Genomic characterization of two Shiga toxin-converting bacteriophages induced from environmental Shiga toxin-producing Escherichia coli.

Authors: ZHANG, YUJIE - Forest Service (FS); Liao, Yen-Te; Salvador, Alexandra; Wu, Vivian

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/13/2021
Publication Date: 2/25/2021
Citation: Zhang, Y., Liao, Y., Salvador, A., Wu, V.C. 2021. Genomic characterization of two Shiga toxin-converting bacteriophages induced from environmental Shiga toxin-producing Escherichia coli. Frontiers in Microbiology. 12. Article 587696. https://doi.org/10.3389/fmicb.2021.587696.
DOI: https://doi.org/10.3389/fmicb.2021.587696

Interpretive Summary: Stx-converting phages, also known as temperate phages, are a type of phages that are induced from Shiga toxin-producing E. coli (STEC) strains. Previous studies have found that Stx-converting phages are able to integrate their phage genomes into the bacterial host genome by transduction and likely contribute to the emergence of new STEC strains. However, the number of genomically characterized Stx-converting phages is scarce. Here, we reported the whole-genome sequencing data of two Stx-converting bacteriophages, Escherichia phage Lys8385Vzw and Lys19259Vzw, induced from E. coli O103:H11 and E. coli O157:H7 strains, respectively. The results showed that Stx1-converting phage Lys8385Vzw and Stx2-converting phage Lys19259Vzw had a total of 68 and 85 genes, respectively. More than 40% of the genes from both phages were identified with known functions that were contributed to the fitness characteristics related to both phages and the pathogenicity of their host strains. The comparison of the selected 15 Stx-converting phages showed the genomic diversity of Stx-converting phages. Furthermore, both genomes of Lys8385Vzw and Lys19259Vzw shared high homology to each of the prophage sequences containing stx genes from the selected five STEC strains, and the results suggested the potential distribution of these two Stx-converting phages among the selected pathogenic STEC strains. The findings of this study demonstrate a variety of the sequenced Stx-converting phages and also provide valuable insight into the potential distribution of Stx-converting phages among pathogenic STEC strains.

Technical Abstract: Shiga toxin, encoded by stx genes located on prophage sequence, is the major pathogenicity of Shiga toxin-producing Escherichia coli (STEC) and is closely associated with the development of hemolytic uremic syndrome. Although numerous Stx prophages sequences have been reported together with their STEC bacterial genomes, the information regarding the genomic characterization of Stx-converting bacteriophages induced from the STEC strains is lacking. The objectives of this study were to genomically characterize two Stx-converting phages and to evaluate their correlation with E. coli. A Stx1-converting phage Lys8385Vzw and a Stx2-converting phage Lys19259Vzw were induced using mitomycin C (0.5 µg/ml) from O103:H11 (RM8385) and O157:H7 (RM19259) strains, respectively. After DNA extraction, both phage DNAs were subjected to fragmentation, DNA library construction using a TruSeq® Nano DNA Library Prep Kit, and whole-genome sequencing using Reagent Kit v2 500 cycle on MiSeq sequencer. Phylogenetic analysis and comparative genomics were used to determine the correlation among these two Stx-converting phages, 13 reference Stx-converting phages, and 10 reference STEC genomes carrying close related Stx prophages. The results showed that both phages Lys8385Vzw and Lys19259Vzw had double-stranded DNA, with a genome size of 50,953 bp and 61,072 bp, respectively. Phylogenetic analysis revealed the 15 Stx-converting phages, all induced from different STEC strains, were divided into three clusters, and those from E. coli O157, in particular, were distributed in each cluster, demonstrating the genomic diversity of these Stx-converting phages. The comparative analysis showed the genes, which encoded the proteins associated with assembly and infection of Stx-converting phages, were conservative and likely related to the phage morphology. Phage Lys8385Vzw shared more than 70% coverage and 95% identity to the Stx prophages of five non-O157 clinical STEC strains, whereas Lys19259Vzw shared 99% coverage and identity to the Stx prophages of five STEC O157 strains from either clinical or environmental samples. The findings of the study demonstrate genomic characterization and variety of Stx-converting phages induced from different STEC strains and provide valuable insights into the potential distribution of Stx-converting phages among STEC strains.