Accessing the accessory genome to better understand the diversity of Shiga toxin-producing Escherichia coli O127:H7 during an outbreak

Shiga-toxin producing Escherichia coli (STEC) O157:H7 is a zoonotic, foodborne gastrointestinal pathogen that can cause a range of symptoms from mild to severe bloody diarrhoea. In a subset of cases, particularly in the young and elderly can lead to life threatening complications such as haemolytic uraemic syndrome (HUS).

STEC O157:H7 has a complex genome with 8% to 15% consisting of homologous prophage regions which leads to ambiguous mapping and difficulty when assembling the genomes with short-read sequencing data. Exploring the accessory genome provides context of mobile genetic elements and reveals large scale structural variation.

David Greig et al. applied Oxford Nanopore technology to achieve complete assemblies of STEC O157:H7 genomes from three different outbreak settings, including (i) environmental exposure (ii) direct contact with animals and (iii) foodborne transmission. The aim of the study was to determine within outbreak variation in the accessory genome.

Within each outbreak, we observed variation in plasmid content, prophage number and characteristics, micro-evolutionary events such as insertions and deletions, and large chromosomal rearrangements. The ability to characterise the accessory genome in this way is the first step to understanding the significance of these changes and their impact on the evolutionary history, virulence and transmission of this zoonotic, foodborne pathogen.