Draft genome of Bordetella pseudohinzii BH370 isolated from trachea and lung tissues of a laboratory mouse.

In this study, we present the draft genome sequence of B. pseudohinzii BH370 recovered from the trachea and lung tissues of an ICR mouse in Malaysia. The genome consists of 4,474,040 bp with a GC content of 66.4%. Annotation using RAST algorithm displayed 5119 protein encoding and 52 RNA genes. The CRISPR-cas genomic sequences previously reported in B. pseudohinzii were identified. The nucleotide sequences of BH370 was deposited into the European Nucleotide Archive under the genome assembly accession number FPJN01000000.

Direct link to deposited data

http://www.ebi.ac.uk/ena/data/view/FPJN01000000

Experimental design, materials and methods

Isolate BH370 obtained from the trachea and lung tissues of an apparently healthy ICR mouse was cultured in Mueller-Hinton broth overnight under aerobic condition at 37 °C. Bacterial genomic DNA was extracted using the Nucleospin Tissue Kit (Macherey-Nagel, Germany) according to the manufacturer's protocol. Whole genome sequencing was performed as previously described [1], with minor modifications. Briefly, the genome library preparation was carried out using the Ion Xpress™ Plus Fragment Library Kit (Thermo Fisher Scientific, USA). Genome libraries of 200-base read fragments were prepared using E-Gel® SizeSelect™ Agarose Gel, 2% (Thermo Fisher Scientific, USA). The sequencing template was prepared using Ion OneTouch™ 200 Template Kit V2 DL (Thermo Fisher Scientific, USA) according to the manufacturer's protocol. Amplified Ion Sphere Particles were enriched using IonPGM Enrichment beads (Thermo Fisher Scientific, USA). Genome sequencing was undertaken using the IonTorrent PGM sequencer (Life Technologies, USA). The raw sequence reads were assembled de novo using SPAdes V3.1.0 [2] as implemented in Torrent Suite V5.0.0. The assembled contigs were functionally annotated with Rapid Annotation using Subsystem Technology (RAST) [3].

Genomic analysis

The non-classical Bordetella species, B. hinzii, has been suggested to cause respiratory infection among laboratory mice [4], and can hence interfere with studies using these animals [5]. Our recent study has suggested that a closely related species could be responsible for some of these infections [5], including laboratory mice infections previously attributed to B. hinzii. The discovery of a new species of the Bordetella genogroup, B. pseudohinzii, isolated from the bronchoalveolar lavage fluid of a C57BL/6 mouse in the USA [6] led us to investigate the species identity of a Bordetella isolate recovered from an ICR mouse. Unlike B. hinzii and other members of the Bordetella genus, B. pseudohinzii is unique in that its genome contains the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated) system [7]. Here, we describe the full genome sequencing of B. pseudohinzii BH370 recovered from the trachea and lung tissues of an ICR mouse.

The draft genome of B. pseudohinzii BH370 was 4,474,040 bp in length, comprising 390 contigs with N50 of 20,945 bp (Table 1). The GC content of the genome sequence was approximately 66.4%. A total of 5119 protein-coding genes and 52 RNAs were predicted using RAST. Out of the 5119 protein-coding genes, 54% of the translated proteins were assigned to subsystem categories according to function (Fig. 1). The CRISPR-cas locus containing the cas9, cas1 and cas2 genes was present in the genome sequence of isolate BH370, confirming its species identity as B. pseudohinzii. Isolate BH370 showed antimicrobial resistance, mainly to β-lactams [2]. This could be influenced by a number of potential virulence genes noted in the genome, including aminoglycoside modifying enzymes (3 genes), β-lactamases (2 genes), fluoroquinolone resistant genes (4 genes), multidrug resistant efflux pumps (8 genes), and the multidrug resistance protein, MarC. In silico analyses also found bacteriocin (7 genes), invasion genes (9 genes), and heavy metal resistant genes (22 genes) to be present in the genome.

Table 1

General genome features of Bordetella pseudohinzii BH370.

Attribute	Chromosome
Genome size (bp)	4,474,040
GC content (%)	66.4
Contigs	390
ORFs	5119
Number of RNAs	52

Fig. 1

Subsystem category distribution of Bordetella pseudohinzii BH370.

Nucleotide accession number

The genome sequences generated in this study are available from the European Nucleotide Archive under the genome assembly accession number FPJN01000000.

Conflict of interest

The authors declare that we have no conflict of interest.

Specifications
Organism	Bordetella pseudohinzii
Strain	BH370
Sequencer or array type	Ion Torrent
Data format	Analyzed
Experimental factors	Microbial strain
Experimental features	Whole genome analysis of B. pseudohinzii BH370
Consent	N/A
Sample source location	Trachea and lung tissues of ICR mouse from the Animal Experimental Unit, Faculty of Medicine, University of Malaya, Malaysia