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EnglishMetagenomic 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 1X. 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.
Zolfo, M.; Tett, A.; Jousson, O.; Donati, C.; Segata, N. (2017). MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. NUCLEIC ACIDS RESEARCH, 45 (2): e7. doi: 10.1093/nar/gkw837 handle: http://hdl.handle.net/10449/35720
| Citation: | Zolfo, M.; Tett, A.; Jousson, O.; Donati, C.; Segata, N. (2017). MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. NUCLEIC ACIDS RESEARCH, 45 (2): e7. doi: 10.1093/nar/gkw837 handle: http://hdl.handle.net/10449/35720 | |
| Internal authors: | ||
| Organization unit: | CRI [2016-02 - today]: UNIT OF COMPUTATIONAL BIOLOGY | |
| Authors: | Zolfo, M.; Tett, A.; Jousson, O.; Donati, C.; Segata, N. | |
| Title: | MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples | |
| Journal: | NUCLEIC ACIDS RESEARCH | |
| Issue Date: | 2017 | |
| Scientific Disciplinary Area: | Settore BIO/19 - MICROBIOLOGIA GENERALE | |
| Keywords ENG: | Metagenomics Population genetics Microbiology | |
| Language: | English | |
| IF: | With Impact Factor ISI | |
| Publication status: | Published | |
| Nature of content: | Articolo in rivista/Article | |
| Digital Object Identifier (DOI): | http://dx.doi.org/10.1093/nar/gkw837 | |
| EU grant: | 7° Programma quadro (FP7) | |
| EU grant agreement number: | 618833 | |
| Appears in Collections: | 01 - Journal article |
Files in This Item:
| File | Description | Type | License | |
|---|---|---|---|---|
| 2017 NAR.pdf | N/A |  | Open AccessView/Open |
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