Genomic characterization of Nontuberculous Mycobacteria
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...
Saved in:
| Published in | Scientific reports Vol. 7; no. 1; p. 45258 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
27.03.2017
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2045-2322 2045-2322 |
| DOI | 10.1038/srep45258 |
Cover
| 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. |
|---|---|
| AbstractList | 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. 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. 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.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. |
| ArticleNumber | 45258 |
| Author | Pecorari, Monica Giacobazzi, Elisabetta Jousson, Olivier Bettua, Clotilde Bertorelli, Roberto Rumpianesi, Fabio Meehan, Conor J. Fregni Serpini, Giulia Segata, Nicola Grottola, Antonella Fabio, Anna Tagliazucchi, Sara De Sanctis, Veronica Tortoli, Enrico Fedrizzi, Tarcisio |
| Author_xml | – sequence: 1 givenname: Tarcisio surname: Fedrizzi fullname: Fedrizzi, Tarcisio organization: Centre for Integrative Biology, University of Trento – sequence: 2 givenname: Conor J. surname: Meehan fullname: Meehan, Conor J. organization: Department of Biomedical Science, Mycobacteriology unit, Institute of Tropical Medicine – sequence: 3 givenname: Antonella surname: Grottola fullname: Grottola, Antonella organization: Microbiology and Virology Unit, University Hospital Polyclinic – sequence: 4 givenname: Elisabetta surname: Giacobazzi fullname: Giacobazzi, Elisabetta organization: Centre for Integrative Biology, University of Trento – sequence: 5 givenname: Giulia surname: Fregni Serpini fullname: Fregni Serpini, Giulia organization: Microbiology and Virology Unit, University Hospital Polyclinic – sequence: 6 givenname: Sara surname: Tagliazucchi fullname: Tagliazucchi, Sara organization: Microbiology and Virology Unit, University Hospital Polyclinic – sequence: 7 givenname: Anna surname: Fabio fullname: Fabio, Anna organization: Microbiology and Virology Unit, University Hospital Polyclinic – sequence: 8 givenname: Clotilde surname: Bettua fullname: Bettua, Clotilde organization: Centre for Integrative Biology, University of Trento – sequence: 9 givenname: Roberto surname: Bertorelli fullname: Bertorelli, Roberto organization: NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento – sequence: 10 givenname: Veronica surname: De Sanctis fullname: De Sanctis, Veronica organization: NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento – sequence: 11 givenname: Fabio surname: Rumpianesi fullname: Rumpianesi, Fabio organization: Microbiology and Virology Unit, University Hospital Polyclinic – sequence: 12 givenname: Monica surname: Pecorari fullname: Pecorari, Monica organization: Microbiology and Virology Unit, University Hospital Polyclinic – sequence: 13 givenname: Olivier surname: Jousson fullname: Jousson, Olivier organization: Centre for Integrative Biology, University of Trento – sequence: 14 givenname: Enrico surname: Tortoli fullname: Tortoli, Enrico email: e.tortoli@libero.it organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute – sequence: 15 givenname: Nicola surname: Segata fullname: Segata, Nicola email: nicola.segata@unitn.it organization: Centre for Integrative Biology, University of Trento |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28345639$$D View this record in MEDLINE/PubMed |
| BookMark | eNptkUtLAzEUhYMoPmoX_gEpuFGhNs-ZZCOIaBV8bHQdMplEI9OkJjOC_npTW0t9BEIu5DuHe-_ZAes-eAPAHoInCBI-StFMKcOMr4FtDCkbYoLx-kq9BfopvcB8GBYUiU2whTmhrCBiG5Rj48PE6YF-VlHp1kT3oVoX_CDYwV3wbVeZqLsmdGlw-65DNWfULtiwqkmmv3h74PHy4uH8anhzP74-P7sZagZpO-SUEMstLizjoqRlKUyt6wIZZEpYC8ZKk4vKcoJLoWphVU0Ys1zQqrDCMtIDp3PfaVdNstb4NqpGTqObqPgug3Ly5493z_IpvElGikKgmcHhwiCG186kVk5c0qZplDd5KIk4R5TmSzJ68At9CV30eTyJBCSEM8hEpvZXO1q28r3TDBzNAR1DyunYJYKgnEUml5FldvSL1a792n8exjX_Ko7nipRd_ZOJK03-gT8BxTenUA |
| CitedBy_id | crossref_primary_10_2106_JBJS_OA_23_00030 crossref_primary_10_1038_s41533_024_00403_9 crossref_primary_10_3389_fmicb_2023_1289182 crossref_primary_10_2903_j_efsa_2019_5824 crossref_primary_10_1016_j_jfma_2020_05_019 crossref_primary_10_3390_microorganisms7050113 crossref_primary_10_1016_j_meegid_2019_01_017 crossref_primary_10_1080_22221751_2023_2276342 crossref_primary_10_1183_16000617_0212_2021 crossref_primary_10_3390_plants11060832 crossref_primary_10_1017_ice_2019_6 crossref_primary_10_1128_mBio_02807_19 crossref_primary_10_1186_s13073_025_01443_7 crossref_primary_10_2174_0115680266276938240108060247 crossref_primary_10_1016_j_copbio_2019_03_010 crossref_primary_10_1038_s41467_022_32122_5 crossref_primary_10_1016_j_snb_2023_135211 crossref_primary_10_1016_j_wroa_2023_100201 crossref_primary_10_1016_j_tcsw_2020_100043 crossref_primary_10_1177_1179548417747529 crossref_primary_10_1186_s12862_019_1447_7 crossref_primary_10_1093_gbe_evz162 crossref_primary_10_1021_acs_jproteome_3c00850 crossref_primary_10_1038_s41598_021_91737_8 crossref_primary_10_1080_21505594_2020_1713690 crossref_primary_10_1099_ijsem_0_004615 crossref_primary_10_3389_ftubr_2023_1243479 crossref_primary_10_1016_j_micres_2024_128039 crossref_primary_10_3390_microorganisms8091380 crossref_primary_10_1093_nargab_lqab070 crossref_primary_10_1111_mmi_15103 crossref_primary_10_3389_fmicb_2021_633510 crossref_primary_10_1007_s12275_018_8372_0 crossref_primary_10_1080_22221751_2019_1637702 crossref_primary_10_30895_2221_996X_2020_20_2_97_102 crossref_primary_10_3389_fmicb_2022_992610 crossref_primary_10_1128_jcm_01626_22 crossref_primary_10_1128_JCM_01924_17 crossref_primary_10_1038_s41598_022_22777_x crossref_primary_10_1128_spectrum_00451_22 crossref_primary_10_3390_molecules23112911 crossref_primary_10_1016_j_chembiol_2019_03_002 crossref_primary_10_2166_h2oj_2022_144 crossref_primary_10_1128_MRA_00547_23 crossref_primary_10_1186_s12870_024_05866_z crossref_primary_10_1128_mSphere_00352_18 crossref_primary_10_3389_fvets_2024_1361788 crossref_primary_10_1002_cmdc_202400303 crossref_primary_10_1016_j_meegid_2018_10_003 crossref_primary_10_1099_ijsem_0_004922 crossref_primary_10_3389_fmed_2021_679755 crossref_primary_10_1038_s41598_024_73768_z crossref_primary_10_1128_JB_00739_17 crossref_primary_10_1099_ijsem_0_002350 crossref_primary_10_1186_s12866_019_1428_4 crossref_primary_10_1183_23120541_00628_2022 crossref_primary_10_1128_MRA_00957_18 crossref_primary_10_1021_acsenvironau_3c00074 crossref_primary_10_1111_zph_12754 crossref_primary_10_1128_spectrum_00856_23 crossref_primary_10_1016_j_vaccine_2025_126720 crossref_primary_10_3390_microorganisms12040665 crossref_primary_10_1016_j_tube_2020_101914 crossref_primary_10_1111_petr_70020 crossref_primary_10_1016_j_jfma_2020_05_006 crossref_primary_10_1099_ijsem_0_002457 crossref_primary_10_3390_antibiotics10080908 crossref_primary_10_1016_j_pdpdt_2022_102839 crossref_primary_10_1016_j_jtemb_2019_02_004 crossref_primary_10_1016_j_thorsurg_2018_09_001 crossref_primary_10_1016_j_onano_2023_100171 crossref_primary_10_1038_s41598_021_89069_8 crossref_primary_10_3390_microorganisms8081249 crossref_primary_10_1080_21505594_2020_1785815 crossref_primary_10_1136_bmjresp_2020_000591 crossref_primary_10_29413_ABS_2019_4_3_17 crossref_primary_10_3390_pathogens12040570 crossref_primary_10_1016_j_meegid_2019_02_028 crossref_primary_10_3389_fmicb_2018_00251 crossref_primary_10_1038_nrmicro_2018_8 crossref_primary_10_1016_j_jiph_2018_05_006 crossref_primary_10_1093_infdis_jiz285 crossref_primary_10_7759_cureus_48270 crossref_primary_10_1128_MRA_00936_18 crossref_primary_10_1016_j_biteb_2023_101389 crossref_primary_10_1093_lambio_ovaf029 crossref_primary_10_1099_mgen_0_000533 crossref_primary_10_3390_microorganisms9112237 crossref_primary_10_1038_s41467_023_42916_w crossref_primary_10_1099_mgen_0_000497 crossref_primary_10_12688_f1000research_22620_2 crossref_primary_10_12688_f1000research_22620_1 crossref_primary_10_1016_j_tube_2024_102516 crossref_primary_10_1016_j_jctube_2020_100150 crossref_primary_10_1186_s12864_021_07972_w crossref_primary_10_3390_microorganisms12071425 crossref_primary_10_3390_ht7040031 crossref_primary_10_1111_hiv_13249 crossref_primary_10_1183_13993003_00795_2019 crossref_primary_10_1093_femsre_fuaa071 crossref_primary_10_1038_s41467_020_16626_6 crossref_primary_10_3389_fvets_2024_1346514 crossref_primary_10_7868_S2587667820050714 crossref_primary_10_3389_fmicb_2021_638047 crossref_primary_10_1016_j_cmi_2020_04_020 crossref_primary_10_1016_j_talanta_2021_123049 crossref_primary_10_1134_S0026261723600477 crossref_primary_10_4103_ijmy_ijmy_175_22 crossref_primary_10_1016_j_chemphyslip_2017_12_006 crossref_primary_10_3390_pathogens10070879 crossref_primary_10_1016_j_diagmicrobio_2022_115757 crossref_primary_10_3390_microorganisms9112220 crossref_primary_10_1016_j_abd_2021_04_005 crossref_primary_10_3389_fmicb_2018_03184 crossref_primary_10_3201_eid2611_191718 crossref_primary_10_1039_D1NP00067E crossref_primary_10_18699_SSMJ20230604 crossref_primary_10_7759_cureus_62210 crossref_primary_10_3389_fpubh_2024_1410672 crossref_primary_10_3389_fmicb_2023_1243371 crossref_primary_10_1038_s41598_019_40922_x crossref_primary_10_4103_ijmr_IJMR_902_20 crossref_primary_10_3390_molecules27165335 crossref_primary_10_1186_s12864_020_07232_3 crossref_primary_10_3389_fmicb_2019_03019 crossref_primary_10_1007_s10096_019_03771_0 crossref_primary_10_1016_j_ijid_2018_04_796 crossref_primary_10_1038_s41598_023_47699_0 crossref_primary_10_1099_ijsem_0_005019 crossref_primary_10_3389_fcimb_2020_00122 crossref_primary_10_3390_microorganisms10091861 crossref_primary_10_3390_vetsci12030275 crossref_primary_10_1016_j_scitotenv_2020_141451 crossref_primary_10_1186_s12864_022_08927_5 crossref_primary_10_36303_JSAVA_229 crossref_primary_10_3389_fmicb_2018_00067 crossref_primary_10_1007_s11033_020_06118_7 crossref_primary_10_1186_s12866_021_02163_9 crossref_primary_10_1186_s12879_020_05626_y crossref_primary_10_1016_j_dib_2025_111368 crossref_primary_10_1128_JCM_01480_17 crossref_primary_10_1177_17534666221148660 crossref_primary_10_1128_MRA_01421_20 crossref_primary_10_3389_fmicb_2019_01887 crossref_primary_10_1038_s41396_020_0600_z crossref_primary_10_1007_s10482_021_01638_z crossref_primary_10_1016_j_meegid_2017_10_013 crossref_primary_10_1038_s41598_019_55464_5 crossref_primary_10_1099_ijsem_0_005378 crossref_primary_10_1099_ijsem_0_006620 crossref_primary_10_3389_fmicb_2022_982679 crossref_primary_10_1016_j_jbc_2022_101859 crossref_primary_10_1186_s12879_020_4936_9 crossref_primary_10_1016_j_mib_2020_01_007 |
| Cites_doi | 10.1093/bioinformatics/btu153 10.1093/nar/gkh340 10.1186/1471-2105-10-421 10.1128/cmr.18.1.81-101.2005 10.1007/s13665-015-0119-3 10.1099/ijs.0.025601-0 10.1016/j.tube.2011.11.005 10.1128/jb.187.22.7667-7679.2005 10.1371/journal.pone.0128773 10.1038/nrmicro1773 10.1093/bioinformatics/btv421 10.1093/bioinformatics/btu033 10.7717/peerj.2584 10.1128/jb.05291-11 10.1371/journal.pone.0147513 10.1371/journal.pone.0050070 10.1101/pdb.prot5408 10.1371/journal.pone.0027980 10.1038/nrmicro.2016.161 10.1016/j.plipres.2005.07.001 10.1128/cmr.14.4.704-726.2001 10.1007/s11010-011-0733-5 10.1137/110845045 10.1055/s-0033-1333568 10.1093/nar/gkn741 10.1016/S0166-218X(96)00062-5 10.1155/2011/497203 10.1186/1471-2164-15-717 10.1111/imr.12251 10.1128/AEM.69.10.6041-6046.2003 10.1371/journal.pone.0087924 10.1038/ncomms3304 10.1111/j.1469-0691.2009.03014.x 10.1093/nar/gkt1253 10.1093/infdis/jiu601 10.1056/NEJMoa1003176 10.1016/j.smim.2014.09.012 10.1371/journal.pmed.1001387 10.1089/cmb.2012.0021 10.1093/gbe/evv035 10.1186/s12916-016-0598-2 10.1016/j.ccm.2015.11.001 10.1111/j.1365-2958.2009.06784.x 10.1016/j.chembiol.2013.11.011 10.1128/jcm.00549-14 10.1111/ijd.12528 10.1099/ijs.0.65658-0 10.1093/nar/gkt1223 10.3389/fmicb.2014.00750 10.1016/j.meegid.2011.05.025 10.1074/jbc.M206538200 10.1186/1944-3277-9-20 10.1097/00006454-199303000-00009 10.1038/srep02101 10.1097/qco.0000000000000104 10.1038/35059006 10.1186/1471-2105-8-64 10.1093/nar/gku1196 10.1016/j.ijid.2015.05.018 10.1093/bioinformatics/btq461 10.7717/peerj.1029 10.1111/j.1365-2958.2004.04041.x 10.1093/nar/gkl791 10.1099/ijs.0.068395-0 10.1128/jb.00749-08 10.1016/j.ccm.2014.10.003 10.1016/s0022-2836(05)80360-2 10.1128/jcm.31.12.3083-3089.1993 10.1128/microbiolspec.MGM2-0025-2013 10.1128/jcm.34.9.2219-2224.1996 10.1128/microbiolspec.MGM2-0003-2013 10.1111/resp.12767 10.1164/rccm.201510-2091OC |
| ContentType | Journal Article |
| Copyright | The Author(s) 2017 Copyright Nature Publishing Group Mar 2017 Copyright © 2017, The Author(s) 2017 The Author(s) |
| Copyright_xml | – notice: The Author(s) 2017 – notice: Copyright Nature Publishing Group Mar 2017 – notice: Copyright © 2017, The Author(s) 2017 The Author(s) |
| DBID | C6C AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7X7 7XB 88A 88E 88I 8FE 8FH 8FI 8FJ 8FK ABUWG AEUYN AFKRA AZQEC BBNVY BENPR BHPHI CCPQU DWQXO FYUFA GHDGH GNUQQ HCIFZ K9. LK8 M0S M1P M2P M7P PHGZM PHGZT PIMPY PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS Q9U 7X8 5PM |
| DOI | 10.1038/srep45258 |
| DatabaseName | Springer Nature OA Free Journals CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Central (Corporate) Health & Medical Collection ProQuest Central (purchase pre-March 2016) Biology Database (Alumni Edition) Medical Database (Alumni Edition) Science Database (Alumni Edition) ProQuest SciTech Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) ProQuest Central (Alumni) ProQuest One Sustainability ProQuest Central UK/Ireland ProQuest Central Essentials - QC Biological Science Collection ProQuest Central Natural Science Collection ProQuest One ProQuest Central Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) Biological Sciences ProQuest Health & Medical Collection Medical Database Science Database Biological Science Database Proquest Central Premium ProQuest One Academic (New) Publicly Available Content Database ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic ProQuest One Academic UKI Edition ProQuest Central China ProQuest Central Basic MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Publicly Available Content Database ProQuest Central Student ProQuest One Academic Middle East (New) ProQuest Central Essentials ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) SciTech Premium Collection ProQuest One Community College ProQuest One Health & Nursing ProQuest Natural Science Collection ProQuest Central China ProQuest Biology Journals (Alumni Edition) ProQuest Central ProQuest One Applied & Life Sciences ProQuest One Sustainability ProQuest Health & Medical Research Collection Health Research Premium Collection Health and Medicine Complete (Alumni Edition) Natural Science Collection ProQuest Central Korea Health & Medical Research Collection Biological Science Collection ProQuest Central (New) ProQuest Medical Library (Alumni) ProQuest Science Journals (Alumni Edition) ProQuest Biological Science Collection ProQuest Central Basic ProQuest Science Journals ProQuest One Academic Eastern Edition ProQuest Hospital Collection Health Research Premium Collection (Alumni) Biological Science Database ProQuest SciTech Collection ProQuest Hospital Collection (Alumni) ProQuest Health & Medical Complete ProQuest Medical Library ProQuest One Academic UKI Edition ProQuest One Academic ProQuest One Academic (New) ProQuest Central (Alumni) MEDLINE - Academic |
| DatabaseTitleList | Publicly Available Content Database MEDLINE CrossRef MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: C6C name: Springer Nature OA Free Journals url: http://www.springeropen.com/ sourceTypes: Publisher – sequence: 2 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database – sequence: 4 dbid: BENPR name: ProQuest Central url: http://www.proquest.com/pqcentral?accountid=15518 sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 2045-2322 |
| ExternalDocumentID | PMC5366915 28345639 10_1038_srep45258 |
| Genre | Journal Article |
| GroupedDBID | 0R~ 3V. 4.4 53G 5VS 7X7 88A 88E 88I 8FE 8FH 8FI 8FJ AAFWJ AAJSJ AAKDD ABDBF ABUWG ACGFS ACSMW ACUHS ADBBV ADRAZ AENEX AEUYN AFKRA AJTQC ALIPV ALMA_UNASSIGNED_HOLDINGS AOIJS AZQEC BAWUL BBNVY BCNDV BENPR BHPHI BPHCQ BVXVI C6C CCPQU DIK DWQXO EBD EBLON EBS EJD ESX FYUFA GNUQQ GROUPED_DOAJ GX1 HCIFZ HH5 HMCUK HYE KQ8 LK8 M0L M1P M2P M48 M7P M~E NAO OK1 PIMPY PQQKQ PROAC PSQYO RNT RNTTT RPM SNYQT UKHRP AASML AAYXX AFPKN CITATION PHGZM PHGZT CGR CUY CVF ECM EIF NPM 7XB 8FK AARCD K9. PJZUB PKEHL PPXIY PQEST PQGLB PQUKI PRINS Q9U 7X8 PUEGO 5PM |
| ID | FETCH-LOGICAL-c504t-8433f8f26f58974779edcd61e1e70d9557ee70bf83279ad9fad355f894b6f9f53 |
| IEDL.DBID | 7X7 |
| ISSN | 2045-2322 |
| IngestDate | Thu Aug 21 14:23:47 EDT 2025 Thu Sep 04 23:46:13 EDT 2025 Wed Aug 13 06:43:03 EDT 2025 Wed Feb 19 02:43:28 EST 2025 Thu Apr 24 23:01:47 EDT 2025 Tue Jul 01 01:32:38 EDT 2025 Fri Feb 21 02:40:08 EST 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 1 |
| Language | English |
| License | This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0 |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c504t-8433f8f26f58974779edcd61e1e70d9557ee70bf83279ad9fad355f894b6f9f53 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 These authors contributed equally to this work. |
| OpenAccessLink | https://www.proquest.com/docview/1903385059?pq-origsite=%requestingapplication% |
| PMID | 28345639 |
| PQID | 1903385059 |
| PQPubID | 2041939 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_5366915 proquest_miscellaneous_1881448143 proquest_journals_1903385059 pubmed_primary_28345639 crossref_primary_10_1038_srep45258 crossref_citationtrail_10_1038_srep45258 springer_journals_10_1038_srep45258 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2017-03-27 |
| PublicationDateYYYYMMDD | 2017-03-27 |
| PublicationDate_xml | – month: 03 year: 2017 text: 2017-03-27 day: 27 |
| PublicationDecade | 2010 |
| PublicationPlace | London |
| PublicationPlace_xml | – name: London – name: England |
| PublicationTitle | Scientific reports |
| PublicationTitleAbbrev | Sci Rep |
| PublicationTitleAlternate | Sci Rep |
| PublicationYear | 2017 |
| Publisher | Nature Publishing Group UK Nature Publishing Group |
| Publisher_xml | – name: Nature Publishing Group UK – name: Nature Publishing Group |
| References | Seemann (CR32) 2014; 30 Coleman, Spain (CR37) 2003; 69 Marrakchi, Laneelle, Daffe (CR55) 2014; 21 Roetzer (CR6) 2013; 10 Onwueme, Vos, Zurita, Ferreras, Quadri (CR56) 2005; 44 Asnicar, Weingart, Tickle, Huttenhower, Segata (CR74) 2015; 3 Falkinham (CR1) 2013; 34 Witney (CR2) 2016; 14 Han (CR31) 2013; 3 Stucki (CR5) 2015; 211 Takayama, Wang, Besra (CR54) 2005; 18 Bankevich (CR29) 2012; 19 Horsburgh, Caldwell, Simonds (CR18) 1993; 12 Fusco da Costa (CR28) 2015; 65 Croucher (CR73) 2015; 43 Bottai, Brosch (CR20) 2009; 73 Stamatakis (CR65) 2014; 30 Edgar (CR64) 2004; 32 Wang (CR27) 2015; 7 Martiniano, Nick, Daley (CR12) 2016; 37 Altschul, Gish, Miller, Myers, Lipman (CR66) 1990; 215 Dhanani (CR71) 2015; 10 CR3 Jorgensen, Kiil, Hansen, Sorensen, Hansen (CR40) 2014; 5 CR7 McDonough (CR51) 2008; 190 Finn (CR41) 2014; 42 Jung (CR16) 2015; 36 Kaser, Ruf, Hauser, Pluschke (CR58) 2010; 2010 Whidden, Beiko, Zeh (CR33) 2013; 42 Novosad, Henkle, Winthrop (CR9) 2015; 4 Rognes, Flouri, Nichols, Quince, Mahe (CR63) 2016; 4 Segata, Bornigen, Morgan, Huttenhower (CR59) 2013; 4 Page (CR38) 2015; 31 Edgar (CR62) 2010; 26 Coscolla, Gagneux (CR8) 2014; 26 Springer (CR35) 1993; 31 Candido (CR11) 2014; 52 CR19 Sayers (CR68) 2009; 37 Das, Ghosh, Mande (CR43) 2011; 6 Warren (CR46) 1996; 34 Sommer, Delcher, Salzberg, Pop (CR70) 2007; 8 McDonough, Hacker, Flores, Pavelka, Braunstein (CR50) 2005; 187 CR53 Land (CR61) 2014; 9 Butler, Guthertz (CR52) 2001; 14 Tortoli (CR25) 2012; 12 Abdallah (CR47) 2007; 5 Zhu, Kosoy, Dittmar (CR72) 2014; 15 Zhang (CR30) 2011; 193 Cole (CR60) 2001; 409 Tortoli (CR15) 2009; 15 Majlessi, Prados-Rosales, Casadevall, Brosch (CR22) 2015; 264 Gardy (CR4) 2011; 364 Benwill, Wallace (CR10) 2014; 27 Tsirigotaki, De Geyter, Sostaric, Economou, Karamanou (CR23) 2017; 15 Mignard, Flandrois (CR26) 2008; 58 Tortoli (CR36) 2011; 61 Constant (CR57) 2002; 277 Smith (CR42) 2012; 7 Tebruegge (CR13) 2016; 11 Powell (CR39) 2014; 42 Lamb, Dawn (CR17) 2014; 53 CR21 Jorgensen, Xu, Hansen, Sorensen, Hansen (CR69) 2014; 9 Sander (CR49) 2004; 52 Hein, Jiang, Wang, Zhang (CR34) 1996; 71 Camacho (CR67) 2009; 10 Zhang, Xie (CR24) 2011; 352 Zhou (CR44) 2007; 35 Sampson (CR45) 2011; 2011 Ligon, Hayden, Braunstein (CR48) 2012; 92 Falkinham (CR14) 2015; 36 E Tortoli (BFsrep45258_CR25) 2012; 12 SL Martiniano (BFsrep45258_CR12) 2016; 37 RC Lamb (BFsrep45258_CR17) 2014; 53 NV Coleman (BFsrep45258_CR37) 2003; 69 C Camacho (BFsrep45258_CR67) 2009; 10 JA McDonough (BFsrep45258_CR51) 2008; 190 JA McDonough (BFsrep45258_CR50) 2005; 187 E Tortoli (BFsrep45258_CR15) 2009; 15 ST Cole (BFsrep45258_CR60) 2001; 409 TS Jorgensen (BFsrep45258_CR69) 2014; 9 LS Ligon (BFsrep45258_CR48) 2012; 92 P Sander (BFsrep45258_CR49) 2004; 52 JL Gardy (BFsrep45258_CR4) 2011; 364 AJ Page (BFsrep45258_CR38) 2015; 31 Q Zhu (BFsrep45258_CR72) 2014; 15 AM Abdallah (BFsrep45258_CR47) 2007; 5 C Whidden (BFsrep45258_CR33) 2013; 42 A Bankevich (BFsrep45258_CR29) 2012; 19 T Rognes (BFsrep45258_CR63) 2016; 4 RD Finn (BFsrep45258_CR41) 2014; 42 ZY Zhang (BFsrep45258_CR30) 2011; 193 SF Altschul (BFsrep45258_CR66) 1990; 215 KC Onwueme (BFsrep45258_CR56) 2005; 44 DD Sommer (BFsrep45258_CR70) 2007; 8 JL Benwill (BFsrep45258_CR10) 2014; 27 S Novosad (BFsrep45258_CR9) 2015; 4 NJ Croucher (BFsrep45258_CR73) 2015; 43 AR Fusco da Costa (BFsrep45258_CR28) 2015; 65 P Constant (BFsrep45258_CR57) 2002; 277 S Mignard (BFsrep45258_CR26) 2008; 58 CE Zhou (BFsrep45258_CR44) 2007; 35 CR Horsburgh Jr. (BFsrep45258_CR18) 1993; 12 J Wang (BFsrep45258_CR27) 2015; 7 ML Land (BFsrep45258_CR61) 2014; 9 PH Candido (BFsrep45258_CR11) 2014; 52 A Roetzer (BFsrep45258_CR6) 2013; 10 S Powell (BFsrep45258_CR39) 2014; 42 RC Edgar (BFsrep45258_CR62) 2010; 26 BFsrep45258_CR19 SE Smith (BFsrep45258_CR42) 2012; 7 T Seemann (BFsrep45258_CR32) 2014; 30 M Kaser (BFsrep45258_CR58) 2010; 2010 M Coscolla (BFsrep45258_CR8) 2014; 26 B Springer (BFsrep45258_CR35) 1993; 31 AA Witney (BFsrep45258_CR2) 2016; 14 A Stamatakis (BFsrep45258_CR65) 2014; 30 BFsrep45258_CR53 D Bottai (BFsrep45258_CR20) 2009; 73 J Hein (BFsrep45258_CR34) 1996; 71 D Stucki (BFsrep45258_CR5) 2015; 211 K Han (BFsrep45258_CR31) 2013; 3 SL Sampson (BFsrep45258_CR45) 2011; 2011 SY Jung (BFsrep45258_CR16) 2015; 36 JO Falkinham 3rd. (BFsrep45258_CR1) 2013; 34 H Marrakchi (BFsrep45258_CR55) 2014; 21 A Tsirigotaki (BFsrep45258_CR23) 2017; 15 R Warren (BFsrep45258_CR46) 1996; 34 L Majlessi (BFsrep45258_CR22) 2015; 264 K Takayama (BFsrep45258_CR54) 2005; 18 N Segata (BFsrep45258_CR59) 2013; 4 EW Sayers (BFsrep45258_CR68) 2009; 37 E Tortoli (BFsrep45258_CR36) 2011; 61 F Asnicar (BFsrep45258_CR74) 2015; 3 BFsrep45258_CR3 RC Edgar (BFsrep45258_CR64) 2004; 32 JO Falkinham 3rd. (BFsrep45258_CR14) 2015; 36 F Zhang (BFsrep45258_CR24) 2011; 352 TS Jorgensen (BFsrep45258_CR40) 2014; 5 C Das (BFsrep45258_CR43) 2011; 6 BFsrep45258_CR7 M Tebruegge (BFsrep45258_CR13) 2016; 11 BFsrep45258_CR21 WR Butler (BFsrep45258_CR52) 2001; 14 AS Dhanani (BFsrep45258_CR71) 2015; 10 20709691 - Bioinformatics. 2010 Oct 1;26(19):2460-1 15034147 - Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 2231712 - J Mol Biol. 1990 Oct 5;215(3):403-10 26026822 - Int J Infect Dis. 2015 Jul;36:62-9 18523191 - Int J Syst Evol Microbiol. 2008 Jun;58(Pt 6):1432-41 11234002 - Nature. 2001 Feb 22;409(6823):1007-11 24503942 - PLoS One. 2014 Feb 04;9(2):e87924 21318182 - Clin Dev Immunol. 2011;2011:497203 25362193 - J Infect Dis. 2015 Apr 15;211(8):1306-16 23460009 - Semin Respir Crit Care Med. 2013 Feb;34(1):95-102 24920766 - J Clin Microbiol. 2014 Aug;52(8):2990-7 19602151 - Mol Microbiol. 2009 Aug;73(3):325-8 17922044 - Nat Rev Microbiol. 2007 Nov;5(11):883-91 21345102 - N Engl J Med. 2011 Feb 24;364(8):730-9 20003500 - BMC Bioinformatics. 2009 Dec 15;10:421 26877911 - Curr Pulmonol Rep. 2015 Sep 1;4(3):152-161 22140496 - PLoS One. 2011;6(11):e27980 25716827 - Genome Biol Evol. 2015 Feb 25;7(3):856-70 25676517 - Clin Chest Med. 2015 Mar;36(1):35-41 22506599 - J Comput Biol. 2012 May;19(5):455-77 24288371 - Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30 26910495 - Am J Respir Crit Care Med. 2016 Sep 1;194(5):621-30 25453224 - Semin Immunol. 2014 Dec;26(6):431-44 24297252 - Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9 25268925 - Curr Opin Infect Dis. 2014 Dec;27(6):506-10 23424287 - PLoS Med. 2013;10(2):e1001387 15186407 - Mol Microbiol. 2004 Jun;52(6):1543-52 27781170 - PeerJ. 2016 Oct 18;4:e2584 18940862 - Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15 16267291 - J Bacteriol. 2005 Nov;187(22):7667-79 26157614 - PeerJ. 2015 Jun 18;3:e1029 27004841 - BMC Med. 2016 Mar 23;14 :46 26812154 - PLoS One. 2016 Jan 26;11(1):e0147513 20360362 - Cold Spring Harb Protoc. 2010 Apr;2010(4):pdb.prot5408 26083489 - PLoS One. 2015 Jun 17;10(6):e0128773 23942190 - Nat Commun. 2013;4:2304 17090593 - Nucleic Acids Res. 2007 Jan;35(Database issue):D391-4 7508452 - J Clin Microbiol. 1993 Dec;31(12):3083-9 19845702 - Clin Microbiol Infect. 2009 Oct;15(10):906-10 22192870 - Tuberculosis (Edinb). 2012 Mar;92(2):121-32 14532060 - Appl Environ Microbiol. 2003 Oct;69(10):6041-6 21685274 - J Bacteriol. 2011 Aug;193(16):4300-1 18658266 - J Bacteriol. 2008 Oct;190(19):6428-38 24374164 - Chem Biol. 2014 Jan 16;21(1):67-85 25780509 - Stand Genomic Sci. 2014 Dec 08;9:20 8095716 - Pediatr Infect Dis J. 1993 Mar;12(3):219-22 20693362 - Int J Syst Evol Microbiol. 2011 Jul;61(Pt 7):1606-11 25414349 - Nucleic Acids Res. 2015 Feb 18;43(3):e15 21258845 - Mol Cell Biochem. 2011 Jun;352(1-2):1-10 26198102 - Bioinformatics. 2015 Nov 15;31(22):3691-3 25703550 - Immunol Rev. 2015 Mar;264(1):25-45 27890920 - Nat Rev Microbiol. 2017 Jan;15(1):21-36 23812535 - Sci Rep. 2013;3:2101 16115688 - Prog Lipid Res. 2005 Sep;44(5):259-302 12138124 - J Biol Chem. 2002 Oct 11;277(41):38148-58 23189179 - PLoS One. 2012;7(11):e50070 27009804 - Respirology. 2016 Aug;21(6):1015-25 25159222 - BMC Genomics. 2014 Aug 26;15:717 15653820 - Clin Microbiol Rev. 2005 Jan;18(1):81-101 25657641 - Front Microbiol. 2015 Jan 22;5:750 26082120 - Microbiol Spectr. 2014 Feb;2(1):MGM2-0025-2013 21684354 - Infect Genet Evol. 2012 Jun;12(4):827-31 11585782 - Clin Microbiol Rev. 2001 Oct;14(4):704-26, table of contents 26857770 - Clin Chest Med. 2016 Mar;37(1):83-96 25487637 - Int J Syst Evol Microbiol. 2015 Feb;65(Pt 2):656-62 8862588 - J Clin Microbiol. 1996 Sep;34(9):2219-24 24642063 - Bioinformatics. 2014 Jul 15;30(14):2068-9 17324286 - BMC Bioinformatics. 2007 Feb 26;8:64 24451623 - Bioinformatics. 2014 May 1;30(9):1312-3 24961147 - Int J Dermatol. 2014 Oct;53(10):1197-204 26104214 - Microbiol Spectr. 2014 Aug;2(4):MGM2-0003-2013 |
| References_xml | – volume: 30 start-page: 2068 year: 2014 end-page: 2069 ident: CR32 article-title: Prokka: rapid prokaryotic genome annotation publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btu153 – volume: 32 start-page: 1792 year: 2004 end-page: 1797 ident: CR64 article-title: MUSCLE: multiple sequence alignment with high accuracy and high throughput publication-title: Nucleic acids research doi: 10.1093/nar/gkh340 – volume: 10 start-page: 421 year: 2009 ident: CR67 article-title: BLAST+: architecture and applications publication-title: BMC bioinformatics doi: 10.1186/1471-2105-10-421 – volume: 18 start-page: 81 year: 2005 end-page: 101 ident: CR54 article-title: Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis publication-title: Clinical microbiology reviews doi: 10.1128/cmr.18.1.81-101.2005 – volume: 4 start-page: 152 year: 2015 end-page: 161 ident: CR9 article-title: The Challenge of Pulmonary Nontuberculous Mycobacterial Infection publication-title: Current pulmonology reports doi: 10.1007/s13665-015-0119-3 – volume: 61 start-page: 1606 year: 2011 end-page: 1611 ident: CR36 article-title: Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex publication-title: International journal of systematic and evolutionary microbiology doi: 10.1099/ijs.0.025601-0 – volume: 92 start-page: 121 year: 2012 end-page: 132 ident: CR48 article-title: The ins and outs of Mycobacterium tuberculosis protein export publication-title: Tuberculosis (Edinburgh, Scotland) doi: 10.1016/j.tube.2011.11.005 – volume: 187 start-page: 7667 year: 2005 end-page: 7679 ident: CR50 article-title: The twin-arginine translocation pathway of Mycobacterium smegmatis is functional and required for the export of mycobacterial beta-lactamases publication-title: Journal of bacteriology doi: 10.1128/jb.187.22.7667-7679.2005 – volume: 10 start-page: e0128773 year: 2015 ident: CR71 article-title: Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens publication-title: PloS One doi: 10.1371/journal.pone.0128773 – volume: 5 start-page: 883 year: 2007 end-page: 891 ident: CR47 article-title: Type VII secretion–mycobacteria show the way publication-title: Nature reviews. Microbiology doi: 10.1038/nrmicro1773 – volume: 31 start-page: 3691 year: 2015 end-page: 3693 ident: CR38 article-title: Roary: rapid large-scale prokaryote pan genome analysis publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btv421 – volume: 30 start-page: 1312 year: 2014 end-page: 1313 ident: CR65 article-title: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btu033 – volume: 4 start-page: e2584 year: 2016 ident: CR63 article-title: VSEARCH: a versatile open source tool for metagenomics publication-title: Peer J doi: 10.7717/peerj.2584 – volume: 193 start-page: 4300 year: 2011 end-page: 4301 ident: CR30 article-title: Complete genome sequence of a novel clinical isolate, the nontuberculous Mycobacterium strain JDM601 publication-title: Journal of bacteriology doi: 10.1128/jb.05291-11 – volume: 11 start-page: e0147513 year: 2016 ident: CR13 article-title: Nontuberculous Mycobacterial Disease in Children - Epidemiology, Diagnosis & Management at a Tertiary Center publication-title: PloS one doi: 10.1371/journal.pone.0147513 – volume: 7 start-page: e50070 year: 2012 ident: CR42 article-title: Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution publication-title: PloS one doi: 10.1371/journal.pone.0050070 – volume: 2010 start-page: pdb.prot5408 year: 2010 ident: CR58 article-title: Optimized DNA preparation from mycobacteria publication-title: Cold Spring Harbor protocols doi: 10.1101/pdb.prot5408 – volume: 6 start-page: e27980 year: 2011 ident: CR43 article-title: Computational analysis of the ESX-1 region of Mycobacterium tuberculosis: insights into the mechanism of type VII secretion system publication-title: PloS One doi: 10.1371/journal.pone.0027980 – volume: 15 start-page: 21 year: 2017 end-page: 36 ident: CR23 article-title: Protein export through the bacterial Sec pathway publication-title: Nature reviews. Microbiology doi: 10.1038/nrmicro.2016.161 – volume: 44 start-page: 259 year: 2005 end-page: 302 ident: CR56 article-title: The dimycocerosate ester polyketide virulence factors of mycobacteria publication-title: Progress in lipid research doi: 10.1016/j.plipres.2005.07.001 – volume: 14 start-page: 704 year: 2001 end-page: 726 ident: CR52 article-title: Mycolic acid analysis by high-performance liquid chromatography for identification of Mycobacterium species publication-title: Clinical microbiology reviews doi: 10.1128/cmr.14.4.704-726.2001 – volume: 352 start-page: 1 year: 2011 end-page: 10 ident: CR24 article-title: Mammalian cell entry gene family of Mycobacterium tuberculosis publication-title: Molecular and cellular biochemistry doi: 10.1007/s11010-011-0733-5 – volume: 42 start-page: 1431 year: 2013 end-page: 1466 ident: CR33 article-title: Fixed-parameter algorithms for maximum agreement forests publication-title: SIAM Journal on Computing doi: 10.1137/110845045 – ident: CR21 – ident: CR19 – volume: 34 start-page: 95 year: 2013 end-page: 102 ident: CR1 article-title: Ecology of nontuberculous mycobacteria–where do human infections come from? publication-title: Seminars in respiratory and critical care medicine doi: 10.1055/s-0033-1333568 – volume: 31 start-page: 3083 year: 1993 end-page: 3089 ident: CR35 article-title: Mycobacterium interjectum, a new species isolated from a patient with chronic lymphadenitis publication-title: Journal of clinical microbiology – volume: 37 start-page: D5 year: 2009 end-page: 15 ident: CR68 article-title: Database resources of the National Center for Biotechnology Information publication-title: Nucleic acids research doi: 10.1093/nar/gkn741 – volume: 71 start-page: 153 year: 1996 end-page: 169 ident: CR34 article-title: On the complexity of comparing evolutionary trees publication-title: Discrete Applied Mathematics doi: 10.1016/S0166-218X(96)00062-5 – volume: 2011 start-page: 497203 year: 2011 ident: CR45 article-title: Mycobacterial PE/PPE proteins at the host-pathogen interface publication-title: Clinical & developmental immunology doi: 10.1155/2011/497203 – volume: 15 start-page: 717 year: 2014 ident: CR72 article-title: HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers publication-title: BMC genomics doi: 10.1186/1471-2164-15-717 – volume: 264 start-page: 25 year: 2015 end-page: 45 ident: CR22 article-title: Release of mycobacterial antigens publication-title: Immunological reviews doi: 10.1111/imr.12251 – volume: 69 start-page: 6041 year: 2003 end-page: 6046 ident: CR37 article-title: Distribution of the coenzyme M pathway of epoxide metabolism among ethene- and vinyl chloride-degrading Mycobacterium strains publication-title: Applied and environmental microbiology doi: 10.1128/AEM.69.10.6041-6046.2003 – volume: 9 start-page: e87924 year: 2014 ident: CR69 article-title: Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome publication-title: PloS One doi: 10.1371/journal.pone.0087924 – volume: 4 start-page: 2304 year: 2013 ident: CR59 article-title: PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes publication-title: Nature communications doi: 10.1038/ncomms3304 – volume: 15 start-page: 906 year: 2009 end-page: 910 ident: CR15 article-title: Clinical manifestations of nontuberculous mycobacteria infections publication-title: Clinical microbiology and infection: the official publication of the European Society of Clinical Microbiology and Infectious Diseases doi: 10.1111/j.1469-0691.2009.03014.x – volume: 42 start-page: D231 year: 2014 end-page: 239 ident: CR39 article-title: eggNOG v4.0: nested orthology inference across 3686 organisms publication-title: Nucleic acids research doi: 10.1093/nar/gkt1253 – volume: 211 start-page: 1306 year: 2015 end-page: 1316 ident: CR5 article-title: Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing publication-title: The Journal of infectious diseases doi: 10.1093/infdis/jiu601 – volume: 364 start-page: 730 year: 2011 end-page: 739 ident: CR4 article-title: Whole-genome sequencing and social-network analysis of a tuberculosis outbreak publication-title: The New England journal of medicine doi: 10.1056/NEJMoa1003176 – volume: 26 start-page: 431 year: 2014 end-page: 444 ident: CR8 article-title: Consequences of genomic diversity in Mycobacterium tuberculosis publication-title: Seminars in immunology doi: 10.1016/j.smim.2014.09.012 – volume: 34 start-page: 2219 year: 1996 end-page: 2224 ident: CR46 article-title: Genotyping of Mycobacterium tuberculosis with additional markers enhances accuracy in epidemiological studies publication-title: Journal of clinical microbiology – volume: 10 start-page: e1001387 year: 2013 ident: CR6 article-title: Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study publication-title: PLoS medicine doi: 10.1371/journal.pmed.1001387 – volume: 19 start-page: 455 year: 2012 end-page: 477 ident: CR29 article-title: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing publication-title: Journal of computational biology: a journal of computational molecular cell biology doi: 10.1089/cmb.2012.0021 – volume: 7 start-page: 856 year: 2015 end-page: 870 ident: CR27 article-title: Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii publication-title: Genome biology and evolution doi: 10.1093/gbe/evv035 – ident: CR53 – volume: 14 start-page: 46 year: 2016 ident: CR2 article-title: Clinical use of whole genome sequencing for Mycobacterium tuberculosis publication-title: BMC medicine doi: 10.1186/s12916-016-0598-2 – volume: 37 start-page: 83 year: 2016 end-page: 96 ident: CR12 article-title: Nontuberculous Mycobacterial Infections in Cystic Fibrosis publication-title: Clinics in chest medicine doi: 10.1016/j.ccm.2015.11.001 – volume: 73 start-page: 325 year: 2009 end-page: 328 ident: CR20 article-title: Mycobacterial PE, PPE and ESX clusters: novel insights into the secretion of these most unusual protein families publication-title: Molecular microbiology doi: 10.1111/j.1365-2958.2009.06784.x – volume: 21 start-page: 67 year: 2014 end-page: 85 ident: CR55 article-title: Mycolic acids: structures, biosynthesis, and beyond publication-title: Chemistry & biology doi: 10.1016/j.chembiol.2013.11.011 – volume: 52 start-page: 2990 year: 2014 end-page: 2997 ident: CR11 article-title: Multidrug-resistant nontuberculous mycobacteria isolated from cystic fibrosis patients publication-title: Journal of clinical microbiology doi: 10.1128/jcm.00549-14 – volume: 53 start-page: 1197 year: 2014 end-page: 1204 ident: CR17 article-title: Cutaneous non-tuberculous mycobacterial infections publication-title: International journal of dermatology doi: 10.1111/ijd.12528 – volume: 58 start-page: 1432 year: 2008 end-page: 1441 ident: CR26 article-title: A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees publication-title: International journal of systematic and evolutionary microbiology doi: 10.1099/ijs.0.65658-0 – volume: 42 start-page: D222 year: 2014 end-page: 230 ident: CR41 article-title: Pfam: the protein families database publication-title: Nucleic acids research doi: 10.1093/nar/gkt1223 – volume: 5 start-page: 750 year: 2014 ident: CR40 article-title: Current strategies for mobilome research publication-title: Frontiers in microbiology doi: 10.3389/fmicb.2014.00750 – volume: 12 start-page: 827 year: 2012 end-page: 831 ident: CR25 article-title: Phylogeny of the genus Mycobacterium: many doubts, few certainties publication-title: Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases doi: 10.1016/j.meegid.2011.05.025 – volume: 277 start-page: 38148 year: 2002 end-page: 38158 ident: CR57 article-title: Role of the pks15/1 gene in the biosynthesis of phenolglycolipids in the Mycobacterium tuberculosis complex. Evidence that all strains synthesize glycosylated p-hydroxybenzoic methyl esters and that strains devoid of phenolglycolipids harbor a frameshift mutation in the pks15/1 gene publication-title: The Journal of biological chemistry doi: 10.1074/jbc.M206538200 – volume: 9 start-page: 20 year: 2014 ident: CR61 article-title: Quality scores for 32,000 genomes publication-title: Standards in genomic sciences doi: 10.1186/1944-3277-9-20 – volume: 12 start-page: 219 year: 1993 end-page: 222 ident: CR18 article-title: Epidemiology of disseminated nontuberculous mycobacterial disease in children with acquired immunodeficiency syndrome publication-title: The Pediatric infectious disease journal doi: 10.1097/00006454-199303000-00009 – ident: CR3 – volume: 3 start-page: 2101 year: 2013 ident: CR31 article-title: Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu publication-title: Scientific reports doi: 10.1038/srep02101 – volume: 27 start-page: 506 year: 2014 end-page: 510 ident: CR10 article-title: Mycobacterium abscessus: challenges in diagnosis and treatment publication-title: Current opinion in infectious diseases doi: 10.1097/qco.0000000000000104 – volume: 409 start-page: 1007 year: 2001 end-page: 1011 ident: CR60 article-title: Massive gene decay in the leprosy bacillus publication-title: Nature doi: 10.1038/35059006 – volume: 8 start-page: 64 year: 2007 ident: CR70 article-title: Minimus: a fast, lightweight genome assembler publication-title: BMC bioinformatics doi: 10.1186/1471-2105-8-64 – volume: 43 start-page: e15 year: 2015 ident: CR73 article-title: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins publication-title: Nucleic acids research doi: 10.1093/nar/gku1196 – volume: 36 start-page: 62 year: 2015 end-page: 69 ident: CR16 article-title: An outbreak of joint and cutaneous infections caused by non-tuberculous mycobacteria after corticosteroid injection publication-title: International journal of infectious diseases: IJID: official publication of the International Society for Infectious Diseases doi: 10.1016/j.ijid.2015.05.018 – volume: 26 start-page: 2460 year: 2010 end-page: 2461 ident: CR62 article-title: Search and clustering orders of magnitude faster than BLAST publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btq461 – volume: 3 start-page: e1029 year: 2015 ident: CR74 article-title: Compact graphical representation of phylogenetic data and metadata with GraPhlAn publication-title: PeerJ doi: 10.7717/peerj.1029 – volume: 52 start-page: 1543 year: 2004 end-page: 1552 ident: CR49 article-title: Lipoprotein processing is required for virulence of Mycobacterium tuberculosis publication-title: Molecular microbiology doi: 10.1111/j.1365-2958.2004.04041.x – volume: 35 start-page: D391 year: 2007 end-page: 394 ident: CR44 article-title: MvirDB–a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications publication-title: Nucleic acids research doi: 10.1093/nar/gkl791 – volume: 65 start-page: 656 year: 2015 end-page: 662 ident: CR28 article-title: Characterization of 17 strains belonging to the Mycobacterium simiae complex and description of Mycobacterium paraense sp. nov publication-title: International journal of systematic and evolutionary microbiology doi: 10.1099/ijs.0.068395-0 – ident: CR7 – volume: 190 start-page: 6428 year: 2008 end-page: 6438 ident: CR51 article-title: Identification of functional Tat signal sequences in Mycobacterium tuberculosis proteins publication-title: Journal of bacteriology doi: 10.1128/jb.00749-08 – volume: 36 start-page: 35 year: 2015 end-page: 41 ident: CR14 article-title: Environmental sources of nontuberculous mycobacteria publication-title: Clinics in chest medicine doi: 10.1016/j.ccm.2014.10.003 – volume: 215 start-page: 403 year: 1990 end-page: 410 ident: CR66 article-title: Basic local alignment search tool publication-title: Journal of molecular biology doi: 10.1016/s0022-2836(05)80360-2 – volume: 31 start-page: 3083 year: 1993 ident: BFsrep45258_CR35 publication-title: Journal of clinical microbiology doi: 10.1128/jcm.31.12.3083-3089.1993 – volume: 8 start-page: 64 year: 2007 ident: BFsrep45258_CR70 publication-title: BMC bioinformatics doi: 10.1186/1471-2105-8-64 – volume: 9 start-page: 20 year: 2014 ident: BFsrep45258_CR61 publication-title: Standards in genomic sciences doi: 10.1186/1944-3277-9-20 – volume: 30 start-page: 2068 year: 2014 ident: BFsrep45258_CR32 publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btu153 – volume: 37 start-page: 83 year: 2016 ident: BFsrep45258_CR12 publication-title: Clinics in chest medicine doi: 10.1016/j.ccm.2015.11.001 – volume: 30 start-page: 1312 year: 2014 ident: BFsrep45258_CR65 publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btu033 – volume: 53 start-page: 1197 year: 2014 ident: BFsrep45258_CR17 publication-title: International journal of dermatology doi: 10.1111/ijd.12528 – volume: 43 start-page: e15 year: 2015 ident: BFsrep45258_CR73 publication-title: Nucleic acids research doi: 10.1093/nar/gku1196 – volume: 26 start-page: 431 year: 2014 ident: BFsrep45258_CR8 publication-title: Seminars in immunology doi: 10.1016/j.smim.2014.09.012 – volume: 3 start-page: 2101 year: 2013 ident: BFsrep45258_CR31 publication-title: Scientific reports doi: 10.1038/srep02101 – volume: 52 start-page: 2990 year: 2014 ident: BFsrep45258_CR11 publication-title: Journal of clinical microbiology doi: 10.1128/jcm.00549-14 – volume: 73 start-page: 325 year: 2009 ident: BFsrep45258_CR20 publication-title: Molecular microbiology doi: 10.1111/j.1365-2958.2009.06784.x – volume: 69 start-page: 6041 year: 2003 ident: BFsrep45258_CR37 publication-title: Applied and environmental microbiology doi: 10.1128/AEM.69.10.6041-6046.2003 – volume: 277 start-page: 38148 year: 2002 ident: BFsrep45258_CR57 publication-title: The Journal of biological chemistry doi: 10.1074/jbc.M206538200 – ident: BFsrep45258_CR21 doi: 10.1128/microbiolspec.MGM2-0025-2013 – volume: 44 start-page: 259 year: 2005 ident: BFsrep45258_CR56 publication-title: Progress in lipid research doi: 10.1016/j.plipres.2005.07.001 – volume: 5 start-page: 750 year: 2014 ident: BFsrep45258_CR40 publication-title: Frontiers in microbiology doi: 10.3389/fmicb.2014.00750 – volume: 264 start-page: 25 year: 2015 ident: BFsrep45258_CR22 publication-title: Immunological reviews doi: 10.1111/imr.12251 – volume: 15 start-page: 21 year: 2017 ident: BFsrep45258_CR23 publication-title: Nature reviews. Microbiology doi: 10.1038/nrmicro.2016.161 – volume: 21 start-page: 67 year: 2014 ident: BFsrep45258_CR55 publication-title: Chemistry & biology doi: 10.1016/j.chembiol.2013.11.011 – volume: 10 start-page: 421 year: 2009 ident: BFsrep45258_CR67 publication-title: BMC bioinformatics doi: 10.1186/1471-2105-10-421 – volume: 9 start-page: e87924 year: 2014 ident: BFsrep45258_CR69 publication-title: PloS One doi: 10.1371/journal.pone.0087924 – volume: 15 start-page: 717 year: 2014 ident: BFsrep45258_CR72 publication-title: BMC genomics doi: 10.1186/1471-2164-15-717 – volume: 61 start-page: 1606 year: 2011 ident: BFsrep45258_CR36 publication-title: International journal of systematic and evolutionary microbiology doi: 10.1099/ijs.0.025601-0 – volume: 14 start-page: 46 year: 2016 ident: BFsrep45258_CR2 publication-title: BMC medicine doi: 10.1186/s12916-016-0598-2 – volume: 352 start-page: 1 year: 2011 ident: BFsrep45258_CR24 publication-title: Molecular and cellular biochemistry doi: 10.1007/s11010-011-0733-5 – volume: 193 start-page: 4300 year: 2011 ident: BFsrep45258_CR30 publication-title: Journal of bacteriology doi: 10.1128/jb.05291-11 – volume: 34 start-page: 2219 year: 1996 ident: BFsrep45258_CR46 publication-title: Journal of clinical microbiology doi: 10.1128/jcm.34.9.2219-2224.1996 – volume: 3 start-page: e1029 year: 2015 ident: BFsrep45258_CR74 publication-title: PeerJ doi: 10.7717/peerj.1029 – volume: 71 start-page: 153 year: 1996 ident: BFsrep45258_CR34 publication-title: Discrete Applied Mathematics doi: 10.1016/S0166-218X(96)00062-5 – volume: 10 start-page: e1001387 year: 2013 ident: BFsrep45258_CR6 publication-title: PLoS medicine doi: 10.1371/journal.pmed.1001387 – volume: 187 start-page: 7667 year: 2005 ident: BFsrep45258_CR50 publication-title: Journal of bacteriology doi: 10.1128/jb.187.22.7667-7679.2005 – volume: 32 start-page: 1792 year: 2004 ident: BFsrep45258_CR64 publication-title: Nucleic acids research doi: 10.1093/nar/gkh340 – volume: 26 start-page: 2460 year: 2010 ident: BFsrep45258_CR62 publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btq461 – volume: 4 start-page: e2584 year: 2016 ident: BFsrep45258_CR63 publication-title: Peer J doi: 10.7717/peerj.2584 – volume: 92 start-page: 121 year: 2012 ident: BFsrep45258_CR48 publication-title: Tuberculosis (Edinburgh, Scotland) doi: 10.1016/j.tube.2011.11.005 – volume: 35 start-page: D391 year: 2007 ident: BFsrep45258_CR44 publication-title: Nucleic acids research doi: 10.1093/nar/gkl791 – volume: 11 start-page: e0147513 year: 2016 ident: BFsrep45258_CR13 publication-title: PloS one doi: 10.1371/journal.pone.0147513 – volume: 12 start-page: 219 year: 1993 ident: BFsrep45258_CR18 publication-title: The Pediatric infectious disease journal doi: 10.1097/00006454-199303000-00009 – volume: 65 start-page: 656 year: 2015 ident: BFsrep45258_CR28 publication-title: International journal of systematic and evolutionary microbiology doi: 10.1099/ijs.0.068395-0 – volume: 18 start-page: 81 year: 2005 ident: BFsrep45258_CR54 publication-title: Clinical microbiology reviews doi: 10.1128/cmr.18.1.81-101.2005 – volume: 2011 start-page: 497203 year: 2011 ident: BFsrep45258_CR45 publication-title: Clinical & developmental immunology doi: 10.1155/2011/497203 – volume: 42 start-page: 1431 year: 2013 ident: BFsrep45258_CR33 publication-title: SIAM Journal on Computing doi: 10.1137/110845045 – volume: 34 start-page: 95 year: 2013 ident: BFsrep45258_CR1 publication-title: Seminars in respiratory and critical care medicine doi: 10.1055/s-0033-1333568 – volume: 4 start-page: 152 year: 2015 ident: BFsrep45258_CR9 publication-title: Current pulmonology reports doi: 10.1007/s13665-015-0119-3 – volume: 211 start-page: 1306 year: 2015 ident: BFsrep45258_CR5 publication-title: The Journal of infectious diseases doi: 10.1093/infdis/jiu601 – volume: 15 start-page: 906 year: 2009 ident: BFsrep45258_CR15 publication-title: Clinical microbiology and infection: the official publication of the European Society of Clinical Microbiology and Infectious Diseases doi: 10.1111/j.1469-0691.2009.03014.x – ident: BFsrep45258_CR53 doi: 10.1128/microbiolspec.MGM2-0003-2013 – ident: BFsrep45258_CR3 – volume: 4 start-page: 2304 year: 2013 ident: BFsrep45258_CR59 publication-title: Nature communications doi: 10.1038/ncomms3304 – volume: 58 start-page: 1432 year: 2008 ident: BFsrep45258_CR26 publication-title: International journal of systematic and evolutionary microbiology doi: 10.1099/ijs.0.65658-0 – ident: BFsrep45258_CR19 doi: 10.1111/resp.12767 – volume: 42 start-page: D222 year: 2014 ident: BFsrep45258_CR41 publication-title: Nucleic acids research doi: 10.1093/nar/gkt1223 – volume: 10 start-page: e0128773 year: 2015 ident: BFsrep45258_CR71 publication-title: PloS One doi: 10.1371/journal.pone.0128773 – volume: 27 start-page: 506 year: 2014 ident: BFsrep45258_CR10 publication-title: Current opinion in infectious diseases doi: 10.1097/qco.0000000000000104 – volume: 52 start-page: 1543 year: 2004 ident: BFsrep45258_CR49 publication-title: Molecular microbiology doi: 10.1111/j.1365-2958.2004.04041.x – volume: 2010 start-page: pdb.prot5408 year: 2010 ident: BFsrep45258_CR58 publication-title: Cold Spring Harbor protocols doi: 10.1101/pdb.prot5408 – volume: 6 start-page: e27980 year: 2011 ident: BFsrep45258_CR43 publication-title: PloS One doi: 10.1371/journal.pone.0027980 – volume: 5 start-page: 883 year: 2007 ident: BFsrep45258_CR47 publication-title: Nature reviews. Microbiology doi: 10.1038/nrmicro1773 – volume: 31 start-page: 3691 year: 2015 ident: BFsrep45258_CR38 publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btv421 – volume: 190 start-page: 6428 year: 2008 ident: BFsrep45258_CR51 publication-title: Journal of bacteriology doi: 10.1128/jb.00749-08 – volume: 14 start-page: 704 year: 2001 ident: BFsrep45258_CR52 publication-title: Clinical microbiology reviews doi: 10.1128/cmr.14.4.704-726.2001 – volume: 36 start-page: 62 year: 2015 ident: BFsrep45258_CR16 publication-title: International journal of infectious diseases: IJID: official publication of the International Society for Infectious Diseases doi: 10.1016/j.ijid.2015.05.018 – volume: 215 start-page: 403 year: 1990 ident: BFsrep45258_CR66 publication-title: Journal of molecular biology doi: 10.1016/s0022-2836(05)80360-2 – volume: 36 start-page: 35 year: 2015 ident: BFsrep45258_CR14 publication-title: Clinics in chest medicine doi: 10.1016/j.ccm.2014.10.003 – volume: 19 start-page: 455 year: 2012 ident: BFsrep45258_CR29 publication-title: Journal of computational biology: a journal of computational molecular cell biology doi: 10.1089/cmb.2012.0021 – volume: 42 start-page: D231 year: 2014 ident: BFsrep45258_CR39 publication-title: Nucleic acids research doi: 10.1093/nar/gkt1253 – volume: 409 start-page: 1007 year: 2001 ident: BFsrep45258_CR60 publication-title: Nature doi: 10.1038/35059006 – volume: 7 start-page: 856 year: 2015 ident: BFsrep45258_CR27 publication-title: Genome biology and evolution doi: 10.1093/gbe/evv035 – volume: 12 start-page: 827 year: 2012 ident: BFsrep45258_CR25 publication-title: Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases doi: 10.1016/j.meegid.2011.05.025 – volume: 37 start-page: D5 year: 2009 ident: BFsrep45258_CR68 publication-title: Nucleic acids research doi: 10.1093/nar/gkn741 – ident: BFsrep45258_CR7 doi: 10.1164/rccm.201510-2091OC – volume: 7 start-page: e50070 year: 2012 ident: BFsrep45258_CR42 publication-title: PloS one doi: 10.1371/journal.pone.0050070 – volume: 364 start-page: 730 year: 2011 ident: BFsrep45258_CR4 publication-title: The New England journal of medicine doi: 10.1056/NEJMoa1003176 – reference: 19602151 - Mol Microbiol. 2009 Aug;73(3):325-8 – reference: 25268925 - Curr Opin Infect Dis. 2014 Dec;27(6):506-10 – reference: 17922044 - Nat Rev Microbiol. 2007 Nov;5(11):883-91 – reference: 25362193 - J Infect Dis. 2015 Apr 15;211(8):1306-16 – reference: 24961147 - Int J Dermatol. 2014 Oct;53(10):1197-204 – reference: 27781170 - PeerJ. 2016 Oct 18;4:e2584 – reference: 27009804 - Respirology. 2016 Aug;21(6):1015-25 – reference: 20709691 - Bioinformatics. 2010 Oct 1;26(19):2460-1 – reference: 26910495 - Am J Respir Crit Care Med. 2016 Sep 1;194(5):621-30 – reference: 21318182 - Clin Dev Immunol. 2011;2011:497203 – reference: 26812154 - PLoS One. 2016 Jan 26;11(1):e0147513 – reference: 23812535 - Sci Rep. 2013;3:2101 – reference: 17324286 - BMC Bioinformatics. 2007 Feb 26;8:64 – reference: 25487637 - Int J Syst Evol Microbiol. 2015 Feb;65(Pt 2):656-62 – reference: 26157614 - PeerJ. 2015 Jun 18;3:e1029 – reference: 15186407 - Mol Microbiol. 2004 Jun;52(6):1543-52 – reference: 26104214 - Microbiol Spectr. 2014 Aug;2(4):MGM2-0003-2013 – reference: 21345102 - N Engl J Med. 2011 Feb 24;364(8):730-9 – reference: 25780509 - Stand Genomic Sci. 2014 Dec 08;9:20 – reference: 24920766 - J Clin Microbiol. 2014 Aug;52(8):2990-7 – reference: 25159222 - BMC Genomics. 2014 Aug 26;15:717 – reference: 16267291 - J Bacteriol. 2005 Nov;187(22):7667-79 – reference: 23189179 - PLoS One. 2012;7(11):e50070 – reference: 20360362 - Cold Spring Harb Protoc. 2010 Apr;2010(4):pdb.prot5408 – reference: 8862588 - J Clin Microbiol. 1996 Sep;34(9):2219-24 – reference: 21258845 - Mol Cell Biochem. 2011 Jun;352(1-2):1-10 – reference: 22140496 - PLoS One. 2011;6(11):e27980 – reference: 14532060 - Appl Environ Microbiol. 2003 Oct;69(10):6041-6 – reference: 26198102 - Bioinformatics. 2015 Nov 15;31(22):3691-3 – reference: 23460009 - Semin Respir Crit Care Med. 2013 Feb;34(1):95-102 – reference: 15034147 - Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 – reference: 25716827 - Genome Biol Evol. 2015 Feb 25;7(3):856-70 – reference: 11585782 - Clin Microbiol Rev. 2001 Oct;14(4):704-26, table of contents – reference: 24503942 - PLoS One. 2014 Feb 04;9(2):e87924 – reference: 24297252 - Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9 – reference: 8095716 - Pediatr Infect Dis J. 1993 Mar;12(3):219-22 – reference: 16115688 - Prog Lipid Res. 2005 Sep;44(5):259-302 – reference: 23942190 - Nat Commun. 2013;4:2304 – reference: 25414349 - Nucleic Acids Res. 2015 Feb 18;43(3):e15 – reference: 25676517 - Clin Chest Med. 2015 Mar;36(1):35-41 – reference: 26857770 - Clin Chest Med. 2016 Mar;37(1):83-96 – reference: 22506599 - J Comput Biol. 2012 May;19(5):455-77 – reference: 25453224 - Semin Immunol. 2014 Dec;26(6):431-44 – reference: 24288371 - Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30 – reference: 24642063 - Bioinformatics. 2014 Jul 15;30(14):2068-9 – reference: 12138124 - J Biol Chem. 2002 Oct 11;277(41):38148-58 – reference: 27890920 - Nat Rev Microbiol. 2017 Jan;15(1):21-36 – reference: 20003500 - BMC Bioinformatics. 2009 Dec 15;10:421 – reference: 26083489 - PLoS One. 2015 Jun 17;10(6):e0128773 – reference: 15653820 - Clin Microbiol Rev. 2005 Jan;18(1):81-101 – reference: 23424287 - PLoS Med. 2013;10(2):e1001387 – reference: 17090593 - Nucleic Acids Res. 2007 Jan;35(Database issue):D391-4 – reference: 18523191 - Int J Syst Evol Microbiol. 2008 Jun;58(Pt 6):1432-41 – reference: 20693362 - Int J Syst Evol Microbiol. 2011 Jul;61(Pt 7):1606-11 – reference: 26082120 - Microbiol Spectr. 2014 Feb;2(1):MGM2-0025-2013 – reference: 18658266 - J Bacteriol. 2008 Oct;190(19):6428-38 – reference: 22192870 - Tuberculosis (Edinb). 2012 Mar;92(2):121-32 – reference: 18940862 - Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15 – reference: 21684354 - Infect Genet Evol. 2012 Jun;12(4):827-31 – reference: 2231712 - J Mol Biol. 1990 Oct 5;215(3):403-10 – reference: 19845702 - Clin Microbiol Infect. 2009 Oct;15(10):906-10 – reference: 7508452 - J Clin Microbiol. 1993 Dec;31(12):3083-9 – reference: 24451623 - Bioinformatics. 2014 May 1;30(9):1312-3 – reference: 21685274 - J Bacteriol. 2011 Aug;193(16):4300-1 – reference: 24374164 - Chem Biol. 2014 Jan 16;21(1):67-85 – reference: 26877911 - Curr Pulmonol Rep. 2015 Sep 1;4(3):152-161 – reference: 26026822 - Int J Infect Dis. 2015 Jul;36:62-9 – reference: 25657641 - Front Microbiol. 2015 Jan 22;5:750 – reference: 11234002 - Nature. 2001 Feb 22;409(6823):1007-11 – reference: 25703550 - Immunol Rev. 2015 Mar;264(1):25-45 – reference: 27004841 - BMC Med. 2016 Mar 23;14 :46 |
| SSID | ssj0000529419 |
| Score | 2.5606186 |
| Snippet | Mycobacterium tuberculosis
and
Mycobacterium leprae
have remained, for many years, the primary species of the genus
Mycobacterium
of clinical and... Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the primary species of the genus Mycobacterium of clinical and... |
| SourceID | pubmedcentral proquest pubmed crossref springer |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 45258 |
| SubjectTerms | 45/22 631/326/107 631/326/325/2482 Chromosome Mapping - methods Gene Transfer, Horizontal Genetic Variation Genome, Bacterial Genomes Genomics Humanities and Social Sciences Humans Leprosy Molecular Sequence Annotation multidisciplinary Mycobacterium Infections, Nontuberculous - microbiology Nontuberculous Mycobacteria - classification Nontuberculous Mycobacteria - genetics Open Reading Frames Opportunist infection Phylogeny Science Sequence Analysis, DNA - methods Species Tuberculosis |
| SummonAdditionalLinks | – databaseName: Scholars Portal Journals: Open Access dbid: M48 link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1LS8NAEB5qRfAivo1WiY-Dl2iSzWZ3DyIi1iK0Jwu9hWyyi0JJa23B_ntn86K1xUMgkFkyzOwy3zA73wDcxOZqReBxJ_QT1wl8Fjs8kNLBYI_RT6dhkJhEsdsLO_3gbUAHDahmbJYG_F6b2pl5Uv3J8O7na_6IB_6haBnn9xhLxqY8xzdgMy8TmRt8JcovKL59VEdUvEKLK5aj0QrEXL0p-adcmkeh9i7slPDRfir8vQcNle3DVjFQcn4A7FXlbcZ2UvMwF22W9kjbvRHGF6kmyWyI6b7dnSd4lnOZ-BD67Zf3545TjkZwEuoGU7QnIZprP9SUm4yACdQxDT3lKeamglKm8EVqPK9MxKnQcYrAQnMRyFALTckRNLNRpk7A9miqNNFpEnPERimTlErPdNzKwFOEEAtuKxNFSckbbsZXDKO8fk14VFvTgqtadFyQZawTalV2jip3RwhLMFdGNCYsuKw_40435Ys4U2iWyOMcsz98UKXjwi31XxAkIRIkuJotOawWMCzay1-yz4-cTZuSMBQeteC6cu2CWn-VP_1f-TPY9k3Yd4njsxY0p5OZOkfQMpUX-Zb8BSRF7f4 priority: 102 providerName: Scholars Portal – databaseName: Springer Nature HAS Fully OA dbid: AAJSJ link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1LSwMxEB60RfAivq1WWR8HL4ubTbJJjkXUUmgvWuht2ewmKJRtaevBf-9kX1r14GFhIRN2mDzmm53JF4CbxJVWMCL9KEwDn4Ui8SXT2kdnj97PZhFLXaA4HEX9MRtM-KQii15WZZUlpWWxTdfVYXfoL-YuBSc3oS0F7rotaPd6g-dB80PFpawYUTV7EJVffdZ9zi8g-bse8kdStPA1j7uwU4FEr1eqtQcbJt-HrfLayI8DEE-mOEzspQ3bcnmY0ptZbzRDL6LNIn2fYlDvDT9SXLGFTHII48eHl_u-X12A4Kc8YCu0GqVW2jCyXDrcLxTqmEXEECOCTHEuDL5oi6tSqCRTNskQPlipmI6sspweQSuf5eYEPMIzY6nN0kQiAsqE5lwTd65WM2IopR24rU0UpxU7uLukYhoXWWoq48aaHbhqROclJcZfQt3aznG1KpYxgg-MiBFzqQ5cNs04n12SIskNmiUmUmKMhw-qdFwOS_MVhEKI9yj2FmsD1gg4ruz1lvztteDM5jSKFOEduK6H9ptaP5U__ZfUGWyHzscH1A9FF1qrxbs5R4Sy0hfV3PwEe_boUA priority: 102 providerName: Springer Nature |
| Title | Genomic characterization of Nontuberculous Mycobacteria |
| URI | https://link.springer.com/article/10.1038/srep45258 https://www.ncbi.nlm.nih.gov/pubmed/28345639 https://www.proquest.com/docview/1903385059 https://www.proquest.com/docview/1881448143 https://pubmed.ncbi.nlm.nih.gov/PMC5366915 |
| Volume | 7 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1Za9tAEB5ah0JfQpNezmHU46EvIl7t_VQckwODTWkb8JvQXiRgZDdxHvzvM6srdVL6oAPtCg0zu_rm2J0B-FrEpRWMqFRkdpiyTBapYsakCPaIfsEJZqOhOJ2Jyys2mfN543C7a5ZVtv_E6kftljb6yE8QuNCaQrzW31d_0lg1KkZXmxIaL2GHoCYSSzfIuex8LDGKxYhuEwpRdYKws4qRPLUNQ890y-dLJJ_ESSv4OX8Du43emIxqQe_BC1_uw6u6kuTmLcgLX-0vTmyXgLneX5ksQzJbIrAYf2vvF2jnJ9ONxUlc9SnewdX52e_xZdrUREgtH7I1MpLSoEImAlfRFJAaaXSCeOLl0GnOpccbE3CiSl04HQqHGkVQmhkRdOD0PfTKZek_QkK484EGZwuFSpGThnND4lZbw4inlPbhW8ui3DYJw2PdikVeBa6pyjtu9uFz13VVZ8n4V6ejls95M1Hu8kex9uFT14xDPMYtitIjW3KiFJp9eCBJH2qxdF9B7QhVQIpvyy2BdR1i-uztlvLmukqjzakQmvA-fGlF-xdZT4k_-D_xh_A6i3g_pGkmj6C3vr33x6itrM2gGpID2BmNJr8meD09m_34iU_HYjyoPAB4njL1ABOn8bc |
| linkProvider | ProQuest |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV3daxQxEB_KlaIvoq0fp1W3VcGXpZdNskkeilhtvdreIdJC37abLxTK7tm7Q-6f829zsl_tteJbHxYWMssOk0l-M5nMDMDbPFytYETGaWIGMUtEHkumdYxgj-jnbcpMcBRH43R4yr6e8bMV-NPmwoRrle2eWG3UtjThjHwHgQu9KcRr9WHyKw5do0J0tW2hkTetFexuVWKsSew4covf6MJNdw8_43y_S5KD_ZNPw7jpMhAbPmAzZI1SL32Sei6DcS2Us8amxBEnBlZxLhy-aI-qL1Rulc8tYrSXiunUKx-6RiAErLJwgNKD1b398bfv3SlPiKMxotqSRlTuIPBNQixRLgPhLev29iXNG5HaCgAPHsKDxnKNPtaq9ghWXLEOa3Uvy8UGiC-uynCOTFcCus7wjEofjUuENu0uzfyinE-j0cLgNlLR5I_h9E7k9QR6RVm4ZxARbp2n3ppcollmheZck5DsqxlxlNI-vG9FlJmmZHnonHGRVaFzKrNOmn3Y7kgndZ2OfxFttnLOmqU6za4Uqw9b3TAushA5yQuHYsmIlOh44oMsPa2npfsL2mdohFL8WixNWEcQCngvjxQ_f1SFvDlNU0V4H960U3uNrZvMP_8_86_h3vBkdJwdH46PXsD9JFgfAxonYhN6s8u5e4m200y_ahQ0gvO7XhN_ARQeL14 |
| linkToPdf | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV3daxQxEB9Ki-KLtNbas62uWsGX5S6bZJM8FBHr2Q979MHCva2bLxTK7rV3h9y_5l_XyX7ptcW3PiwsZJYdJjP5TTKTGYD9PKRWMCLjNDGDmCUijyXTOkawR_TzNmUmbBTPRunRBTsZ8_EK_GnvwoS0ynZNrBZqW5pwRt5H4MLdFOK16vsmLeL8cPhxchWHDlIh0tq206hV5NQtfuP2bXpwfIhz_T5Jhl--fz6Kmw4DseEDNkO2KPXSJ6nnMjjWQjlrbEoccWJgFefC4Yv2qPZC5Vb53CI-e6mYTr3yoWMELv9rgjIW2kaIsejOd0IEjRHVFjOiso-QNwlRRLkMgXf82rvpmbditBX0DdfhaeOzRp9qJduAFVc8g0d1F8vFJoivrrrbHJmu-HN9tzMqfTQqEdS0uzbzy3I-jc4WBheQiiZ_DhcPIq0tWC3Kwm1DRLh1nnprcokOmRWac03CNV_NiKOU9uBDK6LMNMXKQ8-My6wKmlOZddLswduOdFJX6LiPaLeVc9YY6TT7q1I9eNMNo3mFmEleOBRLRqTELSc-yNKLelq6v6Bnhu4nxa_F0oR1BKF09_JI8etnVcKb0zRVhPfgXTu1_7B1m_mX_2f-NTxGS8i-HY9Od-BJEtyOAY0TsQurs-u520OnaaZfVdoZwY-HNocb3nQs-g |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Genomic+characterization+of+Nontuberculous+Mycobacteria&rft.jtitle=Scientific+reports&rft.au=Fedrizzi%2C+Tarcisio&rft.au=Meehan%2C+Conor+J&rft.au=Grottola%2C+Antonella&rft.au=Giacobazzi%2C+Elisabetta&rft.date=2017-03-27&rft.pub=Nature+Publishing+Group&rft.eissn=2045-2322&rft.volume=7&rft.spage=45258&rft_id=info:doi/10.1038%2Fsrep45258&rft.externalDBID=HAS_PDF_LINK |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2045-2322&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2045-2322&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2045-2322&client=summon |