125
Kaldalu N, Mei R, Lewis K (2004) Killing by ampicillin and ofloxacin induces overlapping changes
in Escherichia coli transcription profile. Antimicrob Agents Chemother 48(8):3213–3213.
https://doi.org/10.1128/Aac.48.8.3213.2004
Kaspy I, Rotem E, Weiss N, Ronin I, Balaban NQ, Glaser G (2013) HipA-mediated antibiotic
persistence via phosphorylation of the glutamyl-tRNA-synthetase. Nat Commun 4. https://doi.
org/10.1038/ncomms4001
Keren I, Kaldalu N, Spoering A, Wang YP, Lewis K (2004a) Persister cells and tolerance to antimicrobials. FEMS Microbiol Lett 230(1):13–18. https://doi.org/10.1016/S0378-1097(03)00856-5
Keren I, Shah D, Spoering A, Kaldalu N, Lewis K (2004b) Specialized persister cells and the
mechanism of multidrug tolerance in Escherichia coli. J Bacteriol 186(24):8172–8180. https://
doi.org/10.1128/Jb.186.24.8172-8180.2004
Keren I, Minami S, Rubin E, Lewis K (2011) Characterization and transcriptome analysis of
Mycobacterium tuberculosis persisters. MBio 2(3):e00100–e00111. https://doi.org/10.1128/
mBio.00100-11
Keren I, Mulcahy LR, Lewis K (2012) Persister eradication: lessons from the world of natural
products methods in enzymology, vol 517. Elsevier, pp 387–406
Khakimova M, Ahlgren HG, Harrison JJ, English AM, Nguyen D (2013) The stringent response
controls catalases in Pseudomonas aeruginosa and is required for hydrogen peroxide and antibiotic tolerance. J Bacteriol 195(9):2011–2020. https://doi.org/10.1128/Jb.02061-12
LaFleur MD, Kumamoto CA, Lewis K (2006) Candida albicans biofilms produce antifungaltolerant persister cells. Antimicrob Agents Chemother 50(11):3839–3846. https://doi.
org/10.1128/AAC.00684-06
LaFleur MD, Qi QG, Lewis K (2010) Patients with long-term oral carriage harbor high- persister
mutants of Candida albicans. Antimicrob Agents Chemother 54(1):39–44. https://doi.
org/10.1128/AAC.00860-09
Lechner S, Prax M, Lange B, Huber C, Eisenreich W, Herbig A, Nieselt K, Bertram R (2014)
Metabolic and transcriptional activities of Staphylococcus aureus challenged with high-doses of
daptomycin. Int J Med Microbiol 304(8):931–940. https://doi.org/10.1016/j.ijmm.2014.05.008
Lee HH, Ostrov N, Wong BG, Gold MA, Khalil AS, Church GM (2019a) Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nat Microbiol
4(7):1105–1113. https://doi.org/10.1038/s41564-019-0423-8
Lee JJ, Lee SK, Song N, Nathan TO, Swarts BM, Eum SY, Ehrt S, Cho SN, Eoh H (2019b)
Transient drug-tolerance and permanent drug-resistance rely on the trehalose-catalytic shift in
Mycobacterium tuberculosis. Nat Commun 10. https://doi.org/10.1038/s41467-019-10975-7
Leung V, Levesque CM (2012) A stress-inducible quorum-sensing peptide mediates the formation
of persister cells with noninherited multidrug tolerance. J Bacteriol 194(9):2265–2274. https://
doi.org/10.1128/Jb.06707-11
Leung V, Ajdic D, Koyanagi S, Levesque CM (2015) The formation of streptococcus mutans persisters induced by the quorum-sensing peptide pheromone is affected by the LexA regulator. J
Bacteriol 197(6):1083–1094. https://doi.org/10.1128/Jb.02496-14
Levin BR, Rozen DE (2006) Non-inherited antibiotic resistance. Nat Rev Microbiol 4(7):556–562.
https://doi.org/10.1038/nrmicro1445
Levin-Reisman I, Ronin I, Gefen O, Braniss I, Shoresh N, Balaban NQ (2017) Antibiotic tolerance
facilitates the evolution of resistance. Science 355(6327):826–830. https://doi.org/10.1126/science.aaj2191
Lewis K (2007) Persister cells, dormancy and infectious disease. Nat Rev Microbiol 5(1):48–56.
https://doi.org/10.1038/nrmicro1557
Lewis K (2010) Persister cells. Annu Rev Microbiol 64(1):357–372. https://doi.org/10.1146/
annurev.micro.112408.134306
Li YF, Zhang Y (2007) PhoU is a persistence switch involved in persister formation and tolerance to multiple antibiotics and stresses in Escherichia coli. Antimicrob Agents Chemother
51(6):2092–2099. https://doi.org/10.1128/Aac.00052-07
5 Molecular and Systems Biology Approaches for Analyzing Drug-Tolerant Bacterial…
Kaldalu N, Mei R, Lewis K (2004) Killing by ampicillin and ofloxacin induces overlapping changes
in Escherichia coli transcription profile. Antimicrob Agents Chemother 48(8):3213–3213.
https://doi.org/10.1128/Aac.48.8.3213.2004
Kaspy I, Rotem E, Weiss N, Ronin I, Balaban NQ, Glaser G (2013) HipA-mediated antibiotic
persistence via phosphorylation of the glutamyl-tRNA-synthetase. Nat Commun 4. https://doi.
org/10.1038/ncomms4001
Keren I, Kaldalu N, Spoering A, Wang YP, Lewis K (2004a) Persister cells and tolerance to antimicrobials. FEMS Microbiol Lett 230(1):13–18. https://doi.org/10.1016/S0378-1097(03)00856-5
Keren I, Shah D, Spoering A, Kaldalu N, Lewis K (2004b) Specialized persister cells and the
mechanism of multidrug tolerance in Escherichia coli. J Bacteriol 186(24):8172–8180. https://
doi.org/10.1128/Jb.186.24.8172-8180.2004
Keren I, Minami S, Rubin E, Lewis K (2011) Characterization and transcriptome analysis of
Mycobacterium tuberculosis persisters. MBio 2(3):e00100–e00111. https://doi.org/10.1128/
mBio.00100-11
Keren I, Mulcahy LR, Lewis K (2012) Persister eradication: lessons from the world of natural
products methods in enzymology, vol 517. Elsevier, pp 387–406
Khakimova M, Ahlgren HG, Harrison JJ, English AM, Nguyen D (2013) The stringent response
controls catalases in Pseudomonas aeruginosa and is required for hydrogen peroxide and antibiotic tolerance. J Bacteriol 195(9):2011–2020. https://doi.org/10.1128/Jb.02061-12
LaFleur MD, Kumamoto CA, Lewis K (2006) Candida albicans biofilms produce antifungaltolerant persister cells. Antimicrob Agents Chemother 50(11):3839–3846. https://doi.
org/10.1128/AAC.00684-06
LaFleur MD, Qi QG, Lewis K (2010) Patients with long-term oral carriage harbor high- persister
mutants of Candida albicans. Antimicrob Agents Chemother 54(1):39–44. https://doi.
org/10.1128/AAC.00860-09
Lechner S, Prax M, Lange B, Huber C, Eisenreich W, Herbig A, Nieselt K, Bertram R (2014)
Metabolic and transcriptional activities of Staphylococcus aureus challenged with high-doses of
daptomycin. Int J Med Microbiol 304(8):931–940. https://doi.org/10.1016/j.ijmm.2014.05.008
Lee HH, Ostrov N, Wong BG, Gold MA, Khalil AS, Church GM (2019a) Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nat Microbiol
4(7):1105–1113. https://doi.org/10.1038/s41564-019-0423-8
Lee JJ, Lee SK, Song N, Nathan TO, Swarts BM, Eum SY, Ehrt S, Cho SN, Eoh H (2019b)
Transient drug-tolerance and permanent drug-resistance rely on the trehalose-catalytic shift in
Mycobacterium tuberculosis. Nat Commun 10. https://doi.org/10.1038/s41467-019-10975-7
Leung V, Levesque CM (2012) A stress-inducible quorum-sensing peptide mediates the formation
of persister cells with noninherited multidrug tolerance. J Bacteriol 194(9):2265–2274. https://
doi.org/10.1128/Jb.06707-11
Leung V, Ajdic D, Koyanagi S, Levesque CM (2015) The formation of streptococcus mutans persisters induced by the quorum-sensing peptide pheromone is affected by the LexA regulator. J
Bacteriol 197(6):1083–1094. https://doi.org/10.1128/Jb.02496-14
Levin BR, Rozen DE (2006) Non-inherited antibiotic resistance. Nat Rev Microbiol 4(7):556–562.
https://doi.org/10.1038/nrmicro1445
Levin-Reisman I, Ronin I, Gefen O, Braniss I, Shoresh N, Balaban NQ (2017) Antibiotic tolerance
facilitates the evolution of resistance. Science 355(6327):826–830. https://doi.org/10.1126/science.aaj2191
Lewis K (2007) Persister cells, dormancy and infectious disease. Nat Rev Microbiol 5(1):48–56.
https://doi.org/10.1038/nrmicro1557
Lewis K (2010) Persister cells. Annu Rev Microbiol 64(1):357–372. https://doi.org/10.1146/
annurev.micro.112408.134306
Li YF, Zhang Y (2007) PhoU is a persistence switch involved in persister formation and tolerance to multiple antibiotics and stresses in Escherichia coli. Antimicrob Agents Chemother
51(6):2092–2099. https://doi.org/10.1128/Aac.00052-07
5 Molecular and Systems Biology Approaches for Analyzing Drug-Tolerant Bacterial…