Emergence of OXA-48-producing Klebsiella pneumoniae ST5994, a sister lineage of the high-risk ST307 clone.

INTRODUCTION

Carbapenemase-producing Klebsiella pneumoniae (CP-KP) represents a major public health threat. The global dissemination of antimicrobial resistance is largely driven by high-risk clones (HRCs), such as ST307/OXA-48, ST11/OXA-48 and ST512/KPC-3, which currently dominate the epidemiology of CP-KP in Spain. This study aimed to describe the emergence, dissemination and genomic evolution of an OXA-48-producing K. pneumoniae ST5994 clone in Cantabria, Spain, and to characterize its genomic, phenotypic and epidemiological features.

METHODS

A retrospective genomic surveillance study of CP-KP isolates was conducted in Cantabria from 2021 to 2024. Whole-genome sequencing was used to characterize sequence types, resistome, mobilome, virulome, pangenome and phylogenetic relationships. Antimicrobial susceptibility and biofilm production assays were performed. Fourier-transform infrared (FT-IR) spectroscopy combined with machine learning algorithms was used to develop a rapid method for HRCs discrimination.

RESULTS

Among 448 non-duplicate CP-KP isolates, bla OXA-48 was the predominant carbapenemase. K. pneumoniae ST5994 was first detected in the second quarter of 2023 and rapidly became one of the dominant CP-KP clones at both reference hospital and regional levels over a two-year period, displacing previously prevalent HRCs, such as K. pneumoniae ST11 and K. pneumoniae ST307. The newly identified clone harbored two potentially conjugative plasmids carrying bla OXA-48 carbapenemase and bla CTX-M-15 extended-spectrum beta-lactamase. At the time of writing, eight ST5994 genomes were publicly available, all from the Americas and none carrying a bla OXA-48 gene, therefore this study represents both the first description of this ST in Europe and its first association with OXA-48. Genomic and epidemiological analyses were compatible with sustained dissemination within the regional healthcare network, although the specific transmission pathways could not be established with the available data. Comparative analyses supported a close evolutionary relationship between K. pneumoniae ST307 and ST5994.

CONCLUSIONS

Our findings highlight the rapid emergence and regional replacement capacity of the novel OXA-48-producing K. pneumoniae ST5994. The integration of genomic and phenotypic data provides insights into its evolutionary trajectory and transmission dynamics. Furthermore, the proposed FT-IR-based approach combined with machine learning offers a promising tool for rapid discrimination of HRCs, supporting surveillance and infection control strategies.