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 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: | Unit of Computational Biology # CRI |
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 |
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2017 NAR.pdf | N/A | ![]() | Open AccessView/Open |