Comparative Genomic Analysis of Avibacterium paragallinarum using Next-gen sequencing to characterize Infectious Coryza infections in Domestic Poultry
Open Access
- Author:
- Morgan, Jasmine
- Area of Honors:
- Veterinary and Biomedical Sciences
- Degree:
- Bachelor of Science
- Document Type:
- Thesis
- Thesis Supervisors:
- Meera Surendran Nair, Thesis Supervisor
Robert John Vansaun, Thesis Honors Advisor - Keywords:
- Avian Diseases
Genotyping
Avibacterium
Next-gen sequencing
serotyping
Diagnostics - Abstract:
- Avibacterium paragallinarum is a gram-negative bacterium that has significant impacts on poultry health and economics associated with the presence of reduced egg production when present. The disease caused by the bacterial pathogen is called Infectious Coryza (IC) and prevention of IC relies on the use of biosecurity measures, surveillance, and vaccination. The absence of cross-protection among serovars makes rapid and efficient characterization of A. paragallinarum critical in reducing the risk of entry into poultry flocks. Current diagnostic tools such as conventional microbiology and serotyping are effective but are not as rapid and are labor-intensive causing for there to be a delay in the diagnostic process. Due to this, the goal of our study was to use comparative genome analysis to evaluate if next generation sequencing is a viable tool in diagnosing outbreaks and identifying the associated serogroups rapidly. To accomplish this, we performed comparative genome analysis of 41 clinical isolates collected from 2019 Pennsylvania (PA) IC outbreaks. The microbial genomes were assembled using Tychus and annotated using Prokka. Roary was then use to identify core genes and unique genes to evaluate how Page Serovars varied genetically. The outputs of Roary were then used to construct a phylogenetic tree to evaluate genetic relatedness of the clinical isolates to previously reported reference isolates obtained from NCBI GenBank. The study revealed genetic diversity among the AP serovars with an in-depth understanding of similarities and differences using reference strains and A. paragallinarum isolates from PA. Further an increased level of genetic heterogeneity among isolates compared to the reference genomes shed light to the open nature of the pan-genome.