Expansion of KPC-3-producing Klebsiella pneumoniae ST15-KL19 after the COVID-19 pandemic in northern Portugal

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• Picked for Microbiology (medical) (top studies of the week, 8 November 2026): Genomic epidemiology and resistance evolution of KPC-producing Klebsiella

Abstract

INTRODUCTION: Carbapenemase-producing (CP) Klebsiella pneumoniae are a major public health concern in Portugal, where the population has been dominated by KPC-3-producing ST147-KL64. Following preliminary detection of an unexpectedly high proportion of ST15-KL19 infections after the COVID-19 pandemic, we investigated the recent expansion and clinical relevance of this sublineage. METHODS: All CP K. pneumoniae isolates recovered from hospitalized patients between 2022 and 2023 (n = 267) were characterized by antibiotic susceptibility testing and Fourier-transform infrared spectroscopy, wzi sequencing and multi-locus sequence typing. Representative ST15-KL19 isolates from a baseline (2019-2021) and the recent expansion (2022-2023) periods were selected for whole-genome sequencing and compared with publicly available global genomes to assess phylogenetic relatedness, temporal structure, and potential links to non-human reservoirs. RESULTS: ST15-KL19 emerged as one of the most frequent CP K. pneumoniae sublineages, increasing from 23% to 35% and replacing ST147-KL64 over time. Genomic analyses identified two temporally distinct ST15-KL19 variants. Isolates from the recent expansion period (2022-2023) acquired bla CTX-M-15 and other plasmid-mediated aminoglycoside resistance determinants, concurrently with an IncR plasmid replicon. Phylogenomic analyses revealed that both variants were already circulating in the region before 2019. Together with the high colonization rates at admission (64%), our data suggest repeated introductions from external sources rather than in-hospital evolution. Global comparisons supported regional and intercontinental dissemination from a common ancestor, though a direct foodborne origin could not be established. CONCLUSION: This study documents the recent expansion of a previously minor CP K. pneumoniae sublineage, highlighting how shifts in healthcare ecology can favor adaptive variants or repeated introductions. Continuous molecular surveillance is essential to detect such emerging lineages early and to inform infection control and antimicrobial stewardship strategies.

Abstract as published, via PubMed.