Molecular epidemiology of Klebsiella pneumoniae causing bloodstream infections in a district hospital in Northern Portugal (2016-2018): clonal diversity and detection of hypervirulent strains.

Abstract

Purpose: Klebsiella pneumoniae (Kp) is a major cause of bloodstream infections (BSI) globally. Yet, detailed characterization of invasive isolates, particularly from datasets not biased toward resistance, remains limited. This baseline study, conducted prior to the expansion of carbapenemase producers in Portugal, characterizes multidrug-resistant (MDR) and non-MDR Kp causing BSIs in a northern district hospital to elucidate resistance emergence and dissemination.

Methods: A total of 174 Kp strains isolated from blood cultures of hospitalized patients (2016-2018) were identified by VITEK2 or MALDI-TOF MS. Antibiotic resistance phenotypes were determined by reference methods, β-lactamases screened by PCR/sequencing, and clonal sublineages identified by FT-IR spectroscopy, MLST and/or WGS, including for putative hypervirulent strains (hvKp).

Results: Isolates were categorized as MDR (49%) or non-MDR (51%), with MDR rates nearly double national reports. Most MDR-Kp (67%) produced CTX-M-15, 25% produced carbapenemases (mainly KPC-3 and/or OXA-48/CTX-M-15), and 8% lacked acquired β-lactamases. Half (53%) belonged to three high-risk sublineages (ST147-KL64, ST307-KL102, ST15-KL19), while non-MDR showed greater diversity, with ST14-KL2 most frequent (13%) and consistently resistant to amoxicillin-clavulanate. Several sublineages circulated across both cohorts (e.g., ST307-KL102, ST348-KL62), some with variable β-lactamase content (e.g., ST147-KL64, ST45-KL24). Two hvKp (1.1%) were identified (ST380-KL2, ST268-KL20).

Conclusion: This baseline study reveals a high local burden of MDR-Kp driven by CTX-M-15 and KPC-3-producing high-risk sublineages, underscoring the importance of local surveillance beyond national reporting. High clonal diversity and variable β-lactamase content suggest heterogeneous acquisition and dissemination routes, with resistance often preceding clonal expansion. Though rare, hvKp detection underscores the need for continued surveillance and multicenter monitoring.