title: MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.
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.
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, TN 38123, Italy.
authors.forename: Moreno
authors.initials: M
authors.lastname: Zolfo
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, TN 38123, Italy.
authors.forename: Adrian
authors.initials: A
authors.lastname: Tett
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, TN 38123, Italy.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jousson
authors.affiliation: Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, San Michele all'Adige 38010, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Donati
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, TN 38123, Italy nicola.segata@unitn.it.
authors.forename: Nicola
authors.initials: N
authors.lastname: Segata
mesh_terms: D000465:Algorithms; D000483:Alleles; D001419:Bacteria / Q000145:classification / Q000235:genetics; D000069196:Gastrointestinal Microbiome; D016680:Genome, Bacterial; D006801:Humans; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D058885:Multilocus Sequence Typing / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D064878:Web Browser