Web-Based Genome Analysis of Bacterial Meningitis Pathogens for Public Health Applications Using the Bacterial Meningitis Genomic Analysis Platform (BMGAP)

Abstract

Effective laboratory-based surveillance and public health response to bacterial meningitis depends on timely characterization of bacterial meningitis pathogens. Traditionally, characterizing bacterial meningitis pathogens such as Neisseria meningitidis (Nm) and Haemophilus influenzae (Hi) required several biochemical and molecular tests. Whole genome sequencing (WGS) has enabled the development of pipelines capable of characterizing the given pathogen with equivalent results to many of the traditional tests. Here, we present the Bacterial Meningitis Genomic Analysis Platform (BMGAP): a secure, web-accessible informatics platform that facilitates automated analysis of WGS data in public health laboratories. BMGAP is a pipeline comprised of several components, including both widely used, open-source third-party software and customized analysis modules for the specific target pathogens. BMGAP performs de novo draft genome assembly and identifies the bacterial species by whole-genome comparisons against a curated reference collection of 17 focal species including Nm, Hi, and other closely related species. Genomes identified as Nm or Hi undergo multi-locus sequence typing (MLST) and capsule characterization. Further typing information is captured from Nm genomes, such as peptides for the vaccine antigens FHbp, NadA, and NhbA. Assembled genomes are retained in the BMGAP database, serving as a repository for genomic comparisons. BMGAP’s species identification and capsule characterization modules were validated using PCR and slide agglutination from 446 bacterial invasive isolates (273 Nm from nine different serogroups, 150 Hi from seven different serotypes, and 23 from nine other species) collected from 2017 to 2019 through surveillance programs. Among the validation isolates, BMGAP correctly identified the species for all 440 isolates (100% sensitivity and specificity) and accurately characterized all Nm serogroups (99% sensitivity and 98% specificity) and Hi serotypes (100% sensitivity and specificity). BMGAP provides an automated, multi-species analysis pipeline that can be extended to include additional analysis modules as needed. This provides easy-to-interpret and validated Nm and Hi genome analysis capacity to public health laboratories and collaborators. As the BMGAP database accumulates more genomic data, it grows as a valuable resource for rapid comparative genomic analyses during outbreak investigations.

Molecular diagnostic assays for the detection of common bacterial meningitis pathogens: A narrative review

“…Furthermore, the analysis and comparison of genomes relies on the availability of databases where genomes can be stored, curated and analysed. For example, PubMLST databases (https://pubmlst.org) store and annotate thousands of genomes (with associated metadata) of all four bacterial species included in this review in dedicated genome libraries [82] and BMGAP allows users to deposit and access N. meningitidis and H. influenzae genomes using a secure online portal [83].…”

Concurrent Outbreaks of Hepatitis A, Invasive Meningococcal Disease, and Mpox, Florida, USA, 2021–2022

“…Select specimens were also forwarded to CDC laboratories for additional characterization or confirmation. We analyzed sequencing data by using BPHL’s FLAQ-AMR pipeline ( https://github.com/BPHL-Molecular/flaq_amr ) to assess sequence quality and identify the sequence type (ST) and submitted data to CDC’s Bacterial Meningitis Genome Analysis Platform (BMGAP; https://github.com/CDCgov/BMGAP ) to identify the clonal complex (CC) and to verify serogroup for each isolate ( 19 ). We identified outbreak-associated cases by serogroup, ST, and CC, and constructed phylogenetic trees.…”