Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections

Goswami, C. , Fox, S., Holden, M., Connor, M., Leanord, A. and Evans, T. J. (2018) Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections. Microbial Genomics, 4(6), e000190. (doi: 10.1099/mgen.0.000190) (PMID:29932391) (PMCID:PMC6096937)

Abstract

Bacteraemia caused by Escherichia coli is a growing problem with a significant mortality. The factors that influence the acquisition and outcome of these infections are not clear. Here, we have linked detailed genetic data from the whole-genome sequencing of 162 bacteraemic isolates collected in Scotland, UK, in 2013–2015, with clinical data in order to delineate bacterial and host factors that influence the acquisition in hospital or the community, outcome and antibiotic resistance. We identified four major sequence types (STs) in these isolates: ST131, ST69, ST73 and ST95. Nearly 50 % of the bacteraemic isolates had a urinary origin. ST69 was genetically distinct from the other STs, with significantly less sharing of accessory genes and with a distinct plasmid population. Virulence genes were widespread and diversely distributed between the dominant STs. ST131 was significantly associated with hospital-associated infections (HAIs), and ST69 with those from the community. However, there was no association of ST with outcome, although patients with HAI had a higher immediate mortality compared to those with community-associated infections (CAIs). Genome-wide association studies revealed genes involved in antibiotic persistence as significantly associated with HAIs and those encoding elements of a type VI secretion system with CAIs. Antibiotic resistance was common, and there were networks of correlated resistance genes and phenotypic antibiotic resistance. This study has revealed the complex interactions between the genotype of E. coli and its ability to cause bacteraemia, and some of the determinants influencing hospital or community acquisition. In part, these are shaped by antibiotic usage, but strain-specific factors are also important.

• Item Type: Articles
• Additional Information: The work was funded by the Scottish Executive via the Chief Scientist Office through the provision of a grant to establish the Scottish Healthcare Associated Infection Prevention Institute (SHAIPI).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Goswami, Dr Cosmika and Leanord, Professor Alistair and Evans, Professor Tom and Fox, Dr Stephen
• Authors: Goswami, C., Fox, S., Holden, M., Connor, M., Leanord, A., and Evans, T. J.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: Microbial Genomics
• Publisher: Microbiology Society
• ISSN: 2057-5858
• ISSN (Online): 2057-5858
• Published Online: 22 June 2018
• Copyright Holders: Copyright © 2018 The Authors
• First Published: First published in Microbial Genomics 4(6): e000190
• Publisher Policy: Reproduced under a Creative Commons License