Genome-Wide Analysis and Longitudinal Study of Klebsiella pneumoniae in Portugal: Tracing the Evolution and Spread of Carbapenem Resistance

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) has high incidence in Portugal, causing severe and often fatal infections.

Objectives: Characterize the evolutionary history and epidemiology of CRKP in Portugal over a 40-year period.

Methods: WGS was performed using the Illumina platform. In silico multilocus sequence typing, surface antigen characterization, and resistance gene detection were subsequently carried out. Core and pan-genome analyses were conducted using Roary. Genomic clusters (GCs) were identified based on a 21-SNP threshold. To estimate the divergence times of the most prevalent sequence types (ST) in the dataset, Bayesian evolutionary analysis was performed using BEAST.

Results: Nineteen GCs harboring carbapenemases were identified. The blaKPC-3 gene was the most prevalent carbapenemase, linked to strains circulating in both hospital and community settings, with dissemination patterns at regional, interregional, and international levels. ST15 was the most established sequence type in Portugal, with nine distinct GCs identified in both clinical and environmental samples. Towards the end of 2010s, ST147 and ST13 were responsible for significant outbreaks associated with blaKPC-3.

Conclusions: This study underscores the value of genomic-based surveillance in understanding the evolution of high-risk clones coupled with the spread of AMR determinants. The data obtained highlights a shift in ST predominance across the country from an ST15-dominated period and strongly associated with ESBL dissemination, to the emergence of ST147 and ST13 CRKP clones, the latter associated with international transmission. This work further stresses the importance of cross-border surveillance efforts to monitor the emergence and dissemination of CRKP strains and inform risk assessment and prevention.