Neisseria genomics: current status and future perspectives

Abstract

High-throughput whole genome sequencing has unlocked a multitude of possibilities enabling members of the Neisseria genus to be examined with unprecedented detail, including the human pathogens Neisseria meningitidis and Neisseria gonorrhoeae. To maximise the potential benefit of this for public health, it is becoming increasingly important to ensure that this plethora of data are adequately stored, disseminated and made readily accessible. Investigations facilitating cross-species comparisons as well as the analysis of global datasets will allow differences among and within species and across geographic locations and different times to be identified, improving our understanding of the distinct phenotypes observed. Recent advances in high-throughput platforms that measure the transcriptome, proteome and/or epigenome are also becoming increasingly employed to explore the complexities of Neisseria biology. An integrated approach to the analysis of these is essential to fully understand the impact these may have in the Neisseria genus. This article reviews the current status of some of the tools available for next generation sequence analysis at the dawn of the 'post-genomic' era.

Keywords: Neisseria gonorrhoeae; Omics analyses; Neisseria meningitidis; next-generation sequencing.

Figure 1.

Cumulative number of assembled WGS data deposited in PubMLST.org/neisseria. Graph depicting cumulative whole genome sequence data available in PubMLST dating from 2000 to the end of 2016. Blue lines depict N. meningitidis WGS data starting with relatively few isolates in 2010 and peaking at 5000 isolates at the end of 2016; red depicts N. gonorrhoeae WGS data peaking at over 2000; green all of the other Neisseria species including N. lactamica, N. subflava, N. polysaccharea, N. cinerea, N. mucosa, N. dentiae, N. musculi, N. oralis, N. bacilliformis and N. elongata.

Figure 2.

NGS and analysis pipelines. Most common tools used for the analysis of WGS data. QC checks*: quality control before de novo assembly: poorly identified bases, low quality sequences and/or contaminants such as adaptors. QC checks^$: quality control checks after assembly for mixed samples and bacterial contamination.

Figure 3.

NEIS loci defined in PubMLST. Representative figure of a bacterial cell and some of the loci found across Neisseria species. Green structures represent acquisition receptors; pink indicate antigens; orange import/export elements; blue amino acid import/export; yellow sugar import/export; various metabolic pathways are also indicated. Additional loci have been defined in PubMLST. Figure based on the study by Tettelin et al. (2000).

Figure 4.

Omics platforms. Flow diagram depicting available Omics approaches some of which have been used in Neisseria research. Possible ways in which these approaches can be associated are also indicated.