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.
Highlights
Rapid low-cost whole-genome sequencing (WGS) is revolutionizing microbiology; complementary advances in accessible, reproducible, and rapid analysis techniques are required to realize the potential of these data
This was first demonstrated in bacterial pathogens, such groupings are found in all bacterial populations and communities; precise and universal “species definitions” remain elusive, even after more than 140 years
Phylogenies were reconstructed from multiple rpl and rps loci and from WGS data and were compared; the results showed that the clustering of the rlpF fragments was highly congruent with clusters obtained from concatenated ribosomal MLST (rMLST) sequences and cgMLST sequences [16]
Summary
The genus Neisseria is a group of Gram-negative, oxidase-positive aerobic Betaproteobacteria, which are commonly associated with the dental and mucosal surfaces of animals and humans [12] Most of these organisms are harmless members of the commensal microbiota; the genus contains two important pathogens: N. meningitidis, the meningococcus; and Neisseria gonorrhoeae, the gonococcus. That study demonstrated how reliance on biochemical tests to differentiate N. lactamica from other Neisseria species may be unreliable, given that N. oralis was found to contain intact lactose fermentation lacY and lacZ genes indicative of -galactosidase activity In all of those cases, nucleotide sequence data from multiple loci were readily available from WGS data; such information is not always economically or practically available from all specimens, especially in resource-poor settings. This assay was developed and validated over a matter of a few weeks and proved invaluable in the MenAfriCar study, which required rapid and inexpensive species identification of thousands of samples collected in the African meningitis belt [17]
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