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ARS Home » Southeast Area » Mississippi State, Mississippi » Poultry Research » Research » Research Project #434880

Research Project: Systems Approach to Understanding and Mitigating Avian Escherichia coli Infections and Antimicrobial Resistance in the Poultry Environment

Location: Poultry Research

2021 Annual Report

1. Use proteomics, genomics, and systems biology approaches to identify molecular determinants of pathogenesis, strain variation, and tissue tropism of different Escherichia (E.) coli strains. 2. Identify immunological targets that will confer cross-protection against prevalent E. coli strains in poultry production and develop vaccine platforms that are effective in very young birds, provide cross-protection, and can be easily administered. 3. Develop systems-level capabilities to evaluate the effects of commercial-scale, poultry management practices on animal health and production; microbial ecology, development of antimicrobial resistance and bacterial pathogen transmission to develop mitigation strategies.

Escherichia (E.) coli is a bacterium that commonly inhabits the gastro-intestinal tract of most animals including poultry. While most strains are nonpathogenic, virulent E. coli strains are often associated with disease in poultry (e.g. colibacillosis) and result in significant economic losses to the poultry industry. To combat E. coli-associated disease in poultry, genotypic and phenotypic traits of virulent E. coli isolates associated with previous colibacillosis outbreaks in chickens will be characterized. The knowledge derived from isolate comparisons will be applied to characterization of E. coli-associated disease as well as to the development of a novel and effective vaccine. Further, vaccination platforms will be developed to maximize the delivery of commercially-available and research derived-vaccines. Application techniques to be investigated will include the traditional means of vaccine delivery including spray, drinking water, and eye-drop. However, novel delivery techniques such as in ovo injections will also be assessed for efficient vaccine delivery. In addition, investigations will be performed to determine the impact of poultry management practices on mitigation of E. coli-related disease. Areas of mitigation interest will include practices to limit E. coli transmission rates and the survivability/maintenance of the pathogen within the poultry environment. The impact of dietary additives including prebiotics, probiotics and bacteriophage will also be considered as means to limit the occurrence of E. coli-related disease in poultry.

Progress Report
To date approximately 230 strains of E. coli associated with avian disease (Avian Pathogenic E. coli, APEC) have been isolated and stocked. Of these, 130 strains have been sequenced, characterized, and compared. In addition, 105 strains are being assembled and annotated for comparison in the near future. The development of in ovo vaccine delivery protocols are underway and initial studies indicate a limited impact on embryo viability. Further, APEC strains from infected broilers in the Southeastern United States were separately isolated and stocked, and their associated virulence-associated genes were characterized toward the development of an APEC challenge model to assess protection afforded by APEC vaccines (2.b.). Separately for the accurate determination of environment-associated APEC-like strains, aerosol sampler evaluations have been completed. However, field implementation of the sampling systems to determine on-farm aerosolized E. coli concentrations has been delayed due to travel restrictions and access limitations at commercial farms. UV and EPI mitigation research is proceeding and on-schedule.

1. Aerosolized APEC sampling in poultry houses. ARS researchers in Mississippi State, Mississippi, evaluated three aerosol sampling technologies (media plates, liquid capture, and filter-based) for E. coli sampling performance. The filter-based system showed significantly reduced capture (28% reduction) and airborne concentration (50% reduction) when compared to media plates or liquid capture. Settled airborne E. coli survivability was evaluated and the mean half-life time was 74.3 hours, indicating that post-aerosolization survivability was significantly less than when directly deposited (28 days).