Purpose: The whole genome of the Shiga toxin-negative E. coli O157:H7 strain was sequenced to understand the specific properties that are related to the colonization and adaptation of E. coli O157:H7 strains to feedlot cattle.
Methods: The C1-057 strain was cultured in trypticase soy broth overnight at 37°C and the genomic DNA was extracted. A Pacific Biosciences RSII system was used to obtain the complete genome sequences. A 3-20 kb library of the strain was prepared and sequenced, achieving average genome coverage of >100×. The 3-20 kb continuous-long-read (CLR) data were de novo assembled using the PacBio hierarchical genome assembly process 2 (HGAP2)/Quiver software package. Prophages and putative phage-like elements in the newly sequenced C1-057 strain were analyzed using the prophage-predicting PHAST Web server and were further compared with E. coli O157:H7 Sakai and E. coli K-12.
Results: When fully assembled, the complete genome consisted of the chromosome of 4,783,867 bp and two plasmids of 96,420 bp and 13,853 bp. These sequences were annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP). These sequences have been deposited at GenBank under the accession LAZO00000000. The C1-057 strain shared eight similar predicted prophages with E. coli O157:H7 Sakai and shared three similar predicted prophages with E. coli K-12.
Significance: The distribution of similar types of prophages among E. coli genomes may underpin a possible path that E. coli genomes evolve from non-pathogenic to pathogenic strains. Genomic characterization of this variant Shiga toxin-negative strain may help to develop interventions to prevent the colonization of E. coli O157:H7 in feedlot cattle.