Empowering active surveillance of Carbapenem-resistant Enterobacterales: Insights from one year of genomic surveillance.

BACKGROUND

Healthcare-associated infections (HAIs) in Europe affect millions of patients annually, driving antimicrobial resistance and imposing significant economic burdens. Carbapenem-resistant Enterobacterales (CRE) are particularly concerning due to their ability to spread, making genomic surveillance essential for tracking their transmission.

METHODS

From October 2022 to September 2023, we sequenced and analysed the genome of 340 CRE obtained from patients admitted to Fondazione IRCCS Policlinico San Matteo ( Italy). Sequencing was performed using a short-read approach and genomes were in-silico characterized to identify Sequence Types (STs), antimicrobial resistance and virulence determinants, and plasmid content. Moreover, a core SNP-based phylogeny was performed to identify potential epidemic clusters within the same clone.

RESULTS

Among the 340 CRE isolated from surveillance (N = 234) and other clinical specimens (N = 106), 87.7% belonged to the Klebsiella genus, primarily K. pneumoniae (CR-Kp, N = 284). Escherichia coli (CR-Ec) accounted for 8.5% (N = 29); while the remaining species were Enterobacter spp. (N = 13) and Citrobacter spp. (N = 9). blaKPC and blaNDM gene variants were detected in 55.9% and 25.6% of CRE, respectively. The most prevalent CR-Kp clones were ST307, ST6668, ST258, and ST512, whereas ST131 was dominant among CR-Ec. Large epidemic clusters (ECs; ≥ 5 strains in each clade) were mainly found in CR-Kp associated with ST307 and ST6668, with 80.63% of CR-Kp grouped into nine ECs. Conversely, other species were observed as sporadic cases or within transmission clusters with limited spread.

CONCLUSION

Our comprehensive analysis of CRE circulation at HSM revealed that their dissemination was largely driven by highly successful clones, shedding light on several of them.