Journal
NUCLEIC ACIDS RESEARCH
Volume 45, Issue 2, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkw837
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Funding
- European Union's Seventh Framework Programme under REA grant [FP7/20072013, PCIG13-GA-2013618833]
- Centre for Integrative Biology, University of Trento startup funds
- MIUR 'Futuro in Ricerca' [RBFR13EWWI 001]
- Leo Pharma Foundation
- Fondazione CARITRO Fellowship [Rif.Int.2013.0239, Rif.int.2014.0325]
- 'Terme di Comano'
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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. Lowt-hroughput 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.
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