Ten-year surveillance of carbapenemase producing Enterobacterales in in one of the smallest European countries, including a genomic overview of Klebsiella pneumoniae strains (2019-2023)
Background  Prevalence of non-invasive Carbapenemase producing Enterobacterales (CPE) cases in Luxembourg is unknown and the increase in CPE cases globally indicated an urgent need to review Luxembourg data. Aim  The study aim was to describe the molecular epidemiology of CPEs at national level during the period of 2014 to 2023 with focus on whole genome sequencing results (WGS) for selected Klebsiella pneumoniae (CPE-KPNE) cases. Methods In this retrospective study, antimicrobial sensitivity results and basic demographic characteristics of all suspected CPE samples received by the “laboratoire national de santé” (LNS) were descriptive analysed. In addition, WGS data derived from CPE-K.pneumoniae (CPE-KPNE) cultures using Illumina platform and Ridom™ Seqshere+ software, were analysed to identify transmission chains, virulence and other resistance makers.  Results Overall, 1,136 suspected CPE isolates were received, of which 279 (24.6%) from 191 patients were positive for CPE gene(s). The most frequently detected CPE genotype was OXA-48-like with 37.3% (N=81), closely followed by KPC with 35.5% (N=77) and NDM with 15.7% (N=34). The relative proportions of E.coli harboring CPEs increased substantially over the past 5 years (14% versus 40%) whereas the Klebsiella pneumoniae proportion decreased (66% versus 47%). Only 42% of the CPE detection were from rectal swabs. The CPE-KPNE population was represented by 25 different sequence types, with two larger potential clusters identified. Overall 32% of CPE-KPNE cases (N=19/60) were phenotypically resistant to all tested aminoglycosides, cephalosporines and ciprofloxacin.  Conclusion Enhancing CPE surveillance in Luxembourg would enable a better understanding of the spread of resistant Enterobacterales and the optimization of infection control measures.