characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol
60(Pt 1):249–266. https://doi.org/10.
1099/ijs.0.016949-0
63. Avery OT, Macleod CM, McCarty M (1944)
Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by
a Desoxyribonucleic [sic] acid fraction isolated
from pneumococcus type III. J Exp Med 79
(2):137–158. https://doi.org/10.1084/jem.
79.2.137
64. Agaisse H, Gominet M, Økstad OA, Kolstø
A-B, Lereclus D (1999) PlcR is a pleiotropic
regulator of extracellular virulence factor gene
expression in Bacillus thuringiensis. Mol
Microbiol 32(5):1043–1053. https://doi.
org/10.1046/j.1365-2958.1999.01419.x
65. Slamti L, Perchat S, Gominet M, VilasBoas G, Fouet A, Mock M, Sanchis V,
Chaufaux J, Gohar M, Lereclus D (2004)
Distinct mutations in PlcR explain why some
strains of the Bacillus cereus group are nonhemolytic. J Bacteriol 186(11):3531–3538.
https://doi.org/10.1128/JB.186.11.35313538.2004
66. Sastalla I, Maltese LM, Pomerantseva OM,
Pomerantsev AP, Keane-Myers A, Leppla SH
(2010) Activation of the latent PlcR regulon
in Bacillus anthracis. Microbiology 156
(Pt 10):2982–2993. https://doi.org/10.
1099/mic.0.041418-0
67. Salamitou S, Ramisse F, Brehelin M,
Bourguet D, Gilois N, Gominet M,
Hernandez E, Lereclus D (2000) The plcR
regulon is involved in the opportunistic properties of Bacillus thuringiensis and Bacillus
cereus in mice and insects. Microbiology 146
(Pt 11):2825–2832. https://doi.org/10.
1099/00221287-146-11-2825
68. Callegan MC, Kane ST, Cochran DC, Gilmore MS, Gominet M, Lereclus D (2003)
Relationship of plcR-regulated factors to
Bacillus endophthalmitis virulence. Infect
Immun 71(6):3116–3124. https://doi.org/
10.1128/iai.71.6.3116-3124.2003
69. Roth A, Fischer M, Hamid ME, Michalke S,
Ludwig W, Mauch H (1998) Differentiation
of phylogenetically related slowly growing
mycobacteria based on 16S-23S rRNA gene
internal transcribed spacer sequences. J Clin
Microbiol 36(1):139–147
70. Tortoli E (2003) Impact of genotypic studies
on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev 16
(2):319–354.
https://doi.org/10.1128/
cmr.16.2.319-354.2003
71. Clarridge JE 3rd (2004) Impact of 16S rRNA
gene sequence analysis for identification of
bacteria on clinical microbiology and infectious diseases. Clinical Microbiol Rev 17
(4):840–862, table of contents. https://doi.
org/10.1128/CMR.17.4.840-862.2004
72. Dobner P, Feldmann K, Rifai M, Lo ¨scher T,
Rinder H (1996) Rapid identification of
mycobacterial species by PCR amplification
of hypervariable 16S rRNA gene promoter
region. J Clin Microbiol 34(4):866
73. Kim SH, Shin JH (2018) Identification of
nontuberculous mycobacteria using multilocous sequence analysis of 16S rRNA, hsp65,
and rpoB. J Clin Lab Anal 32(1). https://doi.
org/10.1002/jcla.22184
74. Adekambi T, Drancourt M (2004) Dissection
of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S
rRNA, hsp65, sodA, recA and rpoB gene
sequencing. Int J Syst Evol Microbiol 54
(Pt 6):2095–2105. https://doi.org/10.
1099/ijs.0.63094-0
75. Gevers D, Cohan FM, Lawrence JG, Spratt
BG, Coenye T, Feil EJ, Stackebrandt E, Van
de Peer Y, Vandamme P, Thompson FL,
Swings J (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3
(9):733–739.
https://doi.org/10.1038/
nrmicro1236
76. Glaeser SP, Kampfer P (2015) Multilocus
sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 38(4):237–245.
https://doi.org/10.1016/j.syapm.2015.03.
007
77. Saha MS, Pal S, Sarkar I, Roy A, Das Mohapatra PK, Sen A (2019) Comparative genomics
of Mycobacterium reveals evolutionary trends
of M. avium complex. Genomics 111
(3):426–435.
https://doi.org/10.1016/j.
ygeno.2018.02.019
78. Lu B, Dong HY, Zhao XQ, Liu ZG, Liu HC,
Zhang YY, Jiang Y, Wan KL (2012) A new
multilocus sequence analysis scheme for Mycobacterium tuberculosis. Biomed Environ Sci
25(6):620–629. https://doi.org/10.3967/
0895-3988.2012.06.003
79. Tan JL, Khang TF, Ngeow YF, Choo SW
(2013) A phylogenomic approach to bacterial
subspecies classification: proof of concept in
Mycobacterium abscessus. BMC Genomics
14:879.
https://doi.org/10.1186/14712164-14-879
80. Alexander DC, Marras TK, Ma JH, Mirza S,
Liu D, Kus JV, Soualhine H, Escuyer V,
Warshauer D, Brode SK, Farrell DJ, Jamieson
448
Marco A. Riojas et al.
60(Pt 1):249–266. https://doi.org/10.
1099/ijs.0.016949-0
63. Avery OT, Macleod CM, McCarty M (1944)
Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by
a Desoxyribonucleic [sic] acid fraction isolated
from pneumococcus type III. J Exp Med 79
(2):137–158. https://doi.org/10.1084/jem.
79.2.137
64. Agaisse H, Gominet M, Økstad OA, Kolstø
A-B, Lereclus D (1999) PlcR is a pleiotropic
regulator of extracellular virulence factor gene
expression in Bacillus thuringiensis. Mol
Microbiol 32(5):1043–1053. https://doi.
org/10.1046/j.1365-2958.1999.01419.x
65. Slamti L, Perchat S, Gominet M, VilasBoas G, Fouet A, Mock M, Sanchis V,
Chaufaux J, Gohar M, Lereclus D (2004)
Distinct mutations in PlcR explain why some
strains of the Bacillus cereus group are nonhemolytic. J Bacteriol 186(11):3531–3538.
https://doi.org/10.1128/JB.186.11.35313538.2004
66. Sastalla I, Maltese LM, Pomerantseva OM,
Pomerantsev AP, Keane-Myers A, Leppla SH
(2010) Activation of the latent PlcR regulon
in Bacillus anthracis. Microbiology 156
(Pt 10):2982–2993. https://doi.org/10.
1099/mic.0.041418-0
67. Salamitou S, Ramisse F, Brehelin M,
Bourguet D, Gilois N, Gominet M,
Hernandez E, Lereclus D (2000) The plcR
regulon is involved in the opportunistic properties of Bacillus thuringiensis and Bacillus
cereus in mice and insects. Microbiology 146
(Pt 11):2825–2832. https://doi.org/10.
1099/00221287-146-11-2825
68. Callegan MC, Kane ST, Cochran DC, Gilmore MS, Gominet M, Lereclus D (2003)
Relationship of plcR-regulated factors to
Bacillus endophthalmitis virulence. Infect
Immun 71(6):3116–3124. https://doi.org/
10.1128/iai.71.6.3116-3124.2003
69. Roth A, Fischer M, Hamid ME, Michalke S,
Ludwig W, Mauch H (1998) Differentiation
of phylogenetically related slowly growing
mycobacteria based on 16S-23S rRNA gene
internal transcribed spacer sequences. J Clin
Microbiol 36(1):139–147
70. Tortoli E (2003) Impact of genotypic studies
on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev 16
(2):319–354.
https://doi.org/10.1128/
cmr.16.2.319-354.2003
71. Clarridge JE 3rd (2004) Impact of 16S rRNA
gene sequence analysis for identification of
bacteria on clinical microbiology and infectious diseases. Clinical Microbiol Rev 17
(4):840–862, table of contents. https://doi.
org/10.1128/CMR.17.4.840-862.2004
72. Dobner P, Feldmann K, Rifai M, Lo ¨scher T,
Rinder H (1996) Rapid identification of
mycobacterial species by PCR amplification
of hypervariable 16S rRNA gene promoter
region. J Clin Microbiol 34(4):866
73. Kim SH, Shin JH (2018) Identification of
nontuberculous mycobacteria using multilocous sequence analysis of 16S rRNA, hsp65,
and rpoB. J Clin Lab Anal 32(1). https://doi.
org/10.1002/jcla.22184
74. Adekambi T, Drancourt M (2004) Dissection
of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S
rRNA, hsp65, sodA, recA and rpoB gene
sequencing. Int J Syst Evol Microbiol 54
(Pt 6):2095–2105. https://doi.org/10.
1099/ijs.0.63094-0
75. Gevers D, Cohan FM, Lawrence JG, Spratt
BG, Coenye T, Feil EJ, Stackebrandt E, Van
de Peer Y, Vandamme P, Thompson FL,
Swings J (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3
(9):733–739.
https://doi.org/10.1038/
nrmicro1236
76. Glaeser SP, Kampfer P (2015) Multilocus
sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 38(4):237–245.
https://doi.org/10.1016/j.syapm.2015.03.
007
77. Saha MS, Pal S, Sarkar I, Roy A, Das Mohapatra PK, Sen A (2019) Comparative genomics
of Mycobacterium reveals evolutionary trends
of M. avium complex. Genomics 111
(3):426–435.
https://doi.org/10.1016/j.
ygeno.2018.02.019
78. Lu B, Dong HY, Zhao XQ, Liu ZG, Liu HC,
Zhang YY, Jiang Y, Wan KL (2012) A new
multilocus sequence analysis scheme for Mycobacterium tuberculosis. Biomed Environ Sci
25(6):620–629. https://doi.org/10.3967/
0895-3988.2012.06.003
79. Tan JL, Khang TF, Ngeow YF, Choo SW
(2013) A phylogenomic approach to bacterial
subspecies classification: proof of concept in
Mycobacterium abscessus. BMC Genomics
14:879.
https://doi.org/10.1186/14712164-14-879
80. Alexander DC, Marras TK, Ma JH, Mirza S,
Liu D, Kus JV, Soualhine H, Escuyer V,
Warshauer D, Brode SK, Farrell DJ, Jamieson
448
Marco A. Riojas et al.