Feavers, I. M. | Search bioRxiv

bioRxiv2026

A Life Identification Number Barcoding (LIN Code) System for Neisseria meningitidis: high resolution multi-level typing of meningococci.

Neisseria meningitidis is a commensal member of the human oropharyngeal microbiota that can cause devastating invasive meningococcal disease. This genetically and antigenically diverse accidental pathogen has been a paradigm for the study of bacterial population biology. The meningococcus was the first organism for which a seven-locus multi-locus sequence typing (MLST) scheme was developed. With the addition of sequence-based characterisation of antigen genes, molecular typing has been widely employed to inform surveillance and public health interventions. Following the advent and widespread adoption of whole genome sequencing (WGS), precise delineation of variants is possible. Here, a WGS-based Life Identification Number (LIN) code typing scheme is described, providing a multi-resolution nomenclature for understanding meningococcal population diversity and molecular epidemiology. The LIN codes were developed using a set of 6,131 N. meningitidis genomes, comprising up to 200 isolates from each clonal complex (cc) previously described using MLST. Based on cluster-stability analysis and concordance with ccs, thirteen LIN thresholds described the meningococcal population at different levels of resolution. LIN codes and human-readable nicknames consistent with existent nomenclatures were assigned to the N. meningitidis genomes hosted in the PubMLST. Published outbreaks validated the LIN thresholds, illustrating the potential of this genomic tool in public health management.

microbiology↗

bioRxiv2020

Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index: a Rapid and Accessible Tool that Exploits Genomic Data in Public Health and Clinical Microbiology Applications

As microbial genomics makes increasingly important contributions to clinical and public health microbiology, the interpretation of whole genome sequence data by non-specialists becomes essential. In the absence of capsule-based vaccines, two protein-based vaccines have been used for the prevention of invasive serogroup B meningococcal disease (IMD), since their licensure in 2013/14. These vaccines have different components and different coverage of meningococcal variants. Hence, decisions regarding which vaccine to use in managing serogroup B IMD outbreaks require information about the index case isolate including: (i) the presence of particular vaccine antigen variants; (ii) the expression of vaccine antigens; and (iii) the likely susceptibility of its antigen variants to antibody-dependent bactericidal killing. To obtain this information requires a multitude of laboratory assays, impractical in real-time clinical settings, where the information is most urgently needed. To facilitate assessment for public health and clinical purposes, we synthesised genomic and experimental data from published sources to develop and implement the Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index, which is publicly-available on PubMLST (https://pubmlst.org). Using whole genome sequences or individual gene sequences obtained from IMD isolates or clinical specimens, MenDeVAR provides rapid evidence-based information on the presence and possible immunological cross-reactivity of different meningococcal vaccine antigen variants. The MenDeVAR Index enables practitioners who are not genomics specialists to assess the likely reactivity of vaccines for individual cases, outbreak management, or the assessment of public health vaccine programmes. MenDeVAR has been developed in consultation with, but independently of, both vaccine manufacturers.

genomics↗