Genomics uncover resistant and virulent Klebsiella on foods: a potential risk to human health

Zamudio, Roxana, Yap, Min, Bloomfield, Samuel J., Palau, Raphaëlle, Janecko, Nicol and Mather, Alison E. (2026) Genomics uncover resistant and virulent Klebsiella on foods: a potential risk to human health. Food Microbiology, 133. ISSN 0740-0020

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Abstract

Klebsiella pneumoniae is a bacterium of public health importance due to its association with antimicrobial resistance (AMR) and its role as a major cause of both hospital- and community-acquired infections. While Klebsiella species have been detected in foods, our understanding of their diversity and the potential risks they pose from food is limited. This study aims to comprehensively evaluate the Klebsiella species population and their contribution to the burden of AMR, virulence, and heavy metal tolerance from diverse food samples. We generated short-read sequence data for 570 Klebsiella isolates recovered from 361 food samples, including leafy greens, pork, prawns, chicken, salmon, and shellfish. Genome analysis showed that eleven unique Klebsiella species were present across food commodities, with K. pneumoniae being the most common (28.3 %); food-derived genomes were intermingled with publicly available Klebsiella genomes isolated from human clinical infections. We detected critical AMR genes, blaCTX-M-15, blaCTX-M-27, blaSHV-70, and blaDHA-1, in K. pneumoniae (n = 8) and K. quasipneumoniae (n = 6) from prawns. Additionally, we identified 46 virulent K. pneumoniae and K. quasipneumoniae isolates from domestic and imported food, including two hypervirulent K. pneumoniae isolates from domestic pork samples. Notably, a K. planticola isolate from salmon exhibited the hypermucoviscosity phenotype. AMR and virulence genes on plasmid contigs were widespread across different Klebsiella species, while chromosome-linked genes were mostly species-specific. These results highlight that food can harbour a range of Klebsiella species with resistance and virulence genes typically found in clinical settings, underscoring the need for monitoring foodborne Klebsiella as a potential risk to human health.

Item Type:	Article
Additional Information:	Data availability: All raw Illumina short-reads generated in this study have been deposited in the European Nucleotide Archive (ENA) with 513 genomes under BioProject PRJEB62598 and 57 genomes under BioProject PRJNA1135353. Metadata and individual accession numbers are available in the Supplementary Dataset S1.
Uncontrolled Keywords:	antimicrobial resistance,food safety,hypervirulence,klebsiella,public health,virulence,microbiology,food science,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/2400/2404
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Related URLs:	https://www.scopus.com/pages/publication...
Depositing User:	LivePure Connector
Date Deposited:	13 May 2026 15:05
Last Modified:	14 May 2026 15:16
URI:	https://ueaeprints.uea.ac.uk/id/eprint/103006
DOI:	10.1016/j.fm.2025.104899

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