Comprehensive genome-based reclassifica5on of several pathogenic species within the genera Bordetella and Borrelia

Abstract

In the present study, a polyphasic taxonomic approach was employed to reassess the classification of several species within the genera Bordetella and Borrelia, using genomic, phylogenetic, and phenotypic data. A total of 22 genome sequences of Bordetella were analysed to re-evaluate the taxonomic boundaries among Bordetella pertussis, Bordetella parapertussis, and Bordetella bronchiseptica, which are traditionally regarded as distinct species despite significant genetic overlap. Phylogenetic analyses based on 16S rRNA sequences, whole-genome datasets and the core genome consistently grouped these three taxa into a single monophyletic clade, supported by strong bootstrap values (≥99%). Genomic relatedness indices, including Average Nucleotide Identity (ANI: 98–99%), Average Amino Acid Identity (AAI: 97–99%), and digital DNA–DNA hybridization (dDDH: 85–95%), exceeded recognized species delineation thresholds (ANI/AAI ≥95%, dDDH ≥70%). For the genus Borrelia, the analysis included two distinct groups: the first composed of B. garinii and B. bavariensis, and the second of B. bissettiae, B. kurtenbachii, and B. carolinensis. Phylogenetic trees constructed from both 16S rRNA and whole-genome data revealed strong clustering within each group. ANI values reached 97% between B. garinii and B. bavariensis and ranged between 96% and 98% among the second group. Corresponding dDDH values supported these results, with 77% for the first group and 63%–80% for the second. These values all exceed their corresponding thresholds for species delineation. In both genera, the additional comparative analyses, including orthologous cluster identification and functional subsystem analysis, revealed a high degree of shared gene content and functional similarity among the studied species. Collectively, all these results highlight a high genomic similarity and evolutionary relatedness among the studied taxa. In light of these results, we propose reclassifying B. bronchisep6ca and B. parapertussis as later heterotypic synonyms of B. pertussis within the genus Bordetella. Similarly, within the genus Borrelia, we propose that B. bavariensis be reclassified as a later heterotypic synonym of B. garinii, and that B. kurtenbachii and B. carolinensis be considered later heterotypic synonyms of B. bisse7ae. This comprehensive reclassificaZon clarifies the current taxonomic ambiguities within these clinically significant bacterial genera, thereby enabling more precise identification of pathogenic species which is an essential step for effective clinical diagnosis, epidemiological tracking, and public health management