ArticleBMC bioinformatics2024
refMLST: reference-based multilocus sequence typing enables universal bacterial typing.
Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers, 1 of them a synthesis that pooled it.
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Who cites it
5 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Tracking of multidrug-resistant pathogen clones in Ghana: a systematic review and meta-analysis.BMC medical genomics · 2025Pooled it
- Applicability of Nanopore-only whole-genome sequencing forJournal of clinical microbiology · 2026Article
- Detecting healthcare-associated transmission and antifungal resistance inJournal of clinical microbiology · 2026Article
- Ribotyping for Accurate Identification of Infectious Bacteria in Animal-Derived Foods and Laboratory Samples: Implications for Human Health.Journal of tropical medicine · 2026Review
- A comparative review of three cloud-based platforms for microbial whole genome sequencing analysis.Antimicrobial stewardship & healthcare epidemiology : ASHE · 2026Article
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Authors and funding
8 authors.
Funding
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Abstract
backgroundCommonly used approaches for genomic investigation of bacterial outbreaks, including SNP and gene-by-gene approaches, are limited by the requirement for background genomes and curated allele schemes, respectively. As a result, they only work on a select subset of known organisms, and fail on novel or less studied pathogens. We introduce refMLST, a gene-by-gene approach using the reference genome of a bacterium to form a scalable, reproducible and robust method to perform outbreak investigation.
resultsWhen applied to multiple outbreak causing bacteria including 1263 Salmonella enterica, 331 Yersinia enterocolitica and 6526 Campylobacter jejuni genomes, refMLST enabled consistent clustering, improved resolution, and faster processing in comparison to commonly used tools like chewieSnake.
conclusionsrefMLST is a novel multilocus sequence typing approach that is applicable to any bacterial species with a public reference genome, does not require a curated scheme, and automatically accounts for genetic recombination. AVAILABILITY AND IMPLEMENTATION: refMLST is freely available for academic use at https://bugseq.com/academic .
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