Draft Genome Sequences of Bordetella hinzii and Bordetella trematum.

Bordetella hinzii colonizes the respiratory tracts of poultry but can also infect immunocompromised humans. Bordetella trematum, however, only infects humans, causing ear and wound infections. Here, we present the first draft genome sequences of strains B. hinzii ATCC 51730 and B. trematum CCUG 13902.

GENOME ANNOUNCEMENT

The genus Bordetella is made up of many host-associated species. Bordetella pertussis and Bordetella parapertussis are the etiological agents of whooping cough in humans (1), whereas Bordetella holmesii is associated with septicemia in humans (2). Other members of this genus are associated with animals, such as Bordetella bronchiseptica, found in small mammals, and Bordetella avium, a bird pathogen (3). In contrast, Bordetella petrii is the only environmentally isolated member of this genus (4). These six species are the previously sequenced members of this genus.

Here, we announce the draft genome sequences of two additional members of the Bordetella genus: Bordetella hinzii and Bordetella trematum. B. hinzii colonizes the respiratory tracts of poultry but also has been isolated from immunocompromised humans (5). Alternatively, B. trematum has only been isolated from humans and is found to be associated with ear and wound infections (6). B. hinzii strain ATCC 57130 was isolated from an immunocompromised person, and B. trematum strain CCUG 13902 was isolated from a human leg wound.

The sequencing data for both these strains were obtained from PCR-free random fragment libraries sequenced on the MiSeq (Illumina, Hayward, CA) platform using indexed paired-end 250-nucleotide (nt) v2 chemistry and resulted in ~700-fold coverage for each genome. The nonindexed read length was 250 nt, with 84.4% of the postfilter paired-end reads having Q30 or greater. The sequence reads were subsampled (~2.2 M reads) and assembled into contigs using Velvet (7) with a k-mer of 151. A total of 1,850,984/2,212,976 reads were assembled for B. hinzii and 1,878,624/2,212,458 reads were assembled for B. trematum, resulting in 98 contigs for B. hinzii and 83 contigs for B. trematum. This is the first report of a draft genome sequence of B. hinzii and B. trematum.

The genomes were analyzed with the RAST server (8). A total of 4,586 coding sequences were predicted for B. hinzii, and 4,145 were predicted for B. trematum. For both species, the genes involved with amino acids and their derivatives and those involved with carbohydrates are the major types of predicted genes. Though the overall distributions of the predicted genes among the different subsystem categories are similar between these Bordetella species, one notable difference is the greater number of predicted membrane transport genes in B. hinzii (308 genes) than in B. trematum (184 genes). B. hinzii has predicted genes associated with a type II secretion system (T2SS), whereas these genes were not identified in B. trematum. B. avium (9) and B. petrii are the only other Bordetella species that have homologs of the same T2SS genes as B. hinzii (gspC to gspN), and these are predicted to produce a functional T2SS by KEGG pathway analysis. This may suggest a closer relationship between the two bird-associated species (B. avium and B. hinzii) and B. petrii (isolated from the environment) in comparison with the other Bordetella species.

Nucleotide sequence accession numbers.

These whole-genome shotgun projects have been deposited in GenBank under accession no. AWNM00000000 (B. hinzii) and no. AWNL00000000 (B. trematum). The versions described in this paper are the first versions, accession no. AWNM01000000 and AWNL01000000, respectively.