Whole genome sequencing approach for KPC and OXA-48 co-producing Klebsiella pneumoniae characterization
Background: Whole Genome Sequencing (WGS) provides important information for the characterization, surveillance and monitoring of antimicrobial resistance (AMR) determinants, particularly in case of multi- and extensively-drug resistant microorganisms. We reported the results of WGS analysis carried out for carbapenemases-producing Klebsiella pneumoniae cause of hospital-acquired infections (HAIs) and characterized by a marked resistance profile. Methods: Clinical, phenotypic and genotypic data were collected into the AMR surveillance screening program of University Hospital of Sassari (Italy) during 2020-2021. Genomic DNA was sequenced using the Illumina Nova Seq 6000 platform. Final assemblies were manually curated and carefully verified for the detection of antimicrobial resistance genes, porin mutations, and virulence factors. A phylogenetic analysis was performed by Maximum Likelihood method. Results: All strains belonged to ST 512 and most of them carried the blaKPC-31 variant, several additional resistance genes, OmpK35 truncation and OmpK36 mutation. Phenotypic analysis showed a marked resistance profile to all antibiotics, including novel ß-lactam/ß-lactamases inhibitors (BL/BLI). Conclusion: WGS characterization revealed the presence of several antibiotic resistance determinants and porin mutations in highly resistant K. pneumoniae strains responsible of HAIs. The detection of blaKPC-31 in our hospital wards highlights the importance of genomic surveillance in hospital settings to monitor the emergence of new clones, and the need to improve control and preventive strategies to efficiently contrast AMR.