ArticleNucleic acids research2017
MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Methicillin-resistant Staphylococcus aureus eradication in cystic fibrosis patients: A randomized multicenter study.PloS one · 2019Trial
- Multi-strain Clostridioides difficile infection: Increased detection and clinical implications.The Journal of infection · 2026Article
- Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.Microorganisms · 2026Review
- Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.Nature microbiology · 2025Article
- Early detection and population dynamics ofFrontiers in microbiology · 2025Article
- Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications.Microbial genomics · 2025Article
- Genome assembly ofFrontiers in microbiology · 2025Article
- The oral-gut microbiome axis in health and disease.Nature reviews. Microbiology · 2024Review
- Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases.Cell host & microbe · 2024Article
- Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.International journal of molecular sciences · 2024Article
- Article
- The Skin Microbiome: Current Techniques, Challenges, and Future Directions.Microorganisms · 2023Review
- Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity ofMicroorganisms · 2023Article
- Article
- Comparison of four multilocus sequence typing schemes and amino acid biosynthesis based on genomic analysis of Bacillus subtilis.PloS one · 2023Article
- Metagenomic Approaches Reveal Strain Profiling and Genotyping of Klebsiella pneumoniae from Hospitalized Patients in China.Microbiology spectrum · 2022Article
- Comparative Respiratory Tract Microbiome Between Carbapenem-ResistantFrontiers in microbiology · 2022Article
- Metagenomic Assessment of the Pathogenic Risk of Microorganisms in Sputum of Postoperative Patients With Pulmonary Infection.Frontiers in cellular and infection microbiology · 2022Article
- Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts.Frontiers in bioinformatics · 2022Article
- mixtureS: a novel tool for bacterial strain genome reconstruction from reads.Bioinformatics (Oxford, England) · 2021Article
2 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with >98.5% accuracy at coverages as low as 1×. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples.
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