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ARS Home » Southeast Area » Mississippi State, Mississippi » Poultry Research » Research » Research Project #437284

Research Project: Identification of the Molecular Determinants of Pathogenesis, Strain Variation, and Tissue Tropism of Different E. coli Strains

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. Sequence Avian Pathogenic E. coli (APEC) strains obtained from accredited veterinary diagnostic labs and assemble associated genomes. (1.a) 2. Application of omic techniques to characterize APEC-associated disease factors

Approach:
APEC strains derived from accredited veterinary diagnostic facilities from states with significant poultry industries (e.g., Mississippi State University College of Veterinary Medicine’s Poultry Research and Diagnostic Lab) will be sequenced. In addition, all strain-associated metadata (e.g., bird species, breed, operation, sex, chicken age, and specimen source) will be collected for later analyses and confirmed as E. coli strains via 16S rDNA sequencing. MinION sequencing will be used to identify unique strains of E. coli. Nanopore allows users to select fragment length and sequences the entire fragment up to 1Mb. This will help us quickly obtain complete genomic sequences, especially for those isolates which might have a large genetic diversity from the prototype E. coli strains. To identify the unique strains for further analyses, MinION sequencing will be used to sequence the genomic sequences, including chromosome and plasmids. The whole genomes of at least 100 non-redundant E. coli strains will be sequenced, associated reads will be assessed, and high quality (99% base call accuracy) data will be used for genomic assembly. The short reads will be assembled de novo to create contiguous sequence and the contiguous sequences will be assembled and mapped to the template sequences. Sequences from Nanopore will be used to close the gaps between the reads and could use the alternative template for mapping the reads and assembly, especially those unmapped sequences. Alternatively, hybrid assembly using both short read and long read data may be performed with alternative assemblers (e.g., Unicycler).