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Nucleic Acids Res. 2017 Jan 25;45(2):e7. doi: 10.1093/nar/gkw837. Epub 2016 Sep 19.

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.

Author information

1
Centre for Integrative Biology, University of Trento, Trento, TN 38123, Italy.
2
Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, San Michele all'Adige 38010, Italy.
3
Centre for Integrative Biology, University of Trento, Trento, TN 38123, Italy nicola.segata@unitn.it.

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.

PMID:
27651451
PMCID:
PMC5314789
DOI:
10.1093/nar/gkw837
[Indexed for MEDLINE]
Free PMC Article

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