determine the role that commercial poultry and backyard poultry plays in the zoonotic transmission of avian pathogenic E. coli from birds to humans. In NIH-funded work with Dr. Jay Graham, we are studying the impact of housing backyard chickens in rural Ecuador on the carriage of avian pathogenic E. coli by children within that household. We are combining these efforts with existing projects in the US to determine the relative impacts of housing backyard chickens versus consuming commercial poultry on the transmission of avian E. coli from birds to humans. Further, we are developing enhanced tools by which to predict food source of an isolates from humans based upon its distinguishing host-adaptive markers from the animal source.

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