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bioRxiv · 10.1101/2025.03.03.641253

Unraveling the Gardnerella Pangenome: Insights into Genetic Diversity, Virulence, and Antibiotic Resistance

Teixeira, P.·Sousa, M.·Ribeiro, T. G.·Grosso, F.·Peixe, L.
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Abstract

In recent years, the development of user-friendly and accessible bioinformatic tools has significantly advanced Gardnerella genome analysis. Despite the taxonomic reclassification of the genus in 2019, many studies continue to rely on subgroups/ clades for species identification. This leads to frequent misidentifications, hindering accurate assessments of species-specific features, such as antimicrobial resistance and pathogenic potential. This study aims to address these gaps by employing precise species-level identification to improve our understanding on Gardnerella and its clinical implications. We performed the most extensive pangenome analysis of Gardnerella to date, analyzing 153 genomes (120 from NCBI and 33 newly sequenced). G. vaginalis, G. leopoldii, G. swidsinskii, and G. pickettii species exhibited open pangenomes. The Gardnerella pangenome is highly diverse, with 90% of its genes belonging to the accessory genome. Carbohydrate transport and metabolism contributed the most for the primary genomic differences observed among Gardnerella species. Additionally, the search for antibiotic resistance genes (ARGs) revealed lsaC gene as the most prevalent ARG, potentially conferring resistance to clindamycin, a commonly prescribed antibiotic for treating bacterial vaginosis (BV). The clustering of Gardnerella genomes mimics the core genome phylogeny, pointing to species specific virulence-associated factors, highlighting important factors such as vaginolysin and sialidases. Our comprehensive pangenome analysis shows that Gardnerella species are well-adapted within the urogenital tract, with identified virulence factors and metabolic capabilities potentially enhancing the pathogenicity of some strains. Future studies should explore Gardnerellas ecological interactions and pathogenic mechanisms within the urogenital microbiome. ImportanceIn recent years, the availability of user-friendly and accessible bioinformatics tools has led to a surge in studies analyzing the Gardnerella genome. Despite the redefinition of the genus in 2019, many researchers continue to rely on subgroups or clades for Gardnerella identification. Our study builds upon the updated taxonomy of Gardnerella, offering a more comprehensive understanding of its genetic diversity. By conducting a pangenome analysis of 153 Gardnerella genomes, we uncover significant genetic variability, species-specific virulence factors, and the widespread presence of antibiotic resistance genes, highlighting the urgent need for precise species-level identification. The identification of novel genomic features and antibiotic resistance profiles not only enhances our understanding of Gardnerellas clinical implications but also sheds light on its metabolic and virulence potential. These insights help clarify the pathogenic mechanisms of Gardnerella and provide a more refined understanding of its role in the urogenital microbiome.

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Teixeira, P., Sousa, M., Ribeiro, T. G., Grosso, F., Peixe, L.. 2025-03-07. Unraveling the Gardnerella Pangenome: Insights into Genetic Diversity, Virulence, and Antibiotic Resistance. https://doi.org/10.1101/2025.03.03.641253

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