title: Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages.
abstract: BACKGROUND
  Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. coli O157 facilitates public health surveillance and outbreak investigations, certain phage types are more likely to occupy specific niches and are associated with specific age groups and disease severity. The aim of this study was to analyse the genome sequences of 16 (fourteen T4 and two T7) E. coli O157 typing phages and to determine the genes responsible for the subtle differences in phage type profiles.
  
  
  RESULTS
  The typing phages were sequenced using paired-end Illumina sequencing at The Genome Analysis Centre and the Animal Health and Veterinary Laboratories Agency and bioinformatics programs including Velvet, Brig and Easyfig were used to analyse them. A two-way Euclidian cluster analysis highlighted the associations between groups of phage types and typing phages. The analysis showed that the T7 typing phages (9 and 10) differed by only three genes and that the T4 typing phages formed three distinct groups of similar genomic sequences: Group 1 (1, 8, 11, 12 and 15, 16), Group 2 (3, 6, 7 and 13) and Group 3 (2, 4, 5 and 14). The E. coli O157 phage typing scheme exhibited a significantly modular network linked to the genetic similarity of each group showing that these groups are specialised to infect a subset of phage types.
  
  
  CONCLUSIONS
  Sequencing the typing phage has enabled us to identify the variable genes within each group and to determine how this corresponds to changes in phage type.
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, 61 Colindale Ave, London, NW9 5HT, UK. lauren.cowley@phe.gov.uk.
authors.forename: Lauren A
authors.initials: LA
authors.lastname: Cowley
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Laver Building, North Park Road, Exeter, EX4 4QE, UK. S.J.Beckett@exeter.ac.uk.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Beckett
authors.affiliation: Division of Immunity and Infection, The Roslin Institute, R(D)VS, University of Edinburgh, Edinburgh, EH25 9RG, UK. margo.chase@ed.ac.uk.
authors.forename: Margo
authors.initials: M
authors.lastname: Chase-Topping
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, 61 Colindale Ave, London, NW9 5HT, UK. neil.perry@phe.gov.uk.
authors.forename: Neil
authors.initials: N
authors.lastname: Perry
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, 61 Colindale Ave, London, NW9 5HT, UK. tim.dallman@phe.gov.uk.
authors.forename: Tim J
authors.initials: TJ
authors.lastname: Dallman
authors.affiliation: Division of Immunity and Infection, The Roslin Institute, R(D)VS, University of Edinburgh, Edinburgh, EH25 9RG, UK. david.gally@roslin.ed.ac.uk.
authors.forename: David L
authors.initials: DL
authors.lastname: Gally
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, 61 Colindale Ave, London, NW9 5HT, UK. claire.jenkins1@phe.gov.uk.
authors.forename: Claire
authors.initials: C
authors.lastname: Jenkins
mesh_terms: D017122:Bacteriophage T4 / Q000235:genetics; D001434:Bacteriophage Typing; D001435:Bacteriophages / Q000235:genetics*; D016000:Cluster Analysis; D019295:Computational Biology; D004279:DNA, Viral / Q000032:analysis / Q000302:isolation & purification; D019453:Escherichia coli O157 / Q000821:virology*; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral