Population and Functional Genomics of Neisseria Revealed with Gene-by-Gene Approaches

Abstract

Rapid low-cost whole-genome sequencing (WGS) is revolutionizing microbiology; however, complementary advances in accessible, reproducible, and rapid analysis techniques are required to realize the potential of these data. Here, investigations of the genus Neisseria illustrated the gene-by-gene conceptual approach to the organization and analysis of WGS data. Using the gene and its link to phenotype as a starting point, the BIGSdb database, which powers the PubMLST databases, enables the assembly of large open-access collections of annotated genomes that provide insight into the evolution of the Neisseria, the epidemiology of meningococcal and gonococcal disease, and mechanisms of Neisseria pathogenicity.

FIG 1

Hierarchical approach to WGS data analysis. The data represent the increasing resolution seen in analyzing different and increasing numbers of loci in bacterial genomes (above the diagonal line, shaded), along with their relationship to nomenclature (below the line). 16S rRNA efficiently identifies bacteria to the genus level, whereas conventional locus MLST (sometimes called multilocus sequence analysis [MLSA]) enables resolution within genera and species. The 53-locus rMLST approach allows species identification and resolution within species, while the highest levels of resolution are obtained with whole, core, and/or accessory genome MLST. (Image republished from reference with permission of the publisher.)

FIG 2

Evolutionary relationships among Neisseria species based on concatenated sequences of the 53 ribosomal gene proteins (rMLST). The relationships among different Neisseria species were reconstructed with nucleotide sequences from 49 ribosomal gene proteins. Single asterisks (*) denote a cluster of Neisseria mucosa species in which isolates previously identified as being Neisseria sicca and Neisseria macacae species were found, indicating that rMLST analysis had identified these as being variants of the N. mucosa species. Double asterisks (**) denote a cluster composed of Neisseria subflava species in which isolates previously identified as Neisseria flavescens had clustered. Triple asterisks (***) denote a polyphyletic group comprising N. polysaccharea isolates indicative of the presence of more than one N. polysaccharea species. (Image republished from reference with permission of the publisher.)

FIG 3

Core genome genealogical analysis of a global lineage 5 meningococcal population dating from 1969 through 2008. Lineage 5 meningococci (equivalent to the hyperinvasive ST-32 clonal complex identified by MLST) have been responsible for serogroup B meningococcal disease outbreaks globally for more than 30 years. In this analysis, a total of 1,752 loci (core to the lineage) were compared, identifying the presence of three distinct sublineages which were classified into the “Asian group” (sublineage 5.1), the “North European-Norwegian group” (sublineage 5.2) which contained isolates with PorA type P1.7,16, and a “Latin American group” (sublineage 5.3) with PorA type P1.19.15. (Image republished from reference with permission of the publisher.)