ArticleCommunications biology2020
Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Forensic Microbiology: When, Where and How.Microorganisms · 2024Review
- Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.Microbial genomics · 2024Article
- Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples.Veterinary sciences · 2023Review
- Whole genomes from bacteria collected at diagnostic units around the world 2020.Scientific data · 2023Article
- Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining.Bioinformatics (Oxford, England) · 2023Article
- Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting.Frontiers in microbiology · 2021Article
- Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.One health outlook · 2020Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Public health authorities whole-genome sequence thousands of isolates each month for microbial diagnostics and surveillance of pathogenic bacteria. The computational methods have not kept up with the deluge of data and the need for real-time results. We have therefore created a bioinformatics pipeline for rapid subtyping and continuous phylogenomic analysis of bacterial samples, suited for large-scale surveillance. The data is divided into sets by mapping to reference genomes, then consensus sequences are generated. Nucleotide based genetic distance is calculated between the sequences in each set, and isolates are clustered together at 10 single-nucleotide polymorphisms. Phylogenetic trees are inferred from the non-redundant sequences and the clustered isolates are added back. The method is accurate at grouping outbreak strains together, while discriminating them from non-outbreak strains. The pipeline is applied in Evergreen Online, which processes publicly available sequencing data from foodborne bacterial pathogens on a daily basis, updating phylogenetic trees as needed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.