Comparative genomics identifies the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species

Abstract

Neisseria meningitidis colonizes the nasopharynx and, unlike commensal Neisseria species, is capable of entering the bloodstream, crossing the blood-brain barrier, and invading the meninges. The other pathogenic Neisseria species, Neisseria gonorrhoeae, generally causes an infection which is localized to the genitourinary tract. In order to investigate the genetic basis of this difference in disease profiles, we used a strategy of genomic comparison. We used DNA arrays to compare the genome of N. meningitidis with those of N. gonorrhoeae and Neisseria lactamica, a commensal of the nasopharynx. We thus identified sequences conserved among a representative set of virulent strains which are either specific to N. meningitidis or shared with N. gonorrhoeae but absent from N. lactamica. Though these bacteria express dramatically different pathogenicities, these meningococcal sequences were limited and, in contrast to what has been found in other pathogenic bacterial species, they are not organized in large chromosomal islands.

FIG. 1.

Computer-assisted comparison of publicly available neisserial genome sequences. (A) TBlastN comparison of ORFs in Z2491 against the genomes of N. gonorrhoeae FA1090 and N. meningitidis MC58. The comparison used a minimum E value of 10⁻⁴ as the cutoff for reporting hits, which corresponds to ∼20% amino acid similarity for an ORF of 100 bases and <10% for an ORF of 300 bases or larger. The percentage of homologous amino acids in a Z2491 ORF (abscissa) is plotted against the number of ORFs (ordinate) presenting that percentage of homology. The positions of selected genes are shown. lipA is a meningococcus-specific capsular biosynthesis gene. PolA is a DNA polymerase involved in chromosome replication. The protein PilC1 is an adhesin, PilE is the pilin subunit, and OpaA and PorB are surface antigens. TbpA and TbpB are the membrane transport and surface-exposed components, respectively, of a human transferrin binding and iron acquisition system. Hence, proteins known experimentally to have similar functions but varying sequences in strains of pathogenic neisseriae are found to have between 65 and 80% amino acid similarity and allow a choice of 65% homology as a cutoff to define the presence or absence of a functional homologue in a test strain. (B) Chromosomal distribution of genetic differences. The degree of homology of the N. meningitidis Z2491 ORFs to sequences in the FA1090 genome (percentage amino acid similarity of predicted proteins) is plotted along the length of the Z2491 chromosome. The larger islands of strain-specific DNA are as follows: a, part of the capsule locus NMA0184-NMA0185 and NMA0195-NMA0202; b, two-partner secretion family proteins NMA0687-NMA0698; c and d, phage-related proteins NMA1183-NMA1200 and NMA1298-NMA1324; and e, prophage NMA1820-NMA1883. (C) Chromosomal distribution of differences between N. meningitidis Z2491 and MC58. The homology of ORFs to sequences in the MC58 genome is plotted along the length of the Z2491 chromosome. Note that many of these differences correspond to those between Z2491 and N. gonorrhoeae FA1090 and are hence strain and not species specific.

FIG. 2.

Distribution of reactivities with different Neisseria strains. The histogram shows the distribution of reactivities of amplicons for each of the strains. Related strains are grouped on the basis of previous epidemiological studies (Table 1). Lanes: 1, N. meningitidis Z2491 (serogroup A); 2, Z5463 (serogroup A); 3, MC58 (serogroup B); 4, 94N369 (serogroup B); 5, FAM18 (serogroup C); 6, ROU (serogroup W135); 7, 98068 (serogroup C); 8, Z4673 (serogroup B); 9, N. gonorrhoeae F62; 10, MS11; 11, FA1090; 12, N. lactamica 8064; 13, 9764.

FIG. 3.

Distribution of strain-specific sequences. Distribution along the chromosome of Z2491 of amplicons absent from each of the strains of N. meningitidis (A) and from each of the strains of N. gonorrhoeae and N. lactamica (B). The strains are arranged as in Table 1 and Fig. 2. The peak height represents the difference between the value for an amplicon and the cutoff value, where the sequence is absent from the strain. Only groups of at least two contiguous nonreacting amplicons are shown. Selected genes or groups of genes, meningococcus serogroup A specific (A) and meningococcus specific (B), are named. Strain Z5463 (A) is an isolate from the same epidemic as the reference strain, Z2491, and bears witness to their high sequence homology.