Genome sequencing reveals widespread virulence gene exchange among human Neisseria species

Abstract

Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange.

Figure 1. Phylogenetic relationship of human Neisseria species.

(A) Rooted maximum likelihood Neisseria species tree (GTR + I + γ) based on concatenating the DNA sequences of a subset of 636 core Neisseria genes that are shared with the outgroup C. violaceum. A dagger denotes a bootstrap value of 100. The three N. meningitidis carrier strains are denoted by asterisks. (B) Maximum likelihood Neisseria species tree (GTR + I + γ) based on concatenating the DNA sequences of all 896 core Neisseria genes.

Figure 2. Prevalence of repetitive elements in human Neisseria genomes.

(A) Numbers of repeat sequences (RS), insertion sequences (IS), Correia elements, and DNA Uptake Sequences (DUS) are given for each Neisseria species, with complete copies in parentheses. DUS refers to the canonical DNA uptake sequence GCCGTCTGAA. DUS1 refers to the DUS variant GtCGTCTGAA. Note the high copy number of DUS1 in N. sicca and N. mucosa, highlighted in bold. (B) Absence of repeat elements in the pgd/lpxC locus region in commensals. Nel: N. elongata; Nsi: N. sicca; Nmu: N. mucosa; Nsu: N. subflava; Nfl: N. flavescens; Nci: N. cinerea; Npo: N. polysaccharea; Nla: N. lactamica 23970; Nme: N. meningitidis MC58. Black bars represent dRS3 elements; blue bars represent Correia elements. Orthologous genes are the same color; orange represents a γ-glutamyltranspeptidase present in four commensal genomes; grey represents hypothetical proteins unique to each genome. (C) Absence of large repeat arrays in the murI-tbpA/B-potD-1 locus in commensals. Ngo: N. gonorrhoeae FA1090. Forward slashes (//) represent a break in chromosome contiguity. Orthologous genes are the same color; light blue denotes a hypothetical protein. All other features are the same as in (B).

Figure 3. Virulence gene exchange among human Neisseria species.

(A) Number of genes present in different Neisseria species, out of the 177 genes known or hypothesized to be important for virulence (see methods for details). (B) Heatmap of AU test p-values obtained by comparing individual virulence gene tree topologies. The map is a 69×69 matrix of 69 virulence genes that are present in all Neisseria species (y-axis) and their corresponding topologies (x-axis). Blue indicates a p-value of 1 (trees are similar); red indicates a p-value of 0 (trees are significantly different).

Figure 4. Iron utilization genes in human Neisseria species.

Species and strain names are listed in the phylogenetic tree. N. meningitidis carrier strains are marked with asterisks. Each box represents an individual gene. Genes of the same color belong to the same iron utilization system. Genes connected by a horizontal line are contiguous in the chromosome. Loci confirmed by sequencing to be pseudogenes have a forward slash (/). N. meningitidis and N. gonorrhoeae gene names appear below each column. Genes are listed as locus tags if their iron utilization functions were deduced from other bacteria. General functions appear below the gene names.