Complete Genome Sequence of Bordetella pertussis CS, a Chinese Pertussis Vaccine Strain

Abstract

Bordetella pertussis is the causative agent of pertussis. Here, we report the genome sequence of Bordetella pertussis strain CS, isolated from an infant patient in Beijing and widely used as a vaccine strain for production of an acellular pertussis vaccine in China.

GENOME ANNOUNCEMENT

Bordetella pertussis is a strict human pathogen that is the causative agent of pertussis (whooping cough). Despite widespread immunization with pertussis vaccines, many countries still report outbreaks (1, 12, 14). Resurgence of pertussis has been recently observed in some countries with high vaccination coverage (4, 8, 10). It is suggested that pathogen adaptation may play a role in the reemergence of pertussis (10, 15, 16). In this present work, the complete genome sequence of B. pertussis strain CS, which was isolated from an infant patient in 1951 in Beijing and widely used as a vaccine strain for production of an acellular pertussis vaccine in China, was determined and compared with the published genome of Tohama I (11).

Whole-genome sequencing of B. pertussis CS was performed with a combined strategy of the Sanger shotgun approach (6) and 454 fragment sequencing technology (9). A total of 329,480 reads, giving 28-fold coverage of the genome, were generated using the GS FLX system (454 Life Sciences Corporation) and assembled into 287 contigs with the 454 Newbler assembler. Artificial 1-kb reads representing the Roche/454 assembly were generated using mktrace and assembled with 11,444 paired-end ABI3730 reads (3.2-kb library) using the Phred/Phrap/Consed package (7). Sequence gaps were filled through sequencing of PCR products. Prediction and annotation of protein-encoding genes were performed as described previously (5) and verified manually using the annotation of Tohama I (11).

The complete genome of B. pertussis CS contains a circular 4,124,236-bp chromosome with an average G+C content of 67.3%. There are 3,456 protein-coding sequences with an average size of 327 amino acids, 51 tRNA genes, and three rRNA operons in the genome.

Compared with strain Tohama I, 2 large fragments (>10 kb) were exclusively present in strain CS, of which contained 18 (BPTD_2835 to BPTD_2852) and 21 (BPTD_0387 to BPTD_0407) genes. These differences were involved mainly in the transcriptional regulator system, the metabolism system, mobile elements, and the restriction modification system. The two regions can be found in both Bordetella bronchiseptica and Bordetella parapertussis (11), suggesting that these genes are lost in the Tohama I lineage and are not obtained in CS, which is consistent with the previously reported tendency (2). Both of these two regions were located adjacent to copies of the insertion element IS481, which is present in high numbers in the B. pertussis chromosome and has been reported to provide targets for homologous recombination, resulting in deletion of intervening sequences (3, 13).

Except for the two large insertions above, only 341 polymorphic sites were found between CS and Tohama I, consisting of 301 single nucleotide polymorphisms (SNPs) and 40 small insertion or deletion events (indels). Of the 301 SNPs, 204 were located in open reading frames and 97 were in the intergenic regions, indicating an estimated SNP density of 1 SNP per 13,701 bases. This places B. pertussis to be one of the known most monomorphic human pathogens.

In summary, the complete genome sequence of B. pertussis CS will facilitate additional bioinformatic and phylogenetic analyses and enable in-depth studies of B. pertussis sequence variations.

Nucleotide sequence accession number.

The genome sequence of B. pertussis strain CS has been deposited in GenBank under the accession number CP002695.