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Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages.
BMC Genomics. 2015 Sep 29; 16:733.BG

Abstract

BACKGROUND

Shiga toxin-producing Escherichia coli O157:H7 is a foodborne pathogen that causes severe human diseases including hemolytic uremic syndrome (HUS). The virulence factor that mediates HUS, Shiga toxin (Stx), is encoded within the genome of a lambdoid prophage. Although draft sequences are publicly available for a large number of E. coli O157:H7 strains, the high sequence similarity of stx-converting bacteriophages with other lambdoid prophages poses challenges to accurately assess the organization and plasticity among stx-converting phages due to assembly difficulties.

METHODS

To further explore genome plasticity of stx-converting prophages, we enriched phage DNA from 45 ciprofloxacin-induced cultures for subsequent 454 pyrosequencing to facilitate assembly of the complete phage genomes. In total, 22 stx2a-converting phage genomes were closed.

RESULTS

Comparison of the genomes distinguished nine distinct phage sequence types (PSTs) delineated by variation in obtained sequences, such as single nucleotide polymorphisms (SNPs) and insertion sequence element prevalence and location. These nine PSTs formed three distinct clusters, designated as PST1, PST2 and PST3. The PST2 cluster, identified in two clade 8 strains, was related to stx2a-converting phages previously identified in non-O157 Shiga-toxin producing E. coli (STEC) strains associated with a high incidence of HUS. The PST1 cluster contained phages related to those from E. coli O157:H7 strain Sakai (lineage I, clade 1), and PST3 contained a single phage that was distinct from the rest but most related to the phage from E. coli O157:H7 strain EC4115 (lineage I/II, clade 8). Five strains carried identical stx2a-converting phages (PST1-1) integrated at the same chromosomal locus, but these strains produced different levels of Stx2.

CONCLUSION

The stx2a-converting phages of E. coli O157:H7 can be categorized into at least three phage types. Diversification within a phage type is mainly driven by IS629 and by a small number of SNPs. Polymorphisms between phage genomes may help explain differences in Stx2a production between strains, however our data indicates that genes encoded external to the phage affect toxin production as well.

Authors+Show Affiliations

Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, 78249, USA.Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, 78249, USA.Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, 78249, USA.Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA. egd100@psu.edu. Center of Molecular Immunology and Infectious Disease, The Pennsylvania State University, University Park, PA, 16802, USA. egd100@psu.edu. 427 Food Science Building, The Pennsylvania State University, University Park, PA, 16802, USA. egd100@psu.edu.

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

26416807

Citation

Yin, Shuang, et al. "Escherichia Coli O157:H7 Strains Harbor at Least Three Distinct Sequence Types of Shiga Toxin 2a-converting Phages." BMC Genomics, vol. 16, 2015, p. 733.
Yin S, Rusconi B, Sanjar F, et al. Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages. BMC Genomics. 2015;16:733.
Yin, S., Rusconi, B., Sanjar, F., Goswami, K., Xiaoli, L., Eppinger, M., & Dudley, E. G. (2015). Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages. BMC Genomics, 16, 733. https://doi.org/10.1186/s12864-015-1934-1
Yin S, et al. Escherichia Coli O157:H7 Strains Harbor at Least Three Distinct Sequence Types of Shiga Toxin 2a-converting Phages. BMC Genomics. 2015 Sep 29;16:733. PubMed PMID: 26416807.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages. AU - Yin,Shuang, AU - Rusconi,Brigida, AU - Sanjar,Fatemeh, AU - Goswami,Kakolie, AU - Xiaoli,Lingzi, AU - Eppinger,Mark, AU - Dudley,Edward G, Y1 - 2015/09/29/ PY - 2015/06/09/received PY - 2015/09/15/accepted PY - 2015/9/30/entrez PY - 2015/9/30/pubmed PY - 2016/6/23/medline SP - 733 EP - 733 JF - BMC genomics JO - BMC Genomics VL - 16 N2 - BACKGROUND: Shiga toxin-producing Escherichia coli O157:H7 is a foodborne pathogen that causes severe human diseases including hemolytic uremic syndrome (HUS). The virulence factor that mediates HUS, Shiga toxin (Stx), is encoded within the genome of a lambdoid prophage. Although draft sequences are publicly available for a large number of E. coli O157:H7 strains, the high sequence similarity of stx-converting bacteriophages with other lambdoid prophages poses challenges to accurately assess the organization and plasticity among stx-converting phages due to assembly difficulties. METHODS: To further explore genome plasticity of stx-converting prophages, we enriched phage DNA from 45 ciprofloxacin-induced cultures for subsequent 454 pyrosequencing to facilitate assembly of the complete phage genomes. In total, 22 stx2a-converting phage genomes were closed. RESULTS: Comparison of the genomes distinguished nine distinct phage sequence types (PSTs) delineated by variation in obtained sequences, such as single nucleotide polymorphisms (SNPs) and insertion sequence element prevalence and location. These nine PSTs formed three distinct clusters, designated as PST1, PST2 and PST3. The PST2 cluster, identified in two clade 8 strains, was related to stx2a-converting phages previously identified in non-O157 Shiga-toxin producing E. coli (STEC) strains associated with a high incidence of HUS. The PST1 cluster contained phages related to those from E. coli O157:H7 strain Sakai (lineage I, clade 1), and PST3 contained a single phage that was distinct from the rest but most related to the phage from E. coli O157:H7 strain EC4115 (lineage I/II, clade 8). Five strains carried identical stx2a-converting phages (PST1-1) integrated at the same chromosomal locus, but these strains produced different levels of Stx2. CONCLUSION: The stx2a-converting phages of E. coli O157:H7 can be categorized into at least three phage types. Diversification within a phage type is mainly driven by IS629 and by a small number of SNPs. Polymorphisms between phage genomes may help explain differences in Stx2a production between strains, however our data indicates that genes encoded external to the phage affect toxin production as well. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/26416807/Escherichia_coli_O157:H7_strains_harbor_at_least_three_distinct_sequence_types_of_Shiga_toxin_2a_converting_phages_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1934-1 DB - PRIME DP - Unbound Medicine ER -