Location: Poultry Research
Project Number: 6064-13000-014-001-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 31, 2019
End Date: Jul 30, 2024
Objective:
1. Complete genomic sequencing and genomic assembly (Objective 1)
2. Comparative genomics and determination of genetic features specific for antigenicity, pathogenesis, and tissue tropisms of APEC isolates in comparison to commensal E. coli (Objective 2a).
Approach:
The whole genomes and plasmids of at least 20 additional APEC isolates will be sequenced using MinION sequencing to achieve our goal of characterizing a total of 250 APEC isolates. Additional resequencing will be performed to close gaps and provide additional sequencing depth for some genomes that have not assembled correctly.
Obj. 2 Approach:
Comparative analysis of the genomes and plasmids of the sequenced APEC isolates is being performed. This analysis includes comparison of virulence genes and antibiotic resistance markers between the APEC strains as well as identification virulence determinants and other genes that are found to coincide with specific pathologies, host types, and environmental factors. Initial sparse machine learning models have been developed and are being improved to compare between our sequenced APEC strains and publicly available genomic sequences of commensal and other pathogenic E. coli strains.
