References
1. Sanger F, Air GM, Barrell BG, Brown NL,
Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977) Nucleotide
sequence of bacteriophage phi X174 DNA.
Nature 265(5596):687–695. https://doi.
org/10.1038/265687a0
2. Venter JC, Adams MD, Myers EW et al
(2001) The sequence of the human genome.
Science 291(5507):1304–1351. https://doi.
org/10.1126/science.1058040
3. International Human Genome Sequencing
Consortium (2001) Initial sequencing and
analysis of the human genome. Nature 409
(6822):860–921. https://doi.org/10.1038/
35057062
4. International Human Genome Sequencing
Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature
431(7011):931–945.
https://doi.org/10.
1038/nature03001
5. Nowoshilow S, Schloissnig S, Fei JF, Dahl A,
Pang AWC, Pippel M, Winkler S, Hastie AR,
Young G, Roscito JG, Falcon F, Knapp D,
Powell S, Cruz A, Cao H, Habermann B,
Hiller M, Tanaka EM, Myers EW (2018)
The axolotl genome and the evolution of key
tissue formation regulators. Nature 554
(7690):50–55. https://doi.org/10.1038/
nature25458
6. Wetterstrand K (2019) DNA Sequencing
Costs: Data from the NHGRI Genome
Sequencing Program (GSP). http://www.
genome.gov/sequencingcostsdata. Accessed
Feb 12, 2020
7. National Center for Biotechnology Information, U.S. National Library of Medicine
(2019) GenBank and WGS Statistics.
https://www.ncbi.nlm.nih.gov/genbank/sta
tistics/. Accessed Feb 12, 2020
8. Ko ¨ser CU, Ellington MJ, Peacock SJ (2014)
Whole-genome sequencing to control antimicrobial resistance. Trends Genet 30
(9):401–407.
https://doi.org/10.1016/j.
tig.2014.07.003
9. Magee JG, Ward AC (2015) Mycobacterium.
In: Bergey’s Manual of systematics of archaea
and bacteria. Wiley, Hoboken, New Jersey, pp
1–84.
https://doi.org/10.1002/
9781118960608.gbm00029
10. CLSI (2018) Laboratory detection and identification of mycobacteria, 2nd Ed. edn. Clinical and Laboratory Standards Institute,
Wayne, PA
11. Tortoli E, Meehan CJ, Grottola A, Fregni
Serpini G, Fabio A, Trovato A, Pecorari M,
Cirillo DM (2019) Genome-based taxonomic
revision detects a number of synonymous taxa
in the genus Mycobacterium. Infect Genet
Evol 75:103983. https://doi.org/10.1016/
j.meegid.2019.103983
12. Gupta RS, Lo B, Son J (2018) Phylogenomics
and comparative genomic studies robustly
support division of the genus Mycobacterium
into an emended genus Mycobacterium and
four novel genera. Front Microbiol 9:67.
https://doi.org/10.3389/fmicb.2018.
00067
13. Tortoli E, Brown-Elliott BA, Chalmers JD,
Cirillo DM, Daley CL, Emler S, Floto RA,
Garcia MJ, Hoefsloot W, Koh WJ, Lange C,
Loebinger M, Maurer FP, Morimoto K,
Niemann S, Richter E, Turenne CY,
Vasireddy R, Vasireddy S, Wagner D, Wallace
RJ Jr, Wengenack N, van Ingen J (2019) Same
meat, different gravy: ignore the new names
of mycobacteria. Eur Respir J 54
(1):1900795.
https://doi.org/10.1183/
13993003.00795-2019
14. Fedrizzi T, Meehan CJ, Grottola A,
Giacobazzi
E,
Fregni
Serpini
G,
Tagliazucchi S, Fabio A, Bettua C,
Bertorelli R, De Sanctis V, Rumpianesi F,
Pecorari M, Jousson O, Tortoli E, Segata N
(2017) Genomic characterization of nontuberculous mycobacteria. Sci Rep 7:45258.
https://doi.org/10.1038/srep45258
15. Tortoli E, Fedrizzi T, Meehan CJ, Trovato A,
Grottola A, Giacobazzi E, Serpini GF,
Tagliazucchi S, Fabio A, Bettua C,
Bertorelli R, Frascaro F, De Sanctis V,
Pecorari M, Jousson O, Segata N, Cirillo
DM (2017) The new phylogeny of the genus
Mycobacterium: the old and the news. Infect
Genet Evol 56:19–25. https://doi.org/10.
1016/j.meegid.2017.10.013
16. Rossello ´ -Mo ´ ra R, Amann R (2015) Past and
future species definitions for Bacteria and
Archaea.
Syst
Appl
Microbiol
38
(4):209–216.
https://doi.org/10.1016/j.
syapm.2015.02.001
17. Riojas MA, McGough KJ, Rider-Riojas CJ,
Rastogi N, Hazbon MH (2018) Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that
Mycobacterium africanum, Mycobacterium
bovis, Mycobacterium caprae, Mycobacterium
microti and Mycobacterium pinnipedii are
later heterotypic synonyms of Mycobacterium
tuberculosis. Int J Syst Evol Microbiol 68
(1):324–332.
https://doi.org/10.1099/
ijsem.0.002507
Mycobacterial ID and Characterization Using WGS
445
1. Sanger F, Air GM, Barrell BG, Brown NL,
Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977) Nucleotide
sequence of bacteriophage phi X174 DNA.
Nature 265(5596):687–695. https://doi.
org/10.1038/265687a0
2. Venter JC, Adams MD, Myers EW et al
(2001) The sequence of the human genome.
Science 291(5507):1304–1351. https://doi.
org/10.1126/science.1058040
3. International Human Genome Sequencing
Consortium (2001) Initial sequencing and
analysis of the human genome. Nature 409
(6822):860–921. https://doi.org/10.1038/
35057062
4. International Human Genome Sequencing
Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature
431(7011):931–945.
https://doi.org/10.
1038/nature03001
5. Nowoshilow S, Schloissnig S, Fei JF, Dahl A,
Pang AWC, Pippel M, Winkler S, Hastie AR,
Young G, Roscito JG, Falcon F, Knapp D,
Powell S, Cruz A, Cao H, Habermann B,
Hiller M, Tanaka EM, Myers EW (2018)
The axolotl genome and the evolution of key
tissue formation regulators. Nature 554
(7690):50–55. https://doi.org/10.1038/
nature25458
6. Wetterstrand K (2019) DNA Sequencing
Costs: Data from the NHGRI Genome
Sequencing Program (GSP). http://www.
genome.gov/sequencingcostsdata. Accessed
Feb 12, 2020
7. National Center for Biotechnology Information, U.S. National Library of Medicine
(2019) GenBank and WGS Statistics.
https://www.ncbi.nlm.nih.gov/genbank/sta
tistics/. Accessed Feb 12, 2020
8. Ko ¨ser CU, Ellington MJ, Peacock SJ (2014)
Whole-genome sequencing to control antimicrobial resistance. Trends Genet 30
(9):401–407.
https://doi.org/10.1016/j.
tig.2014.07.003
9. Magee JG, Ward AC (2015) Mycobacterium.
In: Bergey’s Manual of systematics of archaea
and bacteria. Wiley, Hoboken, New Jersey, pp
1–84.
https://doi.org/10.1002/
9781118960608.gbm00029
10. CLSI (2018) Laboratory detection and identification of mycobacteria, 2nd Ed. edn. Clinical and Laboratory Standards Institute,
Wayne, PA
11. Tortoli E, Meehan CJ, Grottola A, Fregni
Serpini G, Fabio A, Trovato A, Pecorari M,
Cirillo DM (2019) Genome-based taxonomic
revision detects a number of synonymous taxa
in the genus Mycobacterium. Infect Genet
Evol 75:103983. https://doi.org/10.1016/
j.meegid.2019.103983
12. Gupta RS, Lo B, Son J (2018) Phylogenomics
and comparative genomic studies robustly
support division of the genus Mycobacterium
into an emended genus Mycobacterium and
four novel genera. Front Microbiol 9:67.
https://doi.org/10.3389/fmicb.2018.
00067
13. Tortoli E, Brown-Elliott BA, Chalmers JD,
Cirillo DM, Daley CL, Emler S, Floto RA,
Garcia MJ, Hoefsloot W, Koh WJ, Lange C,
Loebinger M, Maurer FP, Morimoto K,
Niemann S, Richter E, Turenne CY,
Vasireddy R, Vasireddy S, Wagner D, Wallace
RJ Jr, Wengenack N, van Ingen J (2019) Same
meat, different gravy: ignore the new names
of mycobacteria. Eur Respir J 54
(1):1900795.
https://doi.org/10.1183/
13993003.00795-2019
14. Fedrizzi T, Meehan CJ, Grottola A,
Giacobazzi
E,
Fregni
Serpini
G,
Tagliazucchi S, Fabio A, Bettua C,
Bertorelli R, De Sanctis V, Rumpianesi F,
Pecorari M, Jousson O, Tortoli E, Segata N
(2017) Genomic characterization of nontuberculous mycobacteria. Sci Rep 7:45258.
https://doi.org/10.1038/srep45258
15. Tortoli E, Fedrizzi T, Meehan CJ, Trovato A,
Grottola A, Giacobazzi E, Serpini GF,
Tagliazucchi S, Fabio A, Bettua C,
Bertorelli R, Frascaro F, De Sanctis V,
Pecorari M, Jousson O, Segata N, Cirillo
DM (2017) The new phylogeny of the genus
Mycobacterium: the old and the news. Infect
Genet Evol 56:19–25. https://doi.org/10.
1016/j.meegid.2017.10.013
16. Rossello ´ -Mo ´ ra R, Amann R (2015) Past and
future species definitions for Bacteria and
Archaea.
Syst
Appl
Microbiol
38
(4):209–216.
https://doi.org/10.1016/j.
syapm.2015.02.001
17. Riojas MA, McGough KJ, Rider-Riojas CJ,
Rastogi N, Hazbon MH (2018) Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that
Mycobacterium africanum, Mycobacterium
bovis, Mycobacterium caprae, Mycobacterium
microti and Mycobacterium pinnipedii are
later heterotypic synonyms of Mycobacterium
tuberculosis. Int J Syst Evol Microbiol 68
(1):324–332.
https://doi.org/10.1099/
ijsem.0.002507
Mycobacterial ID and Characterization Using WGS
445