The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom

• Published in: Microbial genomics Vol. 9; no. 10
• Main Authors: Hamilton, William L, Coscione, Suny, Maes, Mailis, Warne, Ben, Pike, Lindsay J, Khokhar, Fahad A, Blane, Beth, Brown, Nicholas M, Gouliouris, Theodore, Dougan, Gordon, Török, M Estée, Baker, Stephen
• Format: Journal Article
• Language: English
• Published: England Microbiology Society 01-10-2023
• Subjects: England; Escherichia coli - genetics; Escherichia coli Infections - epidemiology; Genomics; Hospitals, Teaching; Humans; Sepsis; United Kingdom - epidemiology; England; United Kingdom; whole genome sequencing; genomic epidemiology; Gram negative; Antimicrobial resistance; clinical microbiology; monoclonal antibody; multidrug resistant; E. coli; healthcare-associated infections
• ISSN: 2057-5858; 2057-5858
• DOI: 10.1099/mgen.0.001122

is a ubiquitous component of the human gut microbiome, but is also a common pathogen, causing around 40, 000 bloodstream infections (BSI) in the United Kingdom (UK) annually. The number of
BSI has increased over the last decade in the UK, and emerging antimicrobial resistance (AMR) profiles threaten treatment options. Here, we combined clinical, epidemiological, and whole genome sequencing data with high content imaging to characterise over 300
isolates associated with BSI in a large teaching hospital in the East of England. Overall, only a limited number of sequence types (ST) were responsible for the majority of organisms causing invasive disease. The most abundant (20 % of all isolates) was ST131, of which around 90 % comprised the pandemic O25b:H4 group. ST131-O25b:H4 isolates were frequently multi-drug resistant (MDR), with a high prevalence of extended spectrum β-lactamases (ESBL) and fluoroquinolone resistance. There was no association between AMR phenotypes and the source of
bacteraemia or whether the infection was healthcare-associated. Several clusters of ST131 were genetically similar, potentially suggesting a shared transmission network. However, there was no clear epidemiological associations between these cases, and they included organisms from both healthcare-associated and non-healthcare-associated origins. The majority of ST131 isolates exhibited strong binding with an anti-O25b antibody, raising the possibility of developing rapid diagnostics targeting this pathogen. In summary, our data suggest that a restricted set of MDR
populations can be maintained and spread across both community and healthcare settings in this location, contributing disproportionately to invasive disease and AMR.