Short-Read Whole-Genome Sequencing for Laboratory-Based Surveillance of Bordetella pertussis

Abstract

Bordetella pertussis is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of B. pertussis acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labor-intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole-genome sequencing data generated from 40 clinical B. pertussis isolates and analyzed using the SRST2 bioinformatic package. SRST2 was able to identify aP antigen genotypes for all antigens with the exception of pertactin, possibly due to low read coverage in GC-rich low-complexity regions of variation. Two main genotypes were observed in addition to a singular third genotype that contained an 84-bp deletion that was identified by SRST2 despite the issues in allele calling. This method has the potential to generate large pools of B. pertussis molecular data that can be linked to clinical and epidemiological information to facilitate research of vaccine effectiveness and disease severity in the context of emerging vaccine antigen-deficient strains.KEYWORDS Bordetella pertussis, DNA sequencing, immunization, molecular methods, surveillance studies B ordetella pertussis is a Gram-negative aerobic bacterium that causes respiratory illness in humans and is commonly referred to as whooping cough. Vaccination is the primary recommended preventative public health intervention, and since the end of the 20th century, vaccination programs in most high-income countries have incorporated acellular component vaccines (aP) as replacements for whole-cell vaccines that have been used for over 60 years, largely due to an improved safety profile (1-5). The aP is the result of decades of research into the immunological properties of B. pertussis and its virulence factors using animal models and in vitro experiments to characterize B. pertussis's mode of infection and pathophysiological effects (6-8). In the context of large and frequent B. pertussis outbreaks and decreasing vaccine effectiveness since the introduction of the aP (albeit to various degrees in different regions), additional research has been conducted to examine how vaccination may be influencing the evolution of B. pertussis and the long-term impact on the effectiveness of B. pertussis vaccines (9-14).Allele typing using select virulence factors has been useful in describing changes across larger evolutionary scales and has been a key tool for associating changes in the B. pertussis population with the introduction of aPs (15-17). The virulence factor typing

Tatajuba ― Exploring the distribution of homopolymer tracts

“…pertussis, 7 Bordetella parapertussis, and 10 Bordetella bronchiseptica), using B. pertussis Tohama I (ASM19571v1) as the reference genome. The B. pertussis samples come from bioprojects PRJNA348407, PRJNA356412, PRJEB42353, and PRJEB38438 [18][19][20], while the B. parapertussis and B. bronchiseptica come from bioproject PRJNA287884 [21].…”

Comparative genomics of whole-cell pertussis vaccine strains from India

“…Strains deficient in tracheal colonization factor (virulence associated protein in B. pertussis), were reported from Belgium, Netherland, and the USA [27]. Besides antigenic divergence, massive gene loss, pseudogenes formation and insertion sequence (IS481) mediated genomic rearrangements are among the significant genomic features of the B. pertussis adaptation that became apparent in different comparative genomic studies [28][29][30][31][32][33][34][35]. Recently, a comparative genomic study based on 343 B. pertussis isolates primarily from countries using ACV suggested that adaptive evolution of this pathogen is closely associated with vaccine introduction and emergent strains spread rapidly between countries [28].…”