Genome structural variation in Escherichia coli O157:H7.

Stephen F Fitzgerald,David L Gally,Lesley Allison,Sharif Shaaban,Sue C Tongue,Judith Evans,James L Bono,Madeleine K Henry,Tom N Mcneilly,David Greig,Nadejda Lupolova,Timothy J Dallman

doi:10.1099/mgen.0.000682

Abstract

The human zoonotic pathogen Escherichia coli O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, E. coli O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.

Highlights

Prophage are bacterial viruses integrated into the chromosome of their host and are major drivers of bacterial genome evolution, host and niche adaptation and virulence [1,2,3]
To examine the extent of genomic diversity generated by large- chromosomal rearrangements (LCRs) in the E. coli O157:H7 clonal group, we examined the whole-genome sequences of 72 isolates, the majority of which were generated by PacBio long-read sequencing
Strains analysed were representative of the main E. coli O157:H7 lineages (I, I/II and II) and included multiple sub- Lineage Ic, phage type (PT) 21/28 isolates, which have been responsible for the majority of serious human infections in the UK over the last two decades [11]

Summary

Introduction

Prophage are bacterial viruses integrated into the chromosome of their host and are major drivers of bacterial genome evolution, host and niche adaptation and virulence [1,2,3]. Numerous prophages (typically 16–25) have integrated into the genomes of E. coli O157:H7 strains with an integration bias towards the terminus (Ter) of replication [9] Acquisition of these prophages, many of which are closely related λ-like phages, has driven the evolution of this pathogen by carriage of virulence genes including secreted effector proteins, sRNAs involved in virulence gene regulation and [7, 10], importantly, these prophages include those that encode Shiga-toxin (Stx) subtypes. E. coli O157:H7 strains divide into three phylogenetically distinct lineages (I, I/II and II) Those that represent a serious threat to human health belong to either lineage I or lineage I/II and the majority encode two sub-types of Stx:Stx2a and Stx2c. Stx2a is generally associated with more serious disease [11, 15,16,17,18] and the emergence of E. coli O157:H7 as a zoonotic threat correlates with the introduction of Stx2a-encoding prophage into the E. coli O157:H7 cattle population approximately 50 years ago [11]

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Results

Conclusion