ArticleFrontiers in microbiology2021
Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- A whole genome-based characterization ofFrontiers in microbiology · 2026Article
- Study Protocol for Genomic Epidemiology Investigation of Intensive Care Unit Patient Colonization by Antimicrobial-Resistant ESKAPE Pathogens.Methods and protocols · 2025Article
- MiST: rapid, accurate and flexible (core-genome) multi-locus sequence typing (MLST) allele calling from draft genomes.BMC genomics · 2025Article
- Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation ofJournal of clinical microbiology · 2025Article
- CoDing Sequence Typer (CDST): a fast, simple, decentralized and interoperable solution for bacterial genomic typing and clustering.Microbial genomics · 2025Article
- Longitudinal and cross-sectional sampling and whole genome sequencing ofApplied and environmental microbiology · 2025Article
- Highly Sensitive Suspension Immunoassay for Multiplex Detection, Differentiation, and Quantification of EightToxins · 2025Article
- Compatibility of whole-genome sequencing data from Illumina and Ion Torrent technologies in genome comparison analysis ofMicrobial genomics · 2025Article
- Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens.Nature communications · 2025Article
- Ribotyping Staphylococcus epidermidis Using Probabilistic Sequence Analysis and Levenshtein Distance Algorithm.Current microbiology · 2025Article
- Integration sites ofFrontiers in microbiology · 2025Article
- An inter-laboratory study characterizes the impact of bioinformatic approaches on genome-based cluster detection for foodborne bacterial pathogens.Frontiers in microbiology · 2025Article
- Multinational investigation of aEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2024Article
- A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.Journal of clinical microbiology · 2024Article
- refMLST: reference-based multilocus sequence typing enables universal bacterial typing.BMC bioinformatics · 2024Article
- Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome sequencing (WGS)-based outbreak investigation has proven to be a valuable method for the surveillance of bacterial pathogens. Its utility has been successfully demonstrated using both gene-by-gene (cgMLST or wgMLST) and single-nucleotide polymorphism (SNP)-based approaches. Among the obstacles of implementing a WGS-based routine surveillance is the need for an exchange of large volumes of sequencing data, as well as a widespread reluctance to share sequence and metadata in public repositories, together with a lacking standardization of suitable bioinformatic tools and workflows. To address these issues, we present
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