ArticleMicrobial genomics2024
Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.
Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A standardized core genome multilocus sequence typing and life identification number barcoding framework for globalMicrobial genomics · 2026Article
- Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens.PLoS biology · 2026Article
- Lineage structure and penicillin-binding protein variability in clinicalFrontiers in public health · 2026Article
- A mini review of genome-predicted β-lactam susceptibility inFrontiers in cellular and infection microbiology · 2026Review
- Article
- Life Identification Number (LIN) codes for the genomic taxonomy of Corynebacterium diphtheriae strains.Genome medicine · 2025Article
- Identification ofJournal of proteome research · 2025Article
- Investigating the population structure of Moraxella catarrhalis using a cgMLST scheme and LIN code system.Nature communications · 2025Article
- Development of a core genome multilocus sequence typing scheme and life identification number code classification system forMicrobial genomics · 2025Article
- Development of a core genome multilocus sequence typing scheme and life identification number code classification system forMicrobial genomics · 2025Article
- Utilizing large and diverse bacterial genome datasets to improve the detection and identification ofMicrobial genomics · 2025Article
- Understanding the population structure ofbioRxiv : the preprint server for biology · 2025Article
- Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure ofMicrobial genomics · 2024Article
- Development and implementation of a core genome multilocus sequence typing scheme forMicrobial genomics · 2024Article
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Authors and funding
9 authors.
Funding
Abstract
Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.
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