title: Short-Read Whole-Genome Sequencing for Laboratory-Based Surveillance of Bordetella pertussis.
abstract: Bordetella pertussisis a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance ofB. pertussisacellular 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 clinicalB. pertussisisolates 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 ofB. pertussismolecular 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.
authors.affiliation: Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada alex.marchand-austin@oahpp.ca.|Public Health Ontario Laboratory, Public Health Ontario, Toronto, Canada.
authors.forename: Alex
authors.identifier: 0000-0001-5932-2037
authors.initials: A
authors.lastname: Marchand-Austin
authors.affiliation: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.
authors.forename: Raymond S W
authors.initials: RSW
authors.lastname: Tsang
authors.affiliation: Public Health Ontario Laboratory, Public Health Ontario, Toronto, Canada.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Guthrie
authors.affiliation: Public Health Ontario Laboratory, Public Health Ontario, Toronto, Canada.
authors.forename: Jennifer H
authors.initials: JH
authors.lastname: Ma
authors.affiliation: Public Health Ontario, Toronto, Canada.
authors.forename: Gillian H
authors.initials: GH
authors.lastname: Lim
authors.affiliation: Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada.|Public Health Ontario, Toronto, Canada.|Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.
authors.forename: Natasha S
authors.initials: NS
authors.lastname: Crowcroft
authors.affiliation: Public Health Ontario, Toronto, Canada.|Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.
authors.forename: Shelley L
authors.initials: SL
authors.lastname: Deeks
authors.affiliation: Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada.|Public Health Ontario Laboratory, Public Health Ontario, Toronto, Canada.
authors.forename: David J
authors.initials: DJ
authors.lastname: Farrell
authors.affiliation: Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada.|Public Health Ontario Laboratory, Public Health Ontario, Toronto, Canada.
authors.forename: Frances B
authors.initials: FB
authors.lastname: Jamieson
mesh_terms: D000942:Antigens, Bacterial / Q000235:genetics / Q000276:immunology; D001483:Base Sequence; D001886:Bordetella pertussis / Q000235:genetics* / Q000276:immunology* / Q000302:isolation & purification; D002648:Child; D002675:Child, Preschool; D004269:DNA, Bacterial / Q000235:genetics; D062665:Epidemiological Monitoring; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D007223:Infant; D009864:Ontario; D010567:Pertussis Vaccine / Q000276:immunology*; D017422:Sequence Analysis, DNA; D014917:Whooping Cough / Q000453:epidemiology* / Q000382:microbiology / Q000473:pathology
chemical_list: D000942:Antigens, Bacterial; D004269:DNA, Bacterial; D010567:Pertussis Vaccine
keywords: Bordetella pertussis; DNA sequencing; immunization; molecular methods; surveillance studies