Genomic analysis of bacteriophages from non-O157 shiga toxin-producing Escherichia coli

Abstract

Shiga toxin-producing Escherichia coli (STEC) is the fiercest pathotype among all diarrheic E. coli. STEC O157:H7 has been a predominant serotype for STEC in the United States. However, an increasing number of cases of infections by STEC other than O157 have been reported in recent years. Shiga toxin (Stx) is the most important virulence factor of STEC and is encoded by stx, which is introduced into STEC genome by bacteriophages through gene transduction. A detailed understanding about Stx bacteriophages is necessary to reveal the emergence and pathogenicity of STEC. The very unstable genomes of Stx bacteriophages result in a dynamic phenotypic versatility including virulence, host cell repertoire and tolerance to adversities. Sequencing technology enables us to generate genomic sequence data of bacteriophages at an affordable cost. The project aimed at obtaining genomic DNA sequences of Stx bacteriophages of non-O157 STEC isolates of diverse serotypes. Thirteen bacteriophages were successfully induced from 83 STEC isolates of serotypes O74, O111, O121, O130, O163, O179 and O183. The bacteriophage DNA samples were collected and sequenced using MiSeq Desktop Sequencer (Illumina®, Inc). Automatically assembled sequences were manually compared to E. coli genome sequence available from NCBI (NC_000913.3) to verify the reliability of the sequencing results. Nine verified bacteriophage sequences were aligned to two Stx bacteriophage genomes of NCBI (NC_000924.1 and NC_018846.1) and visible alignment results were obtained. A phylogenetic relationship of the nine phages and the two reference sequences was constructed and gene profiles of each sample sequences were identified. The comparative analysis indicated that recombination events occurred in probacteriophages showed traces. Similarity of bacteriophage genomes correlated to the serotypes of host bacteria based on the comparison of phylogenetic tree and STEC serotypes. Gene identification results showed that nucleotide variance does not show region specificity, silent mutations are frequent in housekeeping genes and virulence genes are conservative among phage samples.