Table 3_Whole-genome sequencing-based characterization of resistome and virulome in Klebsiella pneumoniae isolated from ready-to-eat foods.xlsx

Klebsiella (K.) pneumoniae is a major antimicrobial-resistant pathogen of global concern. It has increasingly been reported outside clinical settings, including food products. However, genomic data on food-derived K. pneumoniae in Egypt remain limited. In this study, we investigated the genomic diversity, antimicrobial susceptibility, and phylogenetic relationships of K. pneumoniae isolated from ready-for-consumption foods obtained from Egyptian supermarkets. Eleven isolates were recovered from dairy products (milk and yogurt) and catfish. Isolates were identified by MALDI-TOF MS and confirmed by whole genome sequencing (WGS). Antimicrobial susceptibility testing (AST) was performed against a panel of clinically relevant antibiotics. Genomic analyses included multilocus sequence typing (MLST), detection of resistance and virulence associated genes, and SNP based phylogenetic reconstruction. The SNP-based phylogenetic analysis was performed using an additional 77 publicly available Egyptian clinical isolates. Most isolates displayed a predominantly susceptible antimicrobial phenotype. Resistance was largely restricted to piperacillin. All genomes carried intrinsic resistance determinants, including multiple blaSHV alleles and fosA variants. These did not correlate with phenotypic resistance to cephalosporins or fosfomycin. MLST revealed heterogeneous lineages, including clinically relevant sequence types ST37 and ST105, as well as a novel sequence type. Phylogenetic analysis showed that some food-derived isolates clustered closely with the genomes of Egyptian clinical isolates. Others formed genetically distinct lineages, indicating diverse origins within the food chain. These findings show that ready-to-eat foods in Egypt can harbor genetically diverse K. pneumoniae strains. Some populations include lineages related to clinical strains, despite limited phenotypic resistance. The study highlights the importance of integrating phenotypic antimicrobial testing with WGS based surveillance. Such integration can better assess the public health significance of foodborne K. pneumoniae within a One Health framework.