Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages.

Lauren A Cowley,Claire Jenkins,David L Gally,Neil Perry,Tim J Dallman,Stephen J Beckett,Margo Chase-Topping

doi:10.1186/s12864-015-1470-z

Lauren A Cowley, Claire Jenkins + Show 5 more

Open Access

https://doi.org/10.1186/s12864-015-1470-z

Copy DOI

Abstract

BackgroundShiga 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.ResultsThe 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.ConclusionSequencing 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1470-z) contains supplementary material, which is available to authorized users.

Highlights

Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome
The analysis showed that the Shiga toxin producing E. coli (STEC) O157 phage typing scheme formed a weak (Qb = 0.1575 (Table 1)) but significantly modular network where the typing phages (TP) groups were each specialised to infect a subset of phage types (PT) (Figure 2)
In this study, the STEC O157 typing phages we clustered into four distinct groups of similar genomic sequences, that broadly correlated with phage typing profile groups determined by two-way Euclidian clustering

Summary

Introduction

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. Escherichia coli O157:H7 is the most prevalent Shiga toxin producing E. coli (STEC) serotype in the UK and has the most severe impact on human health [1]. STEC O157 symptoms can range from mild gastroenteritis to severe bloody diarrhoea and in more extreme cases haemolytic uraemic syndrome (HUS) [2]. A recent Public Health England (PHE) study found incidence to be as high as 1.78 per 100,000 person-years with up to 33% of cases being hospitalised (Gastrointestinal Bacterial Reference Unit (GBRU) in house data).

Objectives

Methods

Results

Discussion

Conclusion