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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.

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


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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