Genome Sequence of Bordetella pertussis Vaccine Strain BP 165

ANNOUNCEMENT

Bordetella pertussis, a Gram-negative bacterium, is the causative agent of pertussis (whooping cough) in humans (1). Despite high vaccination coverage, resurgence of pertussis disease has been reported in many countries. The observed resurgence of whooping cough underlines the need for studies on strain evolution, antigenic divergence at local and global levels, and vaccine-induced adaptation in the pathogen (2). We report here a draft genome sequence of B. pertussis strain BP 165, which is used in the manufacture of acellular pertussis vaccine at the Serum Institute of India. Bordetella pertussis strain BP 165 is a U.S. clinical isolate procured from the Center for Biologics Evaluation and Research (CBER) in the United States. The strain was grown on Bordet-Gengou agar slants supplemented with 15% horse blood and modified Stainer Scholte (SS) medium incubated at 35°C for 3 days.

Genomic DNA was extracted and purified using a genomic DNA Clean and Concentrator-10 kit (Zymo Research) per the manufacturer’s instructions. Whole-genome sequencing was performed using the MiSeq platform (Illumina, San Diego, CA). The MiSeq shotgun library was prepared using an NEBNext Ultra DNA library prep kit and was analyzed with a Bioanalyzer instrument (Agilent Technologies), using a DNA 1000 chip per the manufacturer’s instructions, followed by 2 × 150-bp paired-end sequencing. The 1,245,512 paired-end reads generated were quality filtered with 87-fold mean coverage. Adapter and low-tone sequences were removed using Trimmomatic v0. 35 (3) with a sliding window quality cutoff of Q20. De novo assembly was performed using SPAdes v3.7 (4). A total of 1,186,989 reads were assembled into 264 contigs with an N₅₀ value of 68,043 bp. Genome annotation was performed using the NCBI Prokaryotic Genome Automatic Annotation Pipeline, PATRIC (5), and Rapid Annotations using Subsystems Technology (RAST) tools (6). CRISPR repeats and bacteriophages were predicted using CRISPR Finder (7) and PHAge Search Tool Enhanced Release (PHASTER) tools (8), respectively. Bacterial insertion elements (ISs) were identified by ISfinder (9), and horizontal gene transfer was detected by the genomic island tool IslandViewer (10). All of the programs and tools in the study were used with default settings.

The genome of B. pertussis vaccine strain BP 165 consists of 4,101,762 bp, with a mean GC content of 67.71%. Totals of 3,702 genes, 46 structural tRNAs, 3 rRNAs, and 4 noncoding RNAs (ncRNAs) were predicted. The genome analysis suggested the absence of plasmids, phages, and CRISPRs. Multilocus sequence typing (MLST) analysis demonstrated that B. pertussis strain BP 165 belongs to clonal complex II (sequence type 2 [ST2]) (11). Core genome multilocus sequence typing showed its similarity with global allelic profile 41 (12). The virulence factors were also identified as being prn (1), ptxA (2), ptxC (2), ptxP (1), fim2 (1), fim3 (1), tcfA (2), ompQ (2), and vag8 (2) alleles. Insertion sequences IS481, IS1663, and IS1002 in strain BP 165 were compared with those in the B. pertussis reference strain Tohama-I and B. pertussis CS and were found to be similar (13).

The accessibility of high-quality genome sequences of B. pertussis vaccine strains will allow detailed phylogenetic and bioinformatic studies, which will facilitate better understanding of sequence variations globally, thus opening the way for global surveillance.