Genomic Characterization and Resistance Mechanisms of Carbapenem-Resistant Klebsiella pneumoniae ST101 Isolates from Saudi Arabia

Carbapenem-resistant <i>Klebsiella pneumoniae</i> (CRKP) represents a critical global health threat, with ST101 identified as a major circulating clone in Saudi Arabia. We used whole genome sequencing and plasmid reconstruction to investigate the molecular characteristics of CRKP ST101 isolates from Saudi Arabia (2018-2021), analyzing antimicrobial resistance genes (ARGs), virulence factors, and plasmid structure and replicon types. Clinical isolates were obtained from the Ministry of National Guard Health Affairs (MNGHA) hospitals in Saudi Arabia between 2018 and 2021. Whole-genome sequencing was performed using the Illumina MiSeq^® platform, followed by comprehensive bioinformatic analysis of ARGs, virulence factors, and plasmid content. All ten isolates belonged to ST101 and harbored extensive antimicrobial resistance (AMR) and virulence determinants. Nine isolates (90%) carried <i>bla</i>_OXA-48, with three co-harboring <i>bla</i>_NDM-1, representing dual-carbapenemase producers. These carbapenemase genes were located on plasmids with distinct replicon types, including IncL/M, IncHI1B/IncFIB, and IncFIA/IncR. All isolates were multidrug-resistant (MDR), with half classified as extensively drug-resistant (XDR). Four isolates exhibited hypervirulent profiles, harboring aerobactin and yersiniabactin siderophores. This study provides comprehensive genomic characterization of CRKP ST101 in Saudi Arabia, revealing complex resistance mechanisms mediated by diverse plasmid types. The findings highlight the importance of genomic surveillance to track the evolution and dissemination of high-risk MDR and XDR lineages and inform targeted infection control strategies.