title: Genomic characterization of Nontuberculous Mycobacteria.
abstract: Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the primary species of the genus Mycobacterium of clinical and microbiological interest. The other members of the genus, referred to as nontuberculous mycobacteria (NTM), have long been underinvestigated. In the last decades, however, the number of reports linking various NTM species with human diseases has steadily increased and treatment difficulties have emerged. Despite the availability of whole genome sequencing technologies, limited effort has been devoted to the genetic characterization of NTM species. As a consequence, the taxonomic and phylogenetic structure of the genus remains unsettled and genomic information is lacking to support the identification of these organisms in a clinical setting. In this work, we widen the knowledge of NTMs by reconstructing and analyzing the genomes of 41 previously uncharacterized NTM species. We provide the first comprehensive characterization of the genomic diversity of NTMs and open new venues for the clinical identification of opportunistic pathogens from this genus.
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Tarcisio
authors.initials: T
authors.lastname: Fedrizzi
authors.affiliation: Mycobacteriology unit, Department of Biomedical Science, Institute of Tropical Medicine, Antwerp, Belgium.
authors.forename: Conor J
authors.initials: CJ
authors.lastname: Meehan
authors.affiliation: Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Grottola
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Giacobazzi
authors.affiliation: Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
authors.forename: Giulia
authors.initials: G
authors.lastname: Fregni Serpini
authors.affiliation: Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
authors.forename: Sara
authors.initials: S
authors.lastname: Tagliazucchi
authors.affiliation: Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Fabio
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Clotilde
authors.initials: C
authors.lastname: Bettua
authors.affiliation: NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Bertorelli
authors.affiliation: NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Veronica
authors.initials: V
authors.lastname: De Sanctis
authors.affiliation: Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Rumpianesi
authors.affiliation: Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
authors.forename: Monica
authors.initials: M
authors.lastname: Pecorari
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jousson
authors.affiliation: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.
authors.forename: Enrico
authors.initials: E
authors.lastname: Tortoli
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Segata
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D058977:Molecular Sequence Annotation; D009165:Mycobacterium Infections, Nontuberculous / Q000382:microbiology; D009170:Nontuberculous Mycobacteria / Q000145:classification / Q000235:genetics*; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*