Résumé:
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
