FB (2014) Multilocus sequence typing of
Mycobacterium xenopi. J Clin Microbiol 52
(11):3973–3977. https://doi.org/10.1128/
JCM.01601-14
81. Kolb J, Hillemann D, Mobius P, Reetz J,
Lahiri A, Lewin A, Rusch-Gerdes S, Richter
E (2014) Genetic characterization of German
Mycobacterium avium strains isolated from
different hosts and specimens by multilocus
sequence typing. International journal of
medical microbiology : IJMM 304
(8):941–948.
https://doi.org/10.1016/j.
ijmm.2014.06.001
82. Cheng A, Sun HY, Tsai YT, Chang SY, Wu
UI, Hsueh PR, Sheng WH, Chen YC, Chang
SC (2019) Comparing the Utilities of Different Multilocus Sequence Typing Schemes for
identifying outbreak strains of Mycobacterium
abscessus subsp. massiliense. J Clin Microbiol
58(1).
https://doi.org/10.1128/JCM.
01304-19
83. Macheras E, Konjek J, Roux AL, Thiberge
JM, Bastian S, Leao SC, Palaci M, SivadonTardy V, Gutierrez C, Richter E, RuschGerdes S, Pfyffer GE, Bodmer T, Jarlier V,
Cambau E, Brisse S, Caro V, Rastogi N, Gaillard JL, Heym B (2014) Multilocus sequence
typing scheme for the Mycobacterium abscessus
complex. Res Microbiol 165(2):82–90.
https://doi.org/10.1016/j.resmic.2013.12.
003
84. Wuzinski M, Bak AK, Petkau A, WH BD,
Soualhine H, Sharma MK (2019) A multilocus sequence typing scheme for Mycobacterium abscessus complex (MAB-multilocus
sequence typing) using whole-genome
sequencing data. Int J Mycobacteriol 8
(3):273–280.
https://doi.org/10.4103/
ijmy.ijmy_106_19
85. Hayashi Sant’Anna F, Bach E, Porto RZ,
Guella F, Hayashi Sant’Anna E, Passaglia
LMP (2019) Genomic metrics made easy:
what to do and where to go in the new era
of bacterial taxonomy. Crit Rev Microbiol 45
(2):182–200.
https://doi.org/10.1080/
1040841X.2019.1569587
86. Wayne LG, Moore WEC, Stackebrandt E,
Kandler O, Colwell RR, Krichevsky MI, Tru ¨per HG, Murray RGE, Grimont PAD, Brenner DJ, Starr MP, Moore LH (1987) Report
of the ad hoc committee on reconciliation of
approaches to bacterial systematics. Int J Syst
Evol Microbiol 37(4):463–464. https://doi.
org/10.1099/00207713-37-4-463
87. Auch AF, von Jan M, Klenk HP, Go ¨ker M
(2010) Digital DNA-DNA hybridization for
microbial species delineation by means of
genome-to-genome sequence comparison.
Stand Genomic Sci 2(1):117–134. https://
doi.org/10.4056/sigs.531120
88. Chun J, Oren A, Ventosa A, Christensen H,
Arahal DR, da Costa MS, Rooney AP, Yi H,
Xu XW, De Meyer S, Trujillo ME (2018)
Proposed minimal standards for the use of
genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68
(1):461–466.
https://doi.org/10.1099/
ijsem.0.002516
89. Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the
Bacteria and Archaea. Int J Syst Evol Microbiol 64(Pt 2):316–324. https://doi.org/10.
1099/ijs.0.054171-0
90. Goris J, Konstantinidis KT, Klappenbach JA,
Coenye T, Vandamme P, Tiedje JM (2007)
DNA-DNA hybridization values and their
relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57
(Pt 1):81–91. https://doi.org/10.1099/ijs.
0.64483-0
91. Hugenholtz P, Skarshewski A, Parks DH
(2016) Genome-based microbial taxonomy
coming of age. Cold Spring Harb Perspect
Biol 8(6):a018085. https://doi.org/10.
1101/cshperspect.a018085
92. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides
NC, Pati A (2015) Microbial species delineation using whole genome sequences. Nucleic
Acids Res 43(14):6761–6771. https://doi.
org/10.1093/nar/gkv657
93. Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A
102(7):2567–2572.
https://doi.org/10.
1073/pnas.0409727102
94. Richter M, Rossello ´-Mo ´ra R (2009) Shifting
the genomic gold standard for the prokaryotic
species definition. Proc Natl Acad Sci U S A
106(45):19126–19131. https://doi.org/10.
1073/pnas.0906412106
95. Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes
reveals clear species boundaries. Nat Commun 9(1):5114. https://doi.org/10.1038/
s41467-018-07641-9
96. Lee I, Kim YO, Park SC, Chun J (2015)
OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66
(2):1100–1103. https://doi.org/10.1099/
ijsem.0.000760
97. Meier-Kolthoff JP, Auch AF, Klenk HP,
Go ¨ker M (2013) Genome sequence-based
Mycobacterial ID and Characterization Using WGS
449
Mycobacterium xenopi. J Clin Microbiol 52
(11):3973–3977. https://doi.org/10.1128/
JCM.01601-14
81. Kolb J, Hillemann D, Mobius P, Reetz J,
Lahiri A, Lewin A, Rusch-Gerdes S, Richter
E (2014) Genetic characterization of German
Mycobacterium avium strains isolated from
different hosts and specimens by multilocus
sequence typing. International journal of
medical microbiology : IJMM 304
(8):941–948.
https://doi.org/10.1016/j.
ijmm.2014.06.001
82. Cheng A, Sun HY, Tsai YT, Chang SY, Wu
UI, Hsueh PR, Sheng WH, Chen YC, Chang
SC (2019) Comparing the Utilities of Different Multilocus Sequence Typing Schemes for
identifying outbreak strains of Mycobacterium
abscessus subsp. massiliense. J Clin Microbiol
58(1).
https://doi.org/10.1128/JCM.
01304-19
83. Macheras E, Konjek J, Roux AL, Thiberge
JM, Bastian S, Leao SC, Palaci M, SivadonTardy V, Gutierrez C, Richter E, RuschGerdes S, Pfyffer GE, Bodmer T, Jarlier V,
Cambau E, Brisse S, Caro V, Rastogi N, Gaillard JL, Heym B (2014) Multilocus sequence
typing scheme for the Mycobacterium abscessus
complex. Res Microbiol 165(2):82–90.
https://doi.org/10.1016/j.resmic.2013.12.
003
84. Wuzinski M, Bak AK, Petkau A, WH BD,
Soualhine H, Sharma MK (2019) A multilocus sequence typing scheme for Mycobacterium abscessus complex (MAB-multilocus
sequence typing) using whole-genome
sequencing data. Int J Mycobacteriol 8
(3):273–280.
https://doi.org/10.4103/
ijmy.ijmy_106_19
85. Hayashi Sant’Anna F, Bach E, Porto RZ,
Guella F, Hayashi Sant’Anna E, Passaglia
LMP (2019) Genomic metrics made easy:
what to do and where to go in the new era
of bacterial taxonomy. Crit Rev Microbiol 45
(2):182–200.
https://doi.org/10.1080/
1040841X.2019.1569587
86. Wayne LG, Moore WEC, Stackebrandt E,
Kandler O, Colwell RR, Krichevsky MI, Tru ¨per HG, Murray RGE, Grimont PAD, Brenner DJ, Starr MP, Moore LH (1987) Report
of the ad hoc committee on reconciliation of
approaches to bacterial systematics. Int J Syst
Evol Microbiol 37(4):463–464. https://doi.
org/10.1099/00207713-37-4-463
87. Auch AF, von Jan M, Klenk HP, Go ¨ker M
(2010) Digital DNA-DNA hybridization for
microbial species delineation by means of
genome-to-genome sequence comparison.
Stand Genomic Sci 2(1):117–134. https://
doi.org/10.4056/sigs.531120
88. Chun J, Oren A, Ventosa A, Christensen H,
Arahal DR, da Costa MS, Rooney AP, Yi H,
Xu XW, De Meyer S, Trujillo ME (2018)
Proposed minimal standards for the use of
genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68
(1):461–466.
https://doi.org/10.1099/
ijsem.0.002516
89. Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the
Bacteria and Archaea. Int J Syst Evol Microbiol 64(Pt 2):316–324. https://doi.org/10.
1099/ijs.0.054171-0
90. Goris J, Konstantinidis KT, Klappenbach JA,
Coenye T, Vandamme P, Tiedje JM (2007)
DNA-DNA hybridization values and their
relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57
(Pt 1):81–91. https://doi.org/10.1099/ijs.
0.64483-0
91. Hugenholtz P, Skarshewski A, Parks DH
(2016) Genome-based microbial taxonomy
coming of age. Cold Spring Harb Perspect
Biol 8(6):a018085. https://doi.org/10.
1101/cshperspect.a018085
92. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides
NC, Pati A (2015) Microbial species delineation using whole genome sequences. Nucleic
Acids Res 43(14):6761–6771. https://doi.
org/10.1093/nar/gkv657
93. Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A
102(7):2567–2572.
https://doi.org/10.
1073/pnas.0409727102
94. Richter M, Rossello ´-Mo ´ra R (2009) Shifting
the genomic gold standard for the prokaryotic
species definition. Proc Natl Acad Sci U S A
106(45):19126–19131. https://doi.org/10.
1073/pnas.0906412106
95. Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes
reveals clear species boundaries. Nat Commun 9(1):5114. https://doi.org/10.1038/
s41467-018-07641-9
96. Lee I, Kim YO, Park SC, Chun J (2015)
OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66
(2):1100–1103. https://doi.org/10.1099/
ijsem.0.000760
97. Meier-Kolthoff JP, Auch AF, Klenk HP,
Go ¨ker M (2013) Genome sequence-based
Mycobacterial ID and Characterization Using WGS
449