The Dissemination of Multidrug-Resistant and HypervirulentKlebsiella pneumoniaeClones Across the Kingdom of Saudi Arabia

Abstract

The Gram-negative bacterium Klebsiella pneumoniae is a major human health threat underlying a broad range of community- and hospital-associated infections. The emergence of clonal hypervirulent strains often resistant to last-resort antimicrobial agents has become a global burden as treatment options are limited. The Kingdom of Saudi Arabia (KSA) has a dynamic and diverse population and serves as a major global tourist hub facilitating the dissemination of multidrug-resistant (MDR) strains of K. pneumoniae. To examine the spread of clinically relevant Klebsiella pneumoniae strains, we characterized the population structure and dynamics of multidrug-resistant K. pneumoniae across the KSA hospitals. Methods We conducted a large genomic survey on a Saudi Arabian collection of multidrug-resistant K. pneumoniae isolates from bloodstream and urinary tract infections. The isolates were collected from 32 hospitals located in 15 major cities across the country in 2022 and 2023. We subjected 352 K. pneumoniae isolates to whole-genome sequencing and employed a broad range of genomic epidemiological and phylodynamic methods to analyse population structure and dynamics at high resolution. We employed an integrated short- and long-read sequencing approach to fully characterize multiple plasmids carrying resistance and virulence genes. Results Our results indicate that, despite a diverse K. pneumoniae population underlying hospital infections, the population is characterized by the rapid expansion of a few dominant clones, including ST096 (n=115), ST147 (n=75), ST231 (n=35), ST101 (n=30), ST11 (n=18), ST16 (n=15) and ST14 (n=12). ST2096, ST231, and ST147 clones were estimated to have formed within the past two decades and spread between hospitals across the country on an epidemiological time scale. All STs were genetically linked with globally circulating clones, particularly strains from the Middle East and South Asia. All of the major clones harboured plasmid-borne ESBLs and a range of carbapenemase genes. Plasmidome analysis revealed multiple mosaic plasmids with resistance and virulence gene cassettes, some of which were shared between the major clades and account for multidrug resistant hypervirulent (MDR/hv) phenotype, especially in the ST2096 strains. Integration of phylodynamic data and resistance plasmid profiles showed that the acquisition of plasmids occurred on the same time scales as did the expansion of major clones across the country. Conclusion Taken together, these results indicate the dissemination of MDR and MDR-hv K. pneumoniae strains across the kingdom and provide evidence for pervasive plasmid sharing and horizontal gene transfer of resistance genes. The results demonstrate the independent introduction of endemic ST147, ST231, and ST101 clones into the country and highlight the clinical significance of ST2096 as an emerging clone with dual resistance and virulence risks. These results highlight the need for continuous surveillance of circulating and newly emergent strains (STs) and of their plasmidome footprints carrying MDR determinants.