Neisseria meningitidis has acquired sequences within the capsule locus by horizontal genetic transfer

Abstract

Background: Expression of a capsule from one of serogroups A, B, C, W, X or Y is usually required for Neisseria meningitidis (Nme) to cause invasive meningococcal disease. The capsule is encoded by the capsule locus, cps, which is proposed to have been acquired by a formerly capsule null organism by horizontal genetic transfer (HGT) from another species. Following identification of putative capsule genes in non-pathogenic Neisseria species, this hypothesis is re-examined. Methods: Whole genome sequence data from Neisseria species, including Nme genomes from a diverse range of clonal complexes and capsule genogroups, and non-Neisseria species, were obtained from PubMLST and GenBank. Sequence alignments of genes from the meningococcal cps, and predicted orthologues in other species, were analysed using Neighbor-nets, BOOTSCANing and maximum likelihood phylogenies. Results: The meningococcal cps was highly mosaic within regions B, C and D. A subset of sequences within regions B and C were phylogenetically nested within homologous sequences belonging to N. subflava, consistent with HGT event in which N. subflava was the donor. In the cps of 23/39 isolates, the two copies of region D were highly divergent, with rfbABC’ sequences being more closely related to predicted orthologues in the proposed species N. weixii (GenBank accession number CP023429.1) than the same genes in Nme isolates lacking a capsule. There was also evidence of mosaicism in the rfbABC’ sequences of the remaining 16 isolates, as well as rfbABC from many isolates. Conclusions: Data are consistent with the en bloc acquisition of cps in meningococci from N. subflava, followed by further recombination events with other Neisseria species. Nevertheless, the data cannot refute an alternative model, in which native meningococcal capsule existed prior to undergoing HGT with N. subflava and other species. Within-genus recombination events may have given rise to the diversity of meningococcal capsule serogroups.

Identification of integrative and conjugative elements in pathogenic and commensal Neisseriaceae species via genomic distributions of DNA uptake sequence dialects

“…S1, indicating this species as a likely donor of the clinically relevant GI. The transfer of disease-associated virulence factors from this commensal to pathogenic Neisseria is consistent with a recent study indicating horizontal acquisition of meningococcal capsule locus components from N. subflava [ 46 ].…”

Classification of Neisseria meningitidis genomes with a bag-of-words approach and machine learning

“…The second, with locus ID NEIS0044, encodes an oligopeptide transporter. Little is known about this gene except that it flanks the capsule locus, 48 which encodes the major N. meningitidis VF. The third, ygfZ , encodes a transfer ribonucleic acid (tRNA)-modifying protein that plays a role in iron–sulfur metabolism 42 and contributes to the secretion of cytotoxic necrotizing factor 1, a VF, in outer-membrane vesicles (OMVs) of Escherichia coli .…”

Diversity of the type VI secretion systems in the Neisseria spp

“…lactamica , and N. polysaccharae (, Box E). The latter two species are common commensal species of the human nasopharynx and are known to engage in frequent horizontal gene transfer events [124, 125] therefore this is perhaps not surprising.…”