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Brzostek A, Zaczek A, Dziadek J (2016)
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Gutierrez MC, Fauville M, Niemann S,
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D (2006) Proposal for standardization of
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org/10.1128/JCM.01392-06
145. Couvin D, Zozio T, Rastogi N (2017) SpolSimilaritySearch - a web tool to compare and
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146. Mokrousov I, Rastogi N (2015) Spacer-based
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(2019) Macro-geographical specificities of
the prevailing tuberculosis epidemic as seen
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doi.org/10.1016/j.meegid.2018.12.030
148. Xia E, Teo YY, Ong RT (2016) SpoTyping:
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s13073-016-0270-7
149. Sekyere JO, Asante J (2018) Emerging
mechanisms of antimicrobial resistance in
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150. Ferri M, Ranucci E, Romagnoli P, Giaccone V
(2017) Antimicrobial resistance: a global
emerging threat to public health systems.
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151. Nasiri MJ, Haeili M, Ghazi M, Goudarzi H,
Pormohammad A, Imani Fooladi AA, Feizabadi MM (2017) New insights in to the
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mechanisms in mycobacteria. Front Microbiol 8:681. https://doi.org/10.3389/fmicb.
2017.00681
152. Smith SE, Showers-Corneli P, Dardenne CN,
Harpending HH, Martin DP, Beiko RG
(2012) Comparative genomic and phylogenetic approaches to characterize the role of
genetic recombination in mycobacterial evolution. PLoS One 7(11):e50070. https://doi.
org/10.1371/journal.pone.0050070
153. Adams KN, Takaki K, Connolly LE,
Wiedenhoft H, Winglee K, Humbert O,
Edelstein PH, Cosma CL, Ramakrishnan L
(2011) Drug tolerance in replicating mycobacteria mediated by a macrophage-induced
efflux mechanism. Cell 145(1):39–53.
https://doi.org/10.1016/j.cell.2011.02.
022
154. Louw GE, Warren RM, Gey van Pittius NC,
McEvoy CR, Van Helden PD, Victor TC
(2009) A balancing act: efflux/influx in
mycobacterial drug resistance. Antimicrob
Agents
Chemother
53(8):3181–3189.
https://doi.org/10.1128/AAC.01577-08
155. Stephan J, Mailaender C, Etienne G, Daffe M,
Niederweis M (2004) Multidrug resistance of
a porin deletion mutant of Mycobacterium
smegmatis. Antimicrob Agents Chemother
48(11):4163–4170.
https://doi.org/10.
1128/AAC.48.11.4163-4170.2004
156. Vianna JS, Machado D, Ramis IB, Silva FP,
Bierhals DV, Abril MA, von Groll A, Ramos
DF, Lourenco MCS, Viveiros M, da Silva
PEA (2019) The contribution of efflux
pumps in Mycobacterium abscessus complex
resistance to clarithromycin. Antibiotics
(Basel) 8(3):153. https://doi.org/10.3390/
antibiotics8030153
157. Kapur V, Li LL, Iordanescu S, Hamrick MR,
Wanger A, Kreiswirth BN, Musser JM (1994)
Characterization by automated DNA
452
Marco A. Riojas et al.
rapid annotations using subsystems technology. BMC Genomics 9(1):75
140. Johnson M, Zaretskaya I, Raytselis Y,
Merezhuk Y, McGinnis S, Madden TL
(2008) NCBI BLAST: a better web interface.
Nucleic Acids Res 36(suppl_2):W5–W9
141. Kanehisa M, Furumichi M, Tanabe M, Sato Y,
Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and
drugs. Nucleic Acids Res 45(D1):
D353–D361
142. Federhen S (2012) The NCBI taxonomy
database. Nucleic Acids Res 40(D1):
D136–D143
143. Jagielski T, Minias A, van Ingen J, Rastogi N,
Brzostek A, Zaczek A, Dziadek J (2016)
Methodological and clinical aspects of the
molecular epidemiology of Mycobacterium
tuberculosis and other mycobacteria. Clin
Microbiol Rev 29(2):239–290. https://doi.
org/10.1128/CMR.00055-15
144. Supply P, Allix C, Lesjean S, CardosoOelemann M, Rusch-Gerdes S, Willery E,
Savine E, de Haas P, van Deutekom H,
Roring S, Bifani P, Kurepina N,
Kreiswirth B, Sola C, Rastogi N, Vatin V,
Gutierrez MC, Fauville M, Niemann S,
Skuce R, Kremer K, Locht C, van Soolingen
D (2006) Proposal for standardization of
optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin
Microbiol 44(12):4498–4510. https://doi.
org/10.1128/JCM.01392-06
145. Couvin D, Zozio T, Rastogi N (2017) SpolSimilaritySearch - a web tool to compare and
search similarities between spoligotypes of
Mycobacterium tuberculosis complex. Tuberculosis 105:49–52. https://doi.org/10.
1016/j.tube.2017.04.007
146. Mokrousov I, Rastogi N (2015) Spacer-based
macroarrays for CRISPR genotyping. In:
Lundgren M, Charpentier E, Fineran PC
(eds) CRISPR: methods and protocols.
Springer New York, New York, NY, pp
111–131. https://doi.org/10.1007/978-14939-2687-9_7
147. Couvin D, David A, Zozio T, Rastogi N
(2019) Macro-geographical specificities of
the prevailing tuberculosis epidemic as seen
through SITVIT2, an updated version of the
Mycobacterium tuberculosis genotyping database. Infect Genet Evol 72:31–43. https://
doi.org/10.1016/j.meegid.2018.12.030
148. Xia E, Teo YY, Ong RT (2016) SpoTyping:
fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Genome
Med 8(1):19. https://doi.org/10.1186/
s13073-016-0270-7
149. Sekyere JO, Asante J (2018) Emerging
mechanisms of antimicrobial resistance in
bacteria and fungi: advances in the era of
genomics. Future Microbiol 13:241–262.
https://doi.org/10.2217/fmb-2017-0172
150. Ferri M, Ranucci E, Romagnoli P, Giaccone V
(2017) Antimicrobial resistance: a global
emerging threat to public health systems.
Crit Rev Food Sci Nutr 57(13):2857–2876.
https://doi.org/10.1080/10408398.2015.
1077192
151. Nasiri MJ, Haeili M, Ghazi M, Goudarzi H,
Pormohammad A, Imani Fooladi AA, Feizabadi MM (2017) New insights in to the
intrinsic and acquired drug resistance
mechanisms in mycobacteria. Front Microbiol 8:681. https://doi.org/10.3389/fmicb.
2017.00681
152. Smith SE, Showers-Corneli P, Dardenne CN,
Harpending HH, Martin DP, Beiko RG
(2012) Comparative genomic and phylogenetic approaches to characterize the role of
genetic recombination in mycobacterial evolution. PLoS One 7(11):e50070. https://doi.
org/10.1371/journal.pone.0050070
153. Adams KN, Takaki K, Connolly LE,
Wiedenhoft H, Winglee K, Humbert O,
Edelstein PH, Cosma CL, Ramakrishnan L
(2011) Drug tolerance in replicating mycobacteria mediated by a macrophage-induced
efflux mechanism. Cell 145(1):39–53.
https://doi.org/10.1016/j.cell.2011.02.
022
154. Louw GE, Warren RM, Gey van Pittius NC,
McEvoy CR, Van Helden PD, Victor TC
(2009) A balancing act: efflux/influx in
mycobacterial drug resistance. Antimicrob
Agents
Chemother
53(8):3181–3189.
https://doi.org/10.1128/AAC.01577-08
155. Stephan J, Mailaender C, Etienne G, Daffe M,
Niederweis M (2004) Multidrug resistance of
a porin deletion mutant of Mycobacterium
smegmatis. Antimicrob Agents Chemother
48(11):4163–4170.
https://doi.org/10.
1128/AAC.48.11.4163-4170.2004
156. Vianna JS, Machado D, Ramis IB, Silva FP,
Bierhals DV, Abril MA, von Groll A, Ramos
DF, Lourenco MCS, Viveiros M, da Silva
PEA (2019) The contribution of efflux
pumps in Mycobacterium abscessus complex
resistance to clarithromycin. Antibiotics
(Basel) 8(3):153. https://doi.org/10.3390/
antibiotics8030153
157. Kapur V, Li LL, Iordanescu S, Hamrick MR,
Wanger A, Kreiswirth BN, Musser JM (1994)
Characterization by automated DNA
452
Marco A. Riojas et al.