Whole-Genome Sequencing of Antimicrobial Resistant Klebsiella quasipneumoniae, a Novel Sequence Type 5655 from Retail Fish Market, Assam, India

Sahadevan Sangeetha; Sudha Sajeev; Muneeb K Hamza; Bibek R Shome; Claire Raisen; Mark A Holmes; Gopalan Krishnan Sivaraman

doi:10.1089/fpd.2023.0017

Whole-Genome Sequencing of Antimicrobial Resistant Klebsiella quasipneumoniae, a Novel Sequence Type 5655 from Retail Fish Market, Assam, India

Foodborne Pathog Dis. 2025 Jan 6. doi: 10.1089/fpd.2023.0017. Online ahead of print.

Authors

Sahadevan Sangeetha^{1

2}, Sudha Sajeev², Muneeb K Hamza², Bibek R Shome³, Claire Raisen⁴, Mark A Holmes⁴, Gopalan Krishnan Sivaraman²

Affiliations

¹ Department of Bioscience, Union Christian College, Aluva, Kochi, India.
² Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India.
³ Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India.
⁴ Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.

PMID: 39761073
DOI: 10.1089/fpd.2023.0017

Abstract

Klebsiella quasipneumoniae is a recently described species that can be differentiated from Klebsiella pneumoniae. However, in clinical settings, they are frequently misidentified as K. pneumoniae. In this study, our objective was to conduct genomic characterization and bioinformatics analysis of K. quasipneumoniae subsp. quasipneumoniae (KpII-A) isolated from a sample obtained from a retail fish market in Assam, India. Notably, this particular isolate was identified as K. pneumoniae when identified using BD Pheonix™ M50 (BD Difco, USA). This represents a serious pitfall of conventional microbiological methods for distinguishing between K. pneumoniae and K. quasipneumoniae. In this connection, identifying differences in nuclear gene content is key to avoid misidentification. The isolate was confirmed to be KpII-A using species identification by Mash Screen and whole-genome sequencing by the Illumina platform. We report the draft genome sequence of this strain, comprising of 53 contigs with an average GC content of 58.11%. The annotation revealed 5,095 protein coding sequences, 69 tRNA genes, and 4 rRNA genes. The isolated strain acknowledges the presence of oqxA, oqxB, fosA, and bla_OKP-A-3 antimicrobial resistance genes (ARGs). Additionally two phage genomes were detected in contigs 3 and 19 of the bacterial genome. Based on the multilocus sequence typing and genome sequencing, the isolate was identified as a novel sequence type, ST5655, within the species K. quasipneumoniae under the phylogroup KpII-A. The presence of antimicrobial resistance genes in KpII-A, isolated from retail fish samples, raises concerns regarding transmission across barriers in ecological niches and possible transmission to consumers. Given that fish may serve as a potential vehicle for ARG transmission, our findings are highly relevant and paramount to human health. Moreover, our study supports the robustness of the sequence-based microbial identification.

Keywords: Klebsiella quasipneumoniae subsp. quasipneumoniae; antimicrobial resistance; multilocus sequence typing; retail fish market; whole-genome sequence.