Whole genome shotgun sequencing revealed highly polymorphic genome regions and genes in Escherichia coli O157:H7 isolates collected from a single feedlot

Abstract

Escherichia coli serotype O157:H7 continues to pose a serious health threat to human beings. Cattle, a major reservoir of the pathogen, harbor E. coli O157:H7 in their gastrointestinal tract and shed variable concentrations of E. coli O157:H7 into the environment. Genetic characterization of cattle-shed E. coli O157 strains is of interest to the livestock industry, food business, and public health community. The present study applied whole genome shotgun sequencing (WGS) and single nucleotide variant (SNV) calling to characterize 279 cattle-shed E. coli O157:H7 strains isolated from a single feedlot located in southwestern region of the US. More than 4,000 SNVs were identified among the strains and the resultant phylogenomic tree revealed three major groups. Using the Sakai strain genome as reference, more than 2,000 SNVs were annotated and a detailed SNV map generated. Results clearly revealed highly polymorphic loci along the E. coli O157:H7 genome that aligned with the prophage regions and highly variant genes involved in processing bacterial genetic information. The WGS data were further profiled against a comprehensive virulence factor database (VFDB) for virulence gene identification. Among the total 285 virulence genes identified, only 132 were present in all the strains. There were six virulence genes unique to single isolates. Our findings suggested that the genome variations of the E. coli O157:H7 were mainly attributable to dynamics of certain phages, and the bacterial strains have variable virulence gene profiles, even though they came from a single cattle population, which may explain the differences in pathogenicity, host prevalence, and transmissibility by E. coli O157:H7.

Fig 1. Phylogenomic relatedness of the E. coli O157 strains isolated from cattle feces from a single feedlot.

ML phylogenetic tree; red, strains in clade 6; green, strains in clade 7; blue, strains in clade 8; rosy-brown, strains that could not be assigned to a clade; and purple, E. coli O157:H7 Sakai strain for reference.

Fig 2. Phylogenomic relatedness among the E. coli O157 strains isolated from cattle feces from a single feedlot and the relevant genomes downloaded from the GenBank.

Black, the downloaded genomes; red, strains in clade 6; green, strains in clade 7; blue, strains in clade 8; yellow, E. coli -:H7, including E coli O55:H7; purple, E. coli O157:H7 Sakai strain; and dark red, E. coli K12. Boxes contains the genome accession numbers corresponding to a given cluster.

Fig 3. Single nucleotide variants on E. coli O157:H7 genome.

Pink circular track, SNVs in genes; orange circular track, SNVs in intergenic regions; orange bars, phage regions; and blue arrows, genes.

Fig 4. Number of single nucleotide variants (SNV) per 2, 000 bases along the E. coli Sakai genome.

SNV-rich regions were zoomed in.

Fig 5. E. coli O157:H7 strains clustering based on the differences in the virulence gene profile.

Clusters dominant with strains from the clades 6, 7, and 8 were highlighted in blue, pink and green, respectively.