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

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, bla_CTX-M-15, bla_CTX-M-27, bla_SHV-70, and bla_DHA-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.

Keywords: Antimicrobial resistance; Food safety; Hypervirulence; Klebsiella; Public health; Virulence.