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

• DOI: 10.1099/mgen.0.001314
• Publication Date: 2024-11-04T10:15:53Z
• Authors: Ann E. Snaith; Robert A. Moran; Rebecca J. Hall; Anna Casey; Liz Ratcliffe; Willem van Schaik; Tony Whitehouse; Alan McNally
• Keywords: Colonisation; Carriage; Pandemic

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 understanding extent patient colonisation by multi-drug-resistant organisms (MDROs) large UK ICUs. Previous work ICUs globally uncovered rates transmission MDROs, but situation is less understood. Here, we investigated diversity antibiotic resistance gene (ARG) carriage present one largest Queen Elizabeth Hospital Birmingham (QEHB), focusing primarily E. as both a widespread commensal disseminated pathogen. Samples were taken during highly restrictive coronavirus disease 2019 (COVID-19) control measures May to December 2021. Whole-genome metagenomic sequencing used detect report strain-level patients, sequence types (STs), their dynamics carriage. We found lack multi-drug (MDR) QEHB. Only carbapenemase-producing organism was isolated, Citrobacter carrying bla KPC-2 . There no evidence supporting spread this strain, there little overall nosocomial acquisition or circulation colonising Whilst 22 different STs identified, only 1 strain pandemic ST131 lineage isolated. This non-MDR be clade A associated with low levels resistance. Overall, QEHB had very MDR strains, result that may influenced part strict COVID-19 place time. Employing some these prevention where reasonable all might therefore assist maintaining MDR.