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References
Albrethsen J, Agner J, Piersma SR, Hojrup P, Pham TV, Weldingh K, Jimenez CR, Andersen P,
Rosenkrands I (2013) Proteomic profiling of Mycobacterium tuberculosis identifies nutrientstarvation- responsive toxin-antitoxin systems. Mol Cell Proteomics 12(5):1180–1191. https://
doi.org/10.1074/mcp.M112.018846
Aldridge BB, Fernandez-Suarez M, Heller D, Ambravaneswaran V, Irimia D, Toner M, Fortune
SM (2012) Asymmetry and aging of mycobacterial cells lead to variable growth and antibiotic
susceptibility. Science 335(6064):100–104. https://doi.org/10.1126/science.1216166
Alkasir R, Ma YA, Liu F, Li J, Lv N, Xue Y, Hu YF, Zhu BL (2018) Characterization and
transcriptome analysis of Acinetobacter baumannii persister cells. Microb Drug Resist
24(10):1466–1474. https://doi.org/10.1089/mdr.2017.0341
Allison KR, Brynildsen MP, Collins JJ (2011) Heterogeneous bacterial persisters and engineering
approaches to eliminate them. Curr Opin Microbiol 14(5):593–598. https://doi.org/10.1016/j.
mib.2011.09.002
Amato SM, Fazen CH, Henry TC, Mok WWK, Orman MA, Sandvik EL, Volzing KG, Brynildsen
MP (2014) The role of metabolism in bacterial persistence. Front Microbiol 5. https://doi.
org/10.3389/fmicb.2014.00070
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL,
Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants:
the Keio collection. Mol Syst Biol 2. https://doi.org/10.1038/msb4100050
Babin BM, Atangcho L, van Eldijk MB, Sweredoski MJ, Moradian A, Hess S, Tolker-Nielsen
T, Newman DK, Tirrell DA (2017) Selective proteomic analysis of antibiotic-tolerant cellular subpopulations in Pseudomonas aeruginosa biofilms. MBio 8(5). https://doi.org/10.1128/
mBio.01593-17
Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004) Bacterial persistence as a phenotypic
switch. Science 305(5690):1622–1625. https://doi.org/10.1126/science.1099390
Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson DI, Brynildsen MP,
Bumann D, Camilli A, Collins JJ, Dehio C, Fortune S, Ghigo JM, Hardt WD, Harms A,
Heinemann M, Hung DT, Jenal U, Levin BR, Michiels J, Storz G, Tan MW, Tenson T, Van
Melderen L, Zinkernagel A (2019) Definitions and guidelines for research on antibiotic persistence. Nat Rev Microbiol 17(7):460–460. https://doi.org/10.1038/s41579-019-0207-4
Bernier SP, Lebeaux D, DeFrancesco AS, Valomon A, Soubigou G, Coppee JY, Ghigo JM, Beloin C
(2013) Starvation, together with the SOS response, mediates high biofilm-specific tolerance to
the fluoroquinolone ofloxacin. PLoS Genet 9(1). https://doi.org/10.1371/journal.pgen.1003144
Betts JC, Lukey PT, Robb LC, McAdam RA, Duncan K (2002) Evaluation of a nutrient starvation
model of Mycobacterium tuberculosis persistence by gene and protein expression profiling.
Mol Microbiol 43(3):717–731. https://doi.org/10.1046/j.1365-2958.2002.02779.x
Bigger JJTL (1944) Treatment of staphylococcal infections with penicillin by intermittent sterilisation. Lancet 244(6320):497–500
Blair JMA, Webber MA, Baylay AJ, Ogbolu DO, Piddock LJV (2015) Molecular mechanisms
of antibiotic resistance. Nat Rev Microbiol 13(1):42–51. https://doi.org/10.1038/nrmicro3380
Brooun A, Liu SH, Lewis K (2000) A dose-response study of antibiotic resistance in Pseudomonas
aeruginosa biofilms. Antimicrob Agents Chemother 44(3):640–646. https://doi.org/10.1128/
AAC.44.3.640-646.2000
Camacho LR, Ensergueix D, Perez E, Gicquel B, Guilhot C (1999) Identification of a virulence
gene cluster of Mycobacterium tuberculosis by signature-tagged transposon mutagenesis. Mol
Microbiol 34(2):257–267. https://doi.org/10.1046/j.1365-2958.1999.01593.x
Cameron DR, Shan Y, Zalis EA, Isabella V, Lewis K (2018) A genetic determinant of persister
cell formation in bacterial pathogens. J Bacteriol 200(17). https://doi.org/10.1128/JB.00303-18
Campos AI, Zampieri M (2019) Metabolomics-driven exploration of the chemical drug space
to predict combination antimicrobial therapies. Mol Cell 74(6):1291–1303. https://doi.
org/10.1016/j.molcel.2019.04.001
X. Duan et al.
References
Albrethsen J, Agner J, Piersma SR, Hojrup P, Pham TV, Weldingh K, Jimenez CR, Andersen P,
Rosenkrands I (2013) Proteomic profiling of Mycobacterium tuberculosis identifies nutrientstarvation- responsive toxin-antitoxin systems. Mol Cell Proteomics 12(5):1180–1191. https://
doi.org/10.1074/mcp.M112.018846
Aldridge BB, Fernandez-Suarez M, Heller D, Ambravaneswaran V, Irimia D, Toner M, Fortune
SM (2012) Asymmetry and aging of mycobacterial cells lead to variable growth and antibiotic
susceptibility. Science 335(6064):100–104. https://doi.org/10.1126/science.1216166
Alkasir R, Ma YA, Liu F, Li J, Lv N, Xue Y, Hu YF, Zhu BL (2018) Characterization and
transcriptome analysis of Acinetobacter baumannii persister cells. Microb Drug Resist
24(10):1466–1474. https://doi.org/10.1089/mdr.2017.0341
Allison KR, Brynildsen MP, Collins JJ (2011) Heterogeneous bacterial persisters and engineering
approaches to eliminate them. Curr Opin Microbiol 14(5):593–598. https://doi.org/10.1016/j.
mib.2011.09.002
Amato SM, Fazen CH, Henry TC, Mok WWK, Orman MA, Sandvik EL, Volzing KG, Brynildsen
MP (2014) The role of metabolism in bacterial persistence. Front Microbiol 5. https://doi.
org/10.3389/fmicb.2014.00070
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL,
Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants:
the Keio collection. Mol Syst Biol 2. https://doi.org/10.1038/msb4100050
Babin BM, Atangcho L, van Eldijk MB, Sweredoski MJ, Moradian A, Hess S, Tolker-Nielsen
T, Newman DK, Tirrell DA (2017) Selective proteomic analysis of antibiotic-tolerant cellular subpopulations in Pseudomonas aeruginosa biofilms. MBio 8(5). https://doi.org/10.1128/
mBio.01593-17
Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004) Bacterial persistence as a phenotypic
switch. Science 305(5690):1622–1625. https://doi.org/10.1126/science.1099390
Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson DI, Brynildsen MP,
Bumann D, Camilli A, Collins JJ, Dehio C, Fortune S, Ghigo JM, Hardt WD, Harms A,
Heinemann M, Hung DT, Jenal U, Levin BR, Michiels J, Storz G, Tan MW, Tenson T, Van
Melderen L, Zinkernagel A (2019) Definitions and guidelines for research on antibiotic persistence. Nat Rev Microbiol 17(7):460–460. https://doi.org/10.1038/s41579-019-0207-4
Bernier SP, Lebeaux D, DeFrancesco AS, Valomon A, Soubigou G, Coppee JY, Ghigo JM, Beloin C
(2013) Starvation, together with the SOS response, mediates high biofilm-specific tolerance to
the fluoroquinolone ofloxacin. PLoS Genet 9(1). https://doi.org/10.1371/journal.pgen.1003144
Betts JC, Lukey PT, Robb LC, McAdam RA, Duncan K (2002) Evaluation of a nutrient starvation
model of Mycobacterium tuberculosis persistence by gene and protein expression profiling.
Mol Microbiol 43(3):717–731. https://doi.org/10.1046/j.1365-2958.2002.02779.x
Bigger JJTL (1944) Treatment of staphylococcal infections with penicillin by intermittent sterilisation. Lancet 244(6320):497–500
Blair JMA, Webber MA, Baylay AJ, Ogbolu DO, Piddock LJV (2015) Molecular mechanisms
of antibiotic resistance. Nat Rev Microbiol 13(1):42–51. https://doi.org/10.1038/nrmicro3380
Brooun A, Liu SH, Lewis K (2000) A dose-response study of antibiotic resistance in Pseudomonas
aeruginosa biofilms. Antimicrob Agents Chemother 44(3):640–646. https://doi.org/10.1128/
AAC.44.3.640-646.2000
Camacho LR, Ensergueix D, Perez E, Gicquel B, Guilhot C (1999) Identification of a virulence
gene cluster of Mycobacterium tuberculosis by signature-tagged transposon mutagenesis. Mol
Microbiol 34(2):257–267. https://doi.org/10.1046/j.1365-2958.1999.01593.x
Cameron DR, Shan Y, Zalis EA, Isabella V, Lewis K (2018) A genetic determinant of persister
cell formation in bacterial pathogens. J Bacteriol 200(17). https://doi.org/10.1128/JB.00303-18
Campos AI, Zampieri M (2019) Metabolomics-driven exploration of the chemical drug space
to predict combination antimicrobial therapies. Mol Cell 74(6):1291–1303. https://doi.
org/10.1016/j.molcel.2019.04.001
X. Duan et al.