Genomic and plasmid-level identity between an environmental Klebsiella pneumoniae isolate from India and the high-risk clinical clone HS11286: a comparative genomic analysis of the K. pneumoniae species complex

Abstract Background Klebsiella pneumoniae is a leading cause of multidrug-resistant infection, and its persistence in environmental reservoirs is increasingly recognized as a One Health concern. Objectives To characterize the genomic relatedness of clinical and environmental K. pneumoniae species complex isolates from India to the internationally significant high-risk clinical strain HS11286. Methods Eleven publicly available K. pneumoniae species complex genomes from clinical, river, lake, raw milk, and soil sources were typed using Kleborate and compared by pan-genome (Panaroo) and core-genome phylogenetic analysis (IQ-TREE), average nucleotide identity (fastANI), plasmid replicon typing (PlasmidFinder), and accessory-genome Jaccard similarity. Results One river water isolate, DCP2, shared sequence type ST11, capsule locus KL103 and O-locus OL2α.1 with HS11286, with a whole-genome average nucleotide identity of 99.99%, the highest pairwise value in the dataset. The two isolates formed a fully supported sister pair (bootstrap = 100) with near-zero branch length, shared an identical complement of five plasmid replicon types at matching sequence identity, and carried the same nine resistance gene classes, including KPC-2 and rmtB. Accessory-genome Jaccard similarity between HS11286 and DCP2 was 0.9956, with 436 accessory genes shared exclusively by this pair. Conclusions DCP2 and HS11286 represent the same clonal lineage, sharing near-identical core, accessory and plasmid genomic content despite different countries and years of isolation, providing genomic evidence that environmental water can harbour, and potentially disseminate, high-risk clinical K. pneumoniae clones.