title: Extensive genomic variation within clonal complexes of Neisseria meningitidis.
abstract: Meningococcal disease is a widely distributed complex disease affecting all age categories. It can cause severe meningitis and septicemia, especially in unvaccinated infants and young children. The causative agent, Neisseria meningitidis (Nm), can be phenotypically and genetically differentiated into serogroups and sequence types (STs) and has a highly dynamic population structure. To obtain a deeper understanding of the epidemiology of Nm, we sequenced seven Nm genomes. Large-scale genomic analysis was conducted with these 7 Nm genomes, 27 additional Nm genomes from GenBank, and 4 other Neisseria genomes. We observed extensive homologous recombination in all gene functional categories among different Nm genomes. Homologous recombination is so frequent that it has resulted in numerous chimeric open reading frames, including genes in the capsule biosynthesis cluster and loci targeted by commercial vaccines. Our results reveal that, despite widespread use, evolutionary relationships inferred from the standard seven-gene multilocus sequence typing (MLST) method could not predict virulence gene content or strain phenotype. In fact, up to 28% of the virulence-associated genes could differ between strains of identical STs. Consistent with previous studies, we found that allelic recombination is also associated with alterations in antibiotic susceptibility. Overall, these findings emphasize the extensive genomic plasticity of Nm and the limitations of standard molecular methods to quantify this genotypic and phenotypic diversity.
authors.affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada. haoweilong@gmail.com
authors.forename: Weilong
authors.initials: W
authors.lastname: Hao
authors.forename: Jennifer H
authors.initials: JH
authors.lastname: Ma
authors.forename: Keisha
authors.initials: K
authors.lastname: Warren
authors.forename: Raymond S W
authors.initials: RS
authors.lastname: Tsang
authors.forename: Donald E
authors.initials: DE
authors.lastname: Low
authors.forename: Frances B
authors.initials: FB
authors.lastname: Jamieson
authors.forename: David C
authors.initials: DC
authors.lastname: Alexander
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000595:Amino Acid Sequence; D015373:Bacterial Typing Techniques / Q000379:methods; D001483:Base Sequence; D002648:Child; D004269:DNA, Bacterial / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D059765:Homologous Recombination; D006801:Humans; D008297:Male; D008589:Meningococcal Infections / Q000453:epidemiology* / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D058885:Multilocus Sequence Typing; D009345:Neisseria meningitidis / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D014774:Virulence
chemical_list: D004269:DNA, Bacterial
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