Expansion of KPC-3-producing Klebsiella pneumoniae ST15-KL19 after the COVID-19 pandemic in northern Portugal
- 1UCIBIO, i4HB, Faculdade de Farmácia, Universidade do Porto
- 2Clinical Microbiology Laboratory, Local Healthcare Unit
- 3Infection Control Unit, Local Healthcare Unit
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.
Related
- Genomic epidemiology of dual carbapenemase-producing Klebsiella pneumoniae and identification of an ST23-KL1 blaKPC-2/blaIMP-4 co-producing isolate in a Chinese tertiary hospital
- Characterization of a conjugative IncA plasmid co-harbouring blaNDM-5 and blaVIM-1 in a KPC-producing Klebsiella pneumoniae clinical isolate K27
- Follistatin-like 1 Promotes Neutrophil-mediated Host Defense against Klebsiella pneumoniae
- Genomic Insights into Multi-Drug-Resistant, Klebsiella pneumoniae Isolated from an Infertile Woman: A Comprehensive Analysis of Antibiotic Resistance and Virulence Factors
- Defining nutrient dependencies of intestinal Klebsiella pneumoniae guides rational probiotic engineering
BibTeX
@article{goncalves2026expansion,
title = {{Expansion of KPC-3-producing Klebsiella pneumoniae ST15-KL19 after the COVID-19 pandemic in northern Portugal}},
author = {Ana Beatriz Gonçalves and Antónia Read and Isabel Neves and Natália Pinheiro and Valquíria Alves and Luísa Peixe and Ângela Novais},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1957369},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1957369/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Expansion of KPC-3-producing Klebsiella pneumoniae ST15-KL19 after the COVID-19 pandemic in northern Portugal
AU - Ana Beatriz Gonçalves
AU - Antónia Read
AU - Isabel Neves
AU - Natália Pinheiro
AU - Valquíria Alves
AU - Luísa Peixe
AU - Ângela Novais
PY - 2026
DA - 2026/10/22
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1957369
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1957369/full
AB - 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.
SN - 1664-302X
ER -