A comprehensive resource for Bordetella genomic epidemiology and biodiversity studies

Abstract

The genus Bordetella includes bacteria that are found in the environment and/or associated with humans and other animals. A few closely related species, including Bordetella pertussis, are human pathogens that cause diseases such as whooping cough. Here, we present a large database of Bordetella isolates and genomes and develop genotyping systems for the genus and for the B. pertussis clade. To generate the database, we merge previously existing databases from Oxford University and Institut Pasteur, import genomes from public repositories, and add 83 newly sequenced B. bronchiseptica genomes. The public database currently includes 2582 Bordetella isolates and their provenance data, and 2085 genomes ( https://bigsdb.pasteur.fr/bordetella/ ). We use core-genome multilocus sequence typing (cgMLST) to develop genotyping systems for the whole genus and for B. pertussis, as well as specific schemes to define antigenic, virulence and macrolide resistance profiles. Phylogenetic analyses allow us to redefine evolutionary relationships among known Bordetella species, and to propose potential new species. Our database provides an expandable resource for genotyping of environmental and clinical Bordetella isolates, thus facilitating evolutionary and epidemiological research on whooping cough and other Bordetella infections.

Fig. 1. Phylogenetic analysis of the Bordetella genus.

The phylogenetic tree was obtained based on the concatenated multiple sequence alignments of the 1415 core gene sequences from the cgMLST_genus scheme; recombination was accounted for using Gubbins. The tree was rooted on the branch leading to isolate FB-8, which was the earliest branching genome in a phylogenetic analysis that included the external group Ralstonia solanacearum isolate IBSBF1503 (Supplementary Fig. 2). Leaves are labelled with the identifier of the isolate in the BIGSdb database, followed by the isolate name. Genomic species are labelled as G.S. An interactive iTOL version of the tree can be accessed at: https://itol.embl.de/shared/1l7Fw0AvKOoCF. Source data are provided as a Source Data file.

Fig. 2. Cladogram of the Bordetella bronchiseptica genomic species.

The analysis was performed with 186 B. bronchiseptica genomes, and representatives of the phylogenetic diversity of B. pertussis (9 genomes) and B. parapertussis (9 genomes). The recombination-purged concatenated multiple sequence alignment of 1415 core gene loci (cgMLST_genus scheme) was used. The tree is rooted on lineage II, which is the most divergent clade. Branch lengths were not used to ease readability of groups and isolates; see Supplementary Fig. 5 for the corresponding phylogram. For each isolate, the host is represented using a leaf symbol, where available (see key in Supplementary Fig. 5). The numbers corresponding to T3SS sequence types are indicated along the external circle around the tree; only the identifiers of main T3STs are indicated. An interactive iTOL version of the tree can be accessed at: https://itol.embl.de/shared/1l7Fw0AvKOoCF. Source data are provided as a Source Data file.

Fig. 3. Phylogenetic analysis of Bordetella pertussis.

The phylogenetic tree was obtained based on the recombination-purged concatenated multiple sequence alignments of the 2038 core genome loci of the cgMLST_pertussis scheme. The distribution of macrolide resistance is indicated. The three outer circles represent (from innermost): 23S_rRNA alleles, fhaB alleles, prn alleles and the vaccine antigen sequence types (AgST). Lineages IIa and IIb were defined in Bart et al. 2014 and are labelled in blue. An interactive iTOL version of the tree can be accessed at: https://itol.embl.de/shared/1l7Fw0AvKOoCF. Source data are provided as a Source Data file.