One Health genomic surveillance of Klebsiella pneumoniae in Belgium demonstrates large genomic diversity, presence of ESBLs and carbapenemases and circulation of clones across sectors
7 affiliations
- 1Service Foodborne Pathogens, Sciensano
- 2Fundamental and Applied Research for Animal and Health (FARAH) Center, University of Liège
- 3Transversal Activities in Applied Genomics, Sciensano
- 4Veterinary Bacteriology Service, Sciensano
- 5National Reference Center for Antibiotic-Resistant Gram-Negative Bacilli, CHU UCL Namur
- 6Association Régionale de Santé et d’Identification Animales
- 7Animal Health Care Flanders
Abstract
Klebsiella pneumoniae is an important reservoir and disseminator of antimicrobial resistance (AMR) genes. Multidrug-resistant lineages, particularly extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant strains, represent an important public health threat. This study characterized antimicrobial resistance and genomic diversity of K. pneumoniae across One Health compartments in Belgium and investigated genomic relatedness within and across sectors. Between 2019 and 2022, 888 presumptive K. pneumoniae isolates were collected from diseased animals ( n = 311), wastewater ( n = 299), the food chain ( n = 178), and human clinical samples ( n = 100). Following selection based on isolation source and AMR characteristics, 286 WGS-confirmed K. pneumoniae isolates were characterized for AMR and virulence determinants, plasmid replicons, population structure, and phylogenomic relatedness. Phenotypic and genotypic resistance showed high concordance for third-generation cephalosporins (93.4%) and carbapenems (89.2%). Carbapenemase genes encoding KPC, NDM, OXA-48-like, and VIM enzymes were detected in 67 isolates from humans ( n = 56) and wastewater ( n = 11), but not in food-chain or diseased-animal isolates. Population structure was highly diverse, with ST307, ST15, ST147, and ST11 representing the most frequently detected high-risk lineages. Thirteen novel STs were identified in 18 K. pneumoniae isolates. Seventeen genomic clusters were identified, including 13 within-sector and four cross-sector clusters. Notably, an ST147 cluster comprising two poultry-meat isolates and a human clinical isolate showed no SNP differences, indicating very close genomic relatedness across sectors. Overall, our findings demonstrate a genetically diverse K. pneumoniae population alongside the circulation of clinically relevant high-risk lineages across One Health compartments and support integrated genomic surveillance to better understand their dissemination.
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BibTeX
@article{debergh2026health,
title = {{One Health genomic surveillance of Klebsiella pneumoniae in Belgium demonstrates large genomic diversity, presence of ESBLs and carbapenemases and circulation of clones across sectors}},
author = {Hanne Debergh and Bert Bogaerts and Inge Van Damme and Cécile Boland and Kevin Vanneste and Koenraad van Hoorde and Pierre Bogaerts and Te-Din Huang and Marc Saulmont and Nadine Botteldoorn and Claude Saegerman and Cristina Garcia-Graells},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1933141},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1933141/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - One Health genomic surveillance of Klebsiella pneumoniae in Belgium demonstrates large genomic diversity, presence of ESBLs and carbapenemases and circulation of clones across sectors
AU - Hanne Debergh
AU - Bert Bogaerts
AU - Inge Van Damme
AU - Cécile Boland
AU - Kevin Vanneste
AU - Koenraad van Hoorde
AU - Pierre Bogaerts
AU - Te-Din Huang
AU - Marc Saulmont
AU - Nadine Botteldoorn
AU - Claude Saegerman
AU - Cristina Garcia-Graells
PY - 2026
DA - 2026/10/07
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1933141
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1933141/full
AB - Klebsiella pneumoniae is an important reservoir and disseminator of antimicrobial resistance (AMR) genes. Multidrug-resistant lineages, particularly extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant strains, represent an important public health threat. This study characterized antimicrobial resistance and genomic diversity of K. pneumoniae across One Health compartments in Belgium and investigated genomic relatedness within and across sectors. Between 2019 and 2022, 888 presumptive K. pneumoniae isolates were collected from diseased animals ( n = 311), wastewater ( n = 299), the food chain ( n = 178), and human clinical samples ( n = 100). Following selection based on isolation source and AMR characteristics, 286 WGS-confirmed K. pneumoniae isolates were characterized for AMR and virulence determinants, plasmid replicons, population structure, and phylogenomic relatedness. Phenotypic and genotypic resistance showed high concordance for third-generation cephalosporins (93.4%) and carbapenems (89.2%). Carbapenemase genes encoding KPC, NDM, OXA-48-like, and VIM enzymes were detected in 67 isolates from humans ( n = 56) and wastewater ( n = 11), but not in food-chain or diseased-animal isolates. Population structure was highly diverse, with ST307, ST15, ST147, and ST11 representing the most frequently detected high-risk lineages. Thirteen novel STs were identified in 18 K. pneumoniae isolates. Seventeen genomic clusters were identified, including 13 within-sector and four cross-sector clusters. Notably, an ST147 cluster comprising two poultry-meat isolates and a human clinical isolate showed no SNP differences, indicating very close genomic relatedness across sectors. Overall, our findings demonstrate a genetically diverse K. pneumoniae population alongside the circulation of clinically relevant high-risk lineages across One Health compartments and support integrated genomic surveillance to better understand their dissemination.
SN - 1664-302X
ER -