Hospital-Based Genomic Surveillance of Klebsiella pneumoniae: Trends in Resistance and Infection.

Klebsiella pneumoniae (Kp) is a leading cause of hospital-acquired infections representing a growing threat driven by emerging multidrug resistance (MDR) and hypervirulence. In this study, we aim to characterise the genomic and epidemiological landscape of Kp in a Portuguese regional hospital (Braga) lacking prior genomic data. We performed whole-genome sequencing of 115 Kp isolates collected from colonisation and infection cases. Phylogenetic, resistance, and virulence profiles were integrated with clinical and epidemiological data. Genomic analysis revealed high diversity, with 83.5% of isolates forming evolutionary clusters. Several novel sequence types (STs), as ST2623 and ST1562, were detected for the first time in Portugal to our knowledge. ST45, uncommonly associated with carbapenem resistance, emerged as dominant with multiple blaKPC-3-positive isolates. Results suggest active transmission of carbapenem resistance genes. One hypervirulent carbapenem-resistant ST13 warrants careful surveillance. Virulence-associated yersiniabactin was common (66.9%) but other hypervirulence loci were rare. Epidemiologically, MDR-Kp was associated with older hospitalised patients with prior antibiotic use and invasive procedures, while community-acquired infections were genetically diverse and affected younger patients with comorbidities. An unusually low number of respiratory infections was observed, likely reflecting strict COVID-19 mitigation measures. Although widespread dissemination of hypervirulent or MDR clones was not evident, the emergence of high-risk lineages and the detection of ongoing gene transmission episodes underscore the need for ongoing genomic surveillance. Immediate mitigation strategies could include reducing device use and hospital transfers, given the high prevalence of colonisation.