Klebsiella quasipneumoniae: a novel sequence type 1699 by whole genome sequence analysis from food fish in India

Klebsiella quasipneumoniae, an emerging member of the Klebsiella genus, has recently garnered attention as a clinically significant pathogen capable of causing severe human infections. Despite its pathogenic potential, it is frequently misidentified as Klebsiella pneumoniae due to their close genetic and phenotypic similarities, leading to diagnostic challenges and potential implications for treatment and epidemiological surveillance. This study addresses a critical gap in our understanding of K. quasipneumoniae by applying high-resolution genomic tools to distinguish it from its more well-characterized K. pneumoniae, assessed their AMR profiles and evaluate the limitation of conventional identification methods. Whole genome of a gram-negative K. quasipneumoniae (Klebsiella ST1699) bacterium found in an edible fish bought from a retail market in Assam, India. Whole Genome Sequencing (WGS) using the Illumina sequencing and species identification by Mash Screen confirmed the authenticity of K. quasipneumoniae. We assembled the 5.21 Mb complete genome of Klebsiella ST1699 and harboured several Antimicrobial Resistance Genes (ARGs) viz., blaLAP-2, blaOKP-B-1, fosA, tet(A), Sul2, dfrA14. OqxA and OqxB, and identified as a novel sequence type 1699 K. quasipneumoniae (ST 1699) from the edible fish in the retail market, Assam, India. We also performed comparative genome analysis with 6 other strains of K. quasipneumoniae genome sequences in the NCBI database. K. quasipneumoniae represents a clinically relevant and underrecognized pathogen with significant antimicrobial resistance. Improved molecular diagnostics are essential for accurate identification and effective infection control. Misidentification may contribute to underreporting and inappropriate therapeutic strategies, underscoring the need for heightened awareness and surveillance. Our findings have implications for diagnostic accuracy, resistance surveillance, and the development of targeted therapeutic strategies.