Literature DB >> 34235665

Identification and Characterization of Mycobacterial Species Using Whole-Genome Sequences.

Marco A Riojas1, Andrew M Frank2, Samuel R Greenfield2, Stephen P King2, Conor J Meehan3, Michael Strong4, Alice R Wattam5, Manzour Hernando Hazbón6.   

Abstract

Whole-genome sequencing (WGS) has shown immense value in enabling identification and characterization of bacterial taxa. This is particularly true for mycobacteria, where culture-based characterization becomes delayed by the inherently slow growth rate of these organisms. This chapter reviews the general techniques behind WGS and their optimization, existing techniques for species-level identification and the advantages of WGS for this purpose, and a variety of useful tools for the genomic characterization of mycobacterial strains.

Keywords:  ANI; DNA; Mycobacteria; Sequencing; Species identification; Whole-genome sequence; dDDH

Year:  2021        PMID： 34235665     DOI： 10.1007/978-1-0716-1460-0_19

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  166 in total

1.  Nucleotide sequence of bacteriophage phi X174 DNA.

Authors:  F Sanger; G M Air; B G Barrell; N L Brown; A R Coulson; C A Fiddes; C A Hutchison; P M Slocombe; M Smith
Journal:  Nature       Date:  1977-02-24       Impact factor: 49.962

Review 2.  Past and future species definitions for Bacteria and Archaea.

Authors:  Ramon Rosselló-Móra; Rudolf Amann
Journal:  Syst Appl Microbiol       Date:  2015-02-20       Impact factor: 4.022

3.  Same meat, different gravy: ignore the new names of mycobacteria.

Authors:  Enrico Tortoli; Barbara A Brown-Elliott; James D Chalmers; Daniela M Cirillo; Charles L Daley; Stefan Emler; R Andres Floto; Maria J Garcia; Wouter Hoefsloot; Won-Jung Koh; Christoph Lange; Michael Loebinger; Florian P Maurer; Kozo Morimoto; Stefan Niemann; Elvira Richter; Christine Y Turenne; Ravikiran Vasireddy; Sruthi Vasireddy; Dirk Wagner; Richard J Wallace; Nancy Wengenack; Jakko van Ingen
Journal:  Eur Respir J       Date:  2019-07-11       Impact factor: 16.671

4.  The axolotl genome and the evolution of key tissue formation regulators.

Authors:  Sergej Nowoshilow; Siegfried Schloissnig; Ji-Feng Fei; Andreas Dahl; Andy W C Pang; Martin Pippel; Sylke Winkler; Alex R Hastie; George Young; Juliana G Roscito; Francisco Falcon; Dunja Knapp; Sean Powell; Alfredo Cruz; Han Cao; Bianca Habermann; Michael Hiller; Elly M Tanaka; Eugene W Myers
Journal:  Nature       Date:  2018-01-24       Impact factor: 49.962

5.  Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.

Authors:  Radhey S Gupta; Brian Lo; Jeen Son
Journal:  Front Microbiol       Date:  2018-02-13       Impact factor: 5.640

6.  Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium.

Authors:  Enrico Tortoli; Conor J Meehan; Antonella Grottola; Giulia Fregni Serpini; Anna Fabio; Alberto Trovato; Monica Pecorari; Daniela M Cirillo
Journal:  Infect Genet Evol       Date:  2019-07-26       Impact factor: 3.342

7.  The new phylogeny of the genus Mycobacterium: The old and the news.

Authors:  Enrico Tortoli; Tarcisio Fedrizzi; Conor J Meehan; Alberto Trovato; Antonella Grottola; Elisabetta Giacobazzi; Giulia Fregni Serpini; Sara Tagliazucchi; Anna Fabio; Clotilde Bettua; Roberto Bertorelli; Francesca Frascaro; Veronica De Sanctis; Monica Pecorari; Olivier Jousson; Nicola Segata; Daniela M Cirillo
Journal:  Infect Genet Evol       Date:  2017-10-11       Impact factor: 3.342

8.  The sequence of the human genome.

Authors:  J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal:  Science       Date:  2001-02-16       Impact factor: 47.728

9.  Genomic characterization of Nontuberculous Mycobacteria.

Authors:  Tarcisio Fedrizzi; Conor J Meehan; Antonella Grottola; Elisabetta Giacobazzi; Giulia Fregni Serpini; Sara Tagliazucchi; Anna Fabio; Clotilde Bettua; Roberto Bertorelli; Veronica De Sanctis; Fabio Rumpianesi; Monica Pecorari; Olivier Jousson; Enrico Tortoli; Nicola Segata
Journal:  Sci Rep       Date:  2017-03-27       Impact factor: 4.379

Review 10.  Whole-genome sequencing to control antimicrobial resistance.

Authors:  Claudio U Köser; Matthew J Ellington; Sharon J Peacock
Journal:  Trends Genet       Date:  2014-08-03       Impact factor: 11.639
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