Draft Genome Sequence of a Bordetella pertussis Strain with the Virulence-Associated Allelic Variant ptxP3, Isolated in Italy.

Despite a universal immunization program, pertussis has persisted and resurged, and is of particular concern for infants in terms of morbidity and mortality. Here, we report the genome sequence of a Bordetella pertussis strain with the virulence-associated allelic variant ptxP3, isolated from a 45-day-old infant.

GENOME ANNOUNCEMENT

Pertussis (whooping cough) is the most common vaccine-preventable disease, and despite widespread vaccination, the circulation of Bordetella pertussis, the causative agent of pertussis, has increased in many countries (1–3). One of the hallmarks of the resurgence of pertussis is the presence of polymorphisms in the virulence-associated genes, including the ptx promoter (ptxP); ptxP3, a novel allele for the pertussis toxin promoter, increases pertussis toxin production and is thus considered the most virulent (4). It replaced almost completely ptxP1 among circulating strains and, together with the sequence analysis of other genes, is commonly evaluated for its genetic divergence from the vaccine strain (5).

Here, the draft genome sequence of a B. pertussis strain, isolated from an unvaccinated 45-day-old infant, is reported. The infant coughed for 33 days with paroxysms, and presented apnea and cyanosis. The strain was isolated from nasopharyngeal aspirate and lab-confirmed by routine conventional methods (6, 7). In particular, it showed the allelic profiles for ptxA1, ptxP3, prn 2, and MLVA 26.

Genomic DNA was extracted using the QIAamp DNA minikit (Qiagen, Hilden, Germany) from a culture grown on Charcoal Agar plates at 35°C. The library was prepared from the extracted genomic DNA using the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA, USA), and a 2 × 300 nucleotide (nt) paired-end sequencing run was performed using the Illumina MiSeq platform. The reads were trimmed and de novo assembled using Abyss version 1.5.2 software (8). The assembly of 2,786,692 reads generated 299 contigs >500 nt with 235× coverage. The estimated genome size is 3.9 Mb, with a G+C content of 67.5%.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LFUE00000000. The version described in this paper is the first version, LFUE01000000.