Septicaemia, E. coli bacteraemia, epidemiology, risk factors, health protection, public health
Objectives:
This study utilises whole genome sequencing (WGS) to identify temporal, geographic and genomic risk factors to determine the rise of Escherichia coli bacteraemia (ECB) in Wales.
Methods:
Population-based prospective WGS study. Microbiology laboratories in Wales submitted all non-duplicate isolates of E. coli from blood cultures to the Specialist Antimicrobial Chemotherapy Unit (SACU) between April 2013 and June 2014 for WGS by Cardiff University. The dataset was linked to routine microbiological surveillance data to
obtain isolate antimicrobial resistance (AMR) profiles. Novel AMR profiles and profiles with phylogeography were characterised by polymerase chain reaction and 672 were selected for WGS based on their determined phylogenetic groups. 48 retrospective ECB samples collected between 2007 and 2012 for BSAC’s Bacteraemia Resistance Surveillance Programme were also included.
Results:
720 isolates were WGS for analysis. The
population structure of the cohort is dominated by four key lineages, which are responsible for a disproportionate number of ECB episodes; MLST Sequence Types 131, 69, 95, and 73. These sequence types are distinct
in their virulence and AMR profiles, and have previously been identified as the principal causes of ECB in other parts of the UK. The study identifies that antimicrobial resistance is variable between these MLST sequence
types. The WGS information has been put into context using additional epidemiological data to identify risk factors associated with these key lineages.
Conclusions:
This high-resolution data will provide a
clear target for developing and deploying
interventions to halt the rise of ECB in
Wales.