Genetic Diversity of Clinical Bordetella Pertussis ST2 Strains in comparison with Vaccine Reference Strains of India

Abstract

Objectives: Pertussis is a highly contagious disease of the respiratory tract caused by Bordetella pertussis, a bacterium that lives in the mouth, nose, and throat. Current study reports the highly accurate complete genomes of two clinical B. pertussis strains from India for the first time. Methods: Complete genome sequencing was performed for two B. pertussis strains using Ion Torrent PGM and Oxford nanopore sequencing method. Data was assembled de novo and the sequence annotation was performed through PATRIC and NCBI server. Downstream analyses of the isolates were performed using CGE server databases for antimicrobial resistance genes, plasmids, and sequence types. The phylogenetic analysis was performed using Roary. Results: The analysis revealed insertional elements flanked by IS481, which has been previously regarded as the important component for bacterial evolution. The two B. pertussis clinical strains exhibited diversity through genome degradation when compared to whole-cell vaccine reference strains of India. These isolates harboured multiple genetic virulence traits and toxin subunits, which belonged to sequence type ST2. Conclusion:The genome information of Indian clinical B. pertussis strains will serve as a baseline data to decipher more information on the genome evolution, virulence factors and their role in pathogenesis for effective vaccine strategies.

Characterization of Bordetella pertussis Strains Isolated from India

“…Here, S1, S2, S5 isolates showed allelic profiles similar with the vaccine strains used in India and two isolates previously reported from India (Table 2) [36]. Most dominant circulating allele type for pertussis toxin, ptxP3 was identified in two isolates S3 and S4 used in this study and not observed in two other B. pertussis genomes present in the database from India [36,37].…”

Comparative genomics of whole-cell pertussis vaccine strains from India

“…Genome sequences of two Indian clinical isolates BPD1 (CP034102) and BPD2 (CP034101) are reported. These are the only two isolates reported from India to date [44].…”

“…The study suggests that vaccine strains and clinical isolates displayed gene loss and duplication with no significant impact on overall genome size as the number of gene lost was nearly equal to the number of genes duplicated (Table 4). Genomic deletions and ongoing gene loss are one of the apparent features observed in recent clinical isolates reported from many countries [44,55]. The lost genes majorly belonged to categories of membrane transport and amino acid metabolism.…”

“…The genes identified in the category of amino acid metabolism were related to ABC transporter's components. ABC transporters are a large group of proteins which have cellular functions in import and export various substances, which suggests deletion of such genes might confer a selective advantage as a one of the strategies during adaptation of the organism in highly vaccinated populations [44,48,68]. The duplicated genes in all strains found in COG categories belonged to amino acid and nucleic acid metabolism and post-translation modification (Additional file 5).…”