Location: Poultry Research
2023 Annual Report
Objectives
1. Use proteomics, genomics, and systems biology approaches to identify molecular determinants of pathogenesis, strain variation, and tissue tropism of different 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.
2.a. Identify genetic determinants for antigenicity and pathogenicity of E. coli through comparative genomics and analyses.
2.b. Identification of immunological targets will provide a cross protection against different strains of Avian Pathogenic Escherichia coli (APEC).
2.c. Assess in ovo vaccination technology for delivery of live attenuated APEC vaccines.
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.
3.a.1. Evaluate performance of three bio-aerosol samplers for collecting airborne E. coli attached to dust particles from poultry production environments.
3.a.2. Quantify concentration and size distribution of airborne E. coli in representative US broiler and layer houses.
3.a.3. Evaluate electrostatic particle ionization (EPI) and ultraviolet (UV) radiation to reduce airborne E. coli.
3.b.1. Evaluate effects of litter amendment application rate on E. coli populations in broiler litter.
3.b.2. Assess E. coli populations and antibiotic growth promoter (AGP) residue concentrations in biochar-treated and untreated litter (live study).
3.b.3. Evaluate effects of litter management [top-dressed (TD) vs non-top-dressed] and bedding type (pine vs switchgrass) on litter E. coli populations over successive flocks.
Approach
Proteomic, genomic, and systems biology approaches will be applied to identify molecular determinants of pathogenesis, strain variation, and tissue tropism of different E. coli strains. The E. coli strains analyzed will be isolated from varying diseased poultry flocks and strain genomic & proteomic characteristics and isolate epidemiological factors will be applied model development for greater understanding of pathogenic E. coli and associated disease. To further protect against pathogenic E. coli, immunological targets will be identified that will confer cross-protection against prevalent E. coli strains in poultry production. The genomic and plasmid sequences of various E. coli strains will be aligned, and antigenic factors will be determined. Immunological targets will be identified and assessed via challenge models that provide cross-protection against pathogenic E. coli. In addition, vaccination platforms that are effective in very young birds, provide cross-protection, and can be easily administered will be developed. In ovo technologies will be assessed for delivery of protective vaccines and associated protocols developed. To increase the understanding of environmental E. coli and evaluate risks to poultry and associated antimicrobial resistance, studies will evaluate airborne E. coli associated with dust particles and E. coli linked to poultry litter. Further, mitigation means will be assessed for their impact on environmental E. coli populations.
Progress Report
Per objective 1, thirty-six additional Avian Pathogenic E. Coli (APEC) strains were sequenced, assembled, and annotated for a cumulative total of 225. A manuscript describing the virulence factors associated with 10 isolates and genomic comparisons has been published in a peer reviewed journal (1.a and 2.a). Additional strains are currently being assembled, annotated, and compared. Cooperator has hired a new post-doc to complete this portion of the research. Per Objective 2b, the characterization of APEC isolates from broilers including AST/AMR, growth curve, and WGS analyses continues. The embryo lethality assessments were performed on 29 APEC isolates. The resulting information is being applied to an APEC challenge model. Thirteen vaccine targets have been identified using reverse vaccinology and are currently being evaluated via a cell model. Per Objective 2c, the effects of injecting a live attenuated E. coli vaccine into egg-layer embryos and impacts hatchling development were investigated and published in a peer-reviewed journal.
Accomplishments
1. Escherichia coli (E coli) are common bacteria found in the intestines of animals. However, some E coli strains (avian pathogenic E coli, or APEC) cause infections and disease in poultry at sites other than the intestines. ARS researchers in Starkville, Mississippi, sequenced the genomes of 10 APEC isolates from Mississippi to understand the genomic and pathogenic differences between the strains. The results showed that the strains are genetically very similar to each other when compared to other E coli strains. However, the strains differed significantly in their antimicrobial resistance (AMR) and virulence genes as well as specific cell surface markers. This suggests that a wide range of genomic diversity in virulence factors and AMR genes are present in APEC strains. This suggests that the current limited approaches to controlling APEC and our current limited understanding of APEC are insufficient to control this organism in poultry flocks.
2. Escherichia coli (E. coli) is an opportunistic organism that ordinarily resides in the normal gut microbiota. A subset of E. coli known as Avian Pathogenic E. coli (APEC), as the name suggests, can cause disease in birds including commercial chickens. Commercial layer chickens that provide the nation’s table egg supply are also susceptible to APEC. Most commercial producers vaccinate their commercial layer chickens against APEC. One such vaccine is a modified live vaccine (Poulvac® E.coli, Zoetis) that is applied to birds that are at least 1 day of age. ARS researchers in Starkville, Mississippi, in collaboration with the Poultry Science Department at Mississippi State University investigated the potential to vaccinate commercial layers before 1 day of age (before hatch) by vaccinating the embryonic chicken within the egg (in ovo) to provide for a more precise and controlled delivery and even earlier immunity against APEC infections 3 days before hatch. The research evaluated delivering the vaccine at varying dosages to the amnionic sac or the air cell of the embryonated egg and its effect on the hatch success, bacteria prevalence, and hatched chick body weight. An inverse relationship was found with increasing dosage of the amnion injection decreasing numbers of hatched chicks and the hatched chick body weight. The birds in ovo-vaccinated with the highest dosage (107 CFU/egg) experienced 5.4% mortality while no other treatments experienced any mortality. All dosages of the tested vaccine caused a reduction in body weight in the birds that extended to the 21st day of rearing after hatch by as much as 19 grams in the 107 CFU/egg dosage. The lowest dose tested in the trials (4.4 x 101 CFU/egg) had the least effect on the birds’ final body weight, however, it caused hatch to decrease by approximately 5%. Overall, the in ovo-vaccination of Poulvac E.coli shows promise with needed modifications. The reduction in hatch is the most important factor that will need to be addressed in future research.
Review Publications
Fancher, C.A., Thames, H.T., Colvin, M.G., Smith, M., Easterling, A., Nuthalapati, N., Zhang, L., Kiess, A., Dinh, T., Sudumaran, A. 2021. Prevalence and molecular characteristics of avian pathogenic Escherichia coli in “No Antibiotics Ever” broiler farms. Microbiology Spectrum. 9(3):e00834-21. https://doi.org/10.1128/Spectrum.00834-21.
Li, T., Castaneda, D., Arick, M., Hsu, C., Kiess, A., Zhang, L. 2020. Complete genome sequence of multidrug-resistant avian pathogenic Escherichia coli strain APEC-O2-MS1170. Journal of Global Antimicrobial Resistance. 23:401-403. https://doi.org/10.1016/j.jgar.2020.11.009.
Nguyen, X.D., Zhao, Y., Evans, J.D., Lin, J., Voy, B., Purswell, J.L. 2022. Effect of ultraviolet radiation on reducing airborne Escherichia coli carried by poultry litter particles. Animals. 12(22):3170. https://doi.org/10.3390/ani12223170.
Robinson, K., Assumpcao, A., Arsi, K., Erf, G.F., Donoghue, A.M., Jesudhasan, P. 2022. Effect of Salmonella Typhimurium colonization on microbiome maturation and blood leukocyte populations in broiler chickens. Animals. 12(20):2867. https://doi.org/10.3390/ani12202867.
Robinson, K., Assumpcao, A., Arsi, K., Donoghue, A.M., Jesudhasan, P. 2022. Ability of garlic and ginger oil to reduce Salmonella in post-harvest poultry. Animals. 12(21):2974. https://doi.org/10.3390/ani12212974.
Lindsey, L.L., Collins Elliott, K.E., Fratemi, S.A., Evans, J.D., Mousstaaid, A., Gerard, P.D., Peebles, E.D. 2022. Variable effects of the in ovo administration of an Escherichia coli vaccine in the amnion or air cell on commercial layer embryo and hatchling development. Poultry. 1(4):278-290. https://doi.org/10.3390/poultry1040023.
Panda, A., Booth, S.L. 2022. Nutritional aspects of healthy aging. Medical Clinics of North America. 106(5): 853-864. https://doi.org/10.1016/j.mcna.2022.04.008.
Fancher, C., Zhang, L., Kiess, A., Adhikari, P., Dinh, T., Sukumaran, A. 2020. Avian pathogenic Escherichia coli and clostridium perfringens: Challenges in no antibiotics ever broiler production and potential solutions. Microorganisms. 8(10):1533. https://doi.org/10.3390/microorganisms8101533.
