Longitudinal genomic surveillance of a UK intensive care unit shows a lack of patient colonisation by multi-drug resistant Gram-negative pathogens

Abstract

Vulnerable patients in an intensive care unit (ICU) setting are at high risk of infection from bacteria including gut-colonising Escherichia coli and Klebsiella species. Complex ICU procedures often depend on successful antimicrobial treatment, underscoring the importance of understanding the extent of patient colonisation by multi-drug resistant organisms (MDRO) in large UK ICUs. Previous work on ICUs globally uncovered high rates of colonisation by and transmission of MDRO, but the situation in UK ICUs is less understood. Here, we investigated the diversity and antibiotic resistance gene (ARG) carriage of bacteria present in one of the largest UK ICUs at the Queen Elizabeth Hospital Birmingham (QEHB), focussing primarily on E. coli as both a widespread commensal and a globally disseminated multidrug resistant pathogen. Samples were taken during highly restrictive COVID-19 control measures from May - December 2021. Whole-genome and metagenomic sequencing were used to detect and report strain level colonisation of patients, focussing on E. coli sequence types (STs), their colonisation dynamics, and antimicrobial resistance (AMR) gene carriage. We found a lack of multidrug resistance (MDR) in the QEHB. Only one carbapenemase-producing organism was isolated, a Citrobacter carrying blaKPC-2. There was no evidence supporting the spread of this strain, and there was little evidence overall of nosocomial acquisition or circulation of colonising E. coli. Whilst 22 different E. coli STs were identified, only one strain of the pandemic ST131 lineage was isolated. This ST131 strain was non-MDR and was found to be a clade A strain, associated with low levels of antibiotic resistance. Overall, the QEHB ICU had very low levels of pandemic or MDR strains, a result which may be influenced in part by the strict COVID-19 control measures in place at the time. Employing some of these infection prevention and control measures where reasonable in all ICUs might therefore assist in maintaining low levels of nosocomial MDR.