ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Infectious Agents and Disease
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1546594
This article is part of the Research TopicBacterial Pathogens and Virulence Factor Genes: Diversity and EvolutionView all 17 articles
Genome assembly of Klebsiella michiganensis based on metagenomic nextgeneration sequencing reveals its genomic characteristics in population genetics and molecular epidemiology
Provisionally accepted
- 1Anqing Medical Center of Anhui Medical University, Anqing Municipal Hospital, Anqing, China
- 2Genoxor Medical Science and Technology Inc., Shanghai, China
- 3Navy Medical University, Shanghai, China
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Klebsiella michiganensis, a significant member of the Klebsiella oxytoca complex, has emerged as a potential pathogen in clinical settings. Despite extensive research on the Klebsiella pneumoniae complex, the pathogenicity and drug resistance of the K. oxytoca complex remain understudied, particularly regarding the reconstruction of whole genomes from metagenomic next-generation sequencing (mNGS) data. In this study, bronchoalveolar lavage fluid (BALF) from a 55-year-old woman with a suspected right lung infection in Anhui Province, China, was analyzed using mNGS.Three distinct assembly strategies were employed to reconstruct the genome of K. michiganensis, leading to the identification of a novel ST452 strain, KMLRT2206.Comprehensive genomic analysis of this strain and 206 clinical isolates (genomes downloaded from public databases) revealed the population structure, distribution of drug resistance genes, and virulence factors of K. michiganensis. The results demonstrated significant genetic diversity, with the species divided into three major clades, each exhibiting distinct patterns of drug resistance and virulence genes. Notably, 38.6% of the strains harbored the blaOXY-1-1 gene, highlighting a potential threat of drug resistance. While virulence gene distribution was not correlated with sequence type (ST), significant differences were observed among clades. This study underscores the value of mNGS combined with optimized assembly strategies for accurate species identification within the K. oxytoca complex, providing critical insights for clinical pathogen detection and epidemiological surveillance.
Keywords: Klebsiella michiganensis, genome assembly, MNGs, Genomic characteristics, Epidemiology
Received: 17 Dec 2024; Accepted: 02 Apr 2025.
Copyright: © 2025 Sun, Cai, Li, Chen and Fang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Jingbo Chen, Navy Medical University, Shanghai, China
Yuan Fang, Genoxor Medical Science and Technology Inc., Shanghai, China
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