Typing and classification of non-tuberculous mycobacteria isolates

Background: There are a large and growing number of non-tuberculous mycobacteria (NTM) species that have been isolated, identified, and described in the literature, yet there are many clinical isolates which are not assignable to known species even when the genome has been sequenced. Additionally, a recent manuscript has proposed the reclassification  of the Mycobacterium genus into five distinct genera. Methods: We describe using a community standard fast  average nucleotide identity (ANI) approximation method, MASH, for classifying NTM genomes by comparison to a resource of type strain genomes and proxy genomes. We evaluate the genus reclassification proposal in light of our ANI, MLST, and pan-genome work. Results: We describe here a sequencing study of hundreds of clinical NTM isolates. To aid in characterizing these isolates we defined a multi-locus sequence typing (MLST) schema for NTMs which can differentiate strains at the species and subspecies level using eight ribosomal protein genes. We determined and deposited the allele profiles for 2,802 NTM and Mycobacterium tuberculosis complex strains in PubMLST. Conclusions: The MLST schema and our pan-genome analysis of Mycobacteria can help inform the design of marker-gene diagnostics. The ANI comparisons likewise can assist in the classification of unknown genomes, even from previously unknown species.

[1]  Radhey S. Gupta,et al.  Corrigendum: Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera , 2019, Front. Microbiol..

[2]  T. Horii,et al.  Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles , 2019, Emerging microbes & infections.

[3]  Erin Beck,et al.  Large-scale comparative analysis of microbial pan-genomes using PanOCT , 2018, Bioinform..

[4]  Keith A Jolley,et al.  Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications , 2018, Wellcome open research.

[5]  E. Tortoli.  Commentary: Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera , 2018, Front. Microbiol..

[6]  G. Sutton,et al.  Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes. , 2018, F1000Research.

[7]  G. Sutton,et al.  Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes. , 2018, F1000Research.

[8]  Granger G. Sutton,et al.  GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models , 2018, Bioinform..

[9]  Radhey S. Gupta,et al.  Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera , 2018, Front. Microbiol..

[10]  N. Segata,et al.  The new phylogeny of the genus Mycobacterium: The old and the news. , 2017, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[11]  Erin Beck,et al.  LOCUST: a custom sequence locus typer for classifying microbial isolates , 2017, Bioinform..

[12]  N. Segata,et al.  Genomic characterization of Nontuberculous Mycobacteria , 2017, Scientific Reports.

[13]  Tetsuya Hayashi,et al.  Draft Genome Sequences of Five Rapidly Growing Mycobacterium Species, M. thermoresistibile, M. fortuitum subsp. acetamidolyticum, M. canariasense, M. brisbanense, and M. novocastrense , 2016, Genome Announcements.

[14]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[15]  Natalia N. Ivanova,et al.  Microbial species delineation using whole genome sequences , 2015, Nucleic acids research.

[16]  T. Tatusova,et al.  RefSeq microbial genomes database: new representation and annotation strategy , 2015, Nucleic Acids Research.

[17]  J. Peter Gogarten,et al.  Bioinformatic Genome Comparisons for Taxonomic and Phylogenetic Assignments Using Aeromonas as a Test Case , 2014, mBio.

[18]  E. Tortoli.  Microbiological Features and Clinical Relevance of New Species of the Genus Mycobacterium , 2014, Clinical Microbiology Reviews.

[19]  H. Wiker,et al.  Effect of Non-tuberculous Mycobacteria on Host Biomarkers Potentially Relevant for Tuberculosis Management , 2014, PLoS neglected tropical diseases.

[20]  H. McShane,et al.  Non-tuberculous mycobacteria have diverse effects on BCG efficacy against Mycobacterium tuberculosis , 2014, Tuberculosis.

[21]  C. Ki,et al.  Distribution of Nontuberculous Mycobacteria by Multigene Sequence-Based Typing and Clinical Significance of Isolated Strains , 2014, Journal of Clinical Microbiology.

[22]  J. Chun,et al.  Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. , 2014, International Journal of Systematic and Evolutionary Microbiology.

[23]  Aidan C. Parte,et al.  LPSN—list of prokaryotic names with standing in nomenclature , 2013, Nucleic Acids Res..

[24]  Han Zheng,et al.  Whole-genome sequence comparison as a method for improving bacterial species definition. , 2014, The Journal of general and applied microbiology.

[25]  Dmitry Antipov,et al.  Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products , 2013, J. Comput. Biol..

[26]  F. Drobniewski,et al.  The geographic diversity of nontuberculous mycobacteria isolated from pulmonary samples: an NTM-NET collaborative study , 2013, European Respiratory Journal.

[27]  Alexander F. Auch,et al.  Genome sequence-based species delimitation with confidence intervals and improved distance functions , 2013, BMC Bioinformatics.

[28]  N. Loman,et al.  Defining bacterial species in the genomic era: insights from the genus Acinetobacter , 2012, BMC Microbiology.

[29]  Derrick E. Fouts,et al.  PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species , 2012, Nucleic acids research.

[30]  H. McShane,et al.  Tuberculosis vaccines in clinical trials , 2011, Expert review of vaccines.

[31]  Sarman Singh,et al.  Non-Tuberculous Mycobacteria in TB-Endemic Countries: Are We Neglecting the Danger? , 2010, PLoS neglected tropical diseases.

[32]  E. Tortoli,et al.  Commercial DNA Probes for Mycobacteria Incorrectly Identify a Number of Less Frequently Encountered Species , 2009, Journal of Clinical Microbiology.

[33]  R. Rosselló-Móra,et al.  Shifting the genomic gold standard for the prokaryotic species definition , 2009, Proceedings of the National Academy of Sciences.

[34]  J. Flandrois,et al.  A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees. , 2008, International journal of systematic and evolutionary microbiology.

[35]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[36]  M. Tameris,et al.  Isolation of Non-Tuberculous Mycobacteria in Children Investigated for Pulmonary Tuberculosis , 2006, PloS one.

[37]  K. Konstantinidis,et al.  The bacterial species definition in the genomic era , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[38]  E. Tortoli.  The new mycobacteria: an update. , 2006, FEMS immunology and medical microbiology.

[39]  E. Tortoli.  Impact of Genotypic Studies on Mycobacterial Taxonomy: the New Mycobacteria of the 1990s , 2003, Clinical Microbiology Reviews.

[40]  R. Wallace,,et al.  Clinical and Taxonomic Status of Pathogenic Nonpigmented or Late-Pigmenting Rapidly Growing Mycobacteria , 2002, Clinical Microbiology Reviews.

[41]  E. Tortoli,et al.  Identification of 54 Mycobacterial Species by PCR-Restriction Fragment Length Polymorphism Analysis of the hsp65Gene , 2001, Journal of Clinical Microbiology.

[42]  Nalin Rastogi,et al.  Species-Specific Identification ofMycobacterium leprae by PCR-Restriction Fragment Length Polymorphism Analysis of the hsp65 Gene , 1999, Journal of Clinical Microbiology.

[43]  J. Euzéby.  List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. , 1997, International journal of systematic bacteriology.

[44]  Frank,et al.  Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis , 1993, Journal of clinical microbiology.

[45]  H. A. Sramek,et al.  Agents of newly recognized or infrequently encountered mycobacterial diseases , 1992, Clinical Microbiology Reviews.

[46]  E. Wolinsky.  Nontuberculous mycobacteria and associated diseases. , 2015, The American review of respiratory disease.