123
Cho SH, Goodlett D, Franzblau S (2006) ICAT-based comparative proteomic analysis of nonreplicating persistent Mycobacterium tuberculosis. Tuberculosis 86(6):445–460. https://doi.
org/10.1016/j.tube.2005.10.002
Chua SL, Yam JKH, Hao PL, Adav SS, Salido MM, Liu Y, Givskov M, Sze SK, Tolker-Nielsen T,
Yang L (2016) Selective labelling and eradication of antibiotic-tolerant bacterial populations
in Pseudomonas aeruginosa biofilms. Nat Commun 7. https://doi.org/10.1038/ncomms10750
Claudi B, Sprote P, Chirkova A, Personnic N, Zankl J, Schurmann N, Schmidt A, Bumann D
(2014) Phenotypic variation of Salmonella in host tissues delays eradication by antimicrobial
chemotherapy. Cell 158(4):722–733. https://doi.org/10.1016/j.cell.2014.06.045
Cohen NR, Lobritz MA, Collins JJ (2013) Microbial persistence and the road to drug resistance.
Cell Host Microbe 13(6):632–642. https://doi.org/10.1016/j.chom.2013.05.009
Conlon BP, Rowe SE, Gandt AB, Nuxoll AS, Donegan NP, Zalis EA, Clair G, Adkins JN, Cheung
AL, Lewis K (2016) Persister formation in Staphylococcus aureus is associated with ATP
depletion. Nat Microbiol 1(5). https://doi.org/10.1038/Nmicrobiol.2016.51
Cui P, Niu H, Shi W, Zhang S, Zhang W, Zhang Y (2018) Identification of genes involved in bacteriostatic antibiotic-induced Persister formation. Front Microbiol 9:413. https://doi.org/10.3389/
fmicb.2018.00413
De Groote VN, Verstraeten N, Fauvart M, Kint CI, Verbeeck AM, Beullens S, Cornelis
P, Michiels J (2009) Novel persistence genes in Pseudomonas aeruginosa identified by high-throughput screening. FEMS Microbiol Lett 297(1):73–79. https://doi.
org/10.1111/j.1574-6968.2009.01657.x
Defraine V, Fauvart M, Michiels J (2018) Fighting bacterial persistence: current and emerging antipersister strategies and therapeutics. Drug Resist Updat 38:12–26. https://doi.org/10.1016/j.
drup.2018.03.002
Dhar N, McKinney JD (2010) Mycobacterium tuberculosis persistence mutants identified by
screening in isoniazid-treated mice. P Natl Acad Sci USA 107(27):12275–12280. https://doi.
org/10.1073/pnas.1003219107
Didelot X, Walker AS, Peto TE, Crook DW, Wilson DJ (2016) Within-host evolution of bacterial
pathogens. Nat Rev Microbiol 14(3):150–162. https://doi.org/10.1038/nrmicro.2015.13
Dorr T, Lewis K, Vulic M (2009) SOS response induces persistence to fluoroquinolones in
Escherichia coli. PLoS Genet 5(12). https://doi.org/10.1371/journal.pgen.1000760
Dorr T, Vulic M, Lewis K (2010) Ciprofloxacin causes persister formation by inducing the TisB
toxin in Escherichia coli. PLoS Biol 8(2). https://doi.org/10.1371/journal.pbio.1000317
Duan XK, Li YS, Du QL, Huang QQ, Guo SY, Xu MM, Lin YP, Liu ZD, Xie JP (2016)
Mycobacterium Lysine epsilon-aminotransferase is a novel alarmone metabolism related
persister gene via dysregulating the intracellular amino acid level. Sci Rep 6. https://doi.
org/10.1038/srep19695
Eng RH, Padberg FT, Smith SM, Tan EN, Cherubin CE (1991) Bactericidal effects of antibiotics
on slowly growing and nongrowing bacteria. Antimicrob Agents Chemother 35(9):1824–1828.
https://doi.org/10.1128/aac.35.9.1824
Figueira R, Watson KG, Holden DW, Helaine S (2013) Identification of salmonella pathogenicity island-2 type III secretion system effectors involved in intramacrophage replication of
S. enterica serovar typhimurium: implications for rational vaccine design. MBio 4(2). https://
doi.org/10.1128/mBio.00065-13
Fisher RA, Gollan B, Helaine S (2017) Persistent bacterial infections and persister cells. Nat Rev
Microbiol 15(8):453–464. https://doi.org/10.1038/nrmicro.2017.42
Fridman O, Goldberg A, Ronin I, Shoresh N, Balaban NQ (2014) Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. Nature 513(7518):418–421. https://
doi.org/10.1038/nature13469
Fu Y, Waldor MK, Mekalanos JJ (2013) Tn-Seq analysis of Vibrio cholerae intestinal colonization reveals a role for T6SS-mediated antibacterial activity in the host. Cell Host Microbe
14(6):652–663. https://doi.org/10.1016/j.chom.2013.11.001
Gallagher LA, Shendure J, Manoil C (2011) Genome-scale identification of resistance functions
in Pseudomonas aeruginosa using Tn-seq. MBio 2(1). https://doi.org/10.1128/mBio.00315-10
5 Molecular and Systems Biology Approaches for Analyzing Drug-Tolerant Bacterial…
Cho SH, Goodlett D, Franzblau S (2006) ICAT-based comparative proteomic analysis of nonreplicating persistent Mycobacterium tuberculosis. Tuberculosis 86(6):445–460. https://doi.
org/10.1016/j.tube.2005.10.002
Chua SL, Yam JKH, Hao PL, Adav SS, Salido MM, Liu Y, Givskov M, Sze SK, Tolker-Nielsen T,
Yang L (2016) Selective labelling and eradication of antibiotic-tolerant bacterial populations
in Pseudomonas aeruginosa biofilms. Nat Commun 7. https://doi.org/10.1038/ncomms10750
Claudi B, Sprote P, Chirkova A, Personnic N, Zankl J, Schurmann N, Schmidt A, Bumann D
(2014) Phenotypic variation of Salmonella in host tissues delays eradication by antimicrobial
chemotherapy. Cell 158(4):722–733. https://doi.org/10.1016/j.cell.2014.06.045
Cohen NR, Lobritz MA, Collins JJ (2013) Microbial persistence and the road to drug resistance.
Cell Host Microbe 13(6):632–642. https://doi.org/10.1016/j.chom.2013.05.009
Conlon BP, Rowe SE, Gandt AB, Nuxoll AS, Donegan NP, Zalis EA, Clair G, Adkins JN, Cheung
AL, Lewis K (2016) Persister formation in Staphylococcus aureus is associated with ATP
depletion. Nat Microbiol 1(5). https://doi.org/10.1038/Nmicrobiol.2016.51
Cui P, Niu H, Shi W, Zhang S, Zhang W, Zhang Y (2018) Identification of genes involved in bacteriostatic antibiotic-induced Persister formation. Front Microbiol 9:413. https://doi.org/10.3389/
fmicb.2018.00413
De Groote VN, Verstraeten N, Fauvart M, Kint CI, Verbeeck AM, Beullens S, Cornelis
P, Michiels J (2009) Novel persistence genes in Pseudomonas aeruginosa identified by high-throughput screening. FEMS Microbiol Lett 297(1):73–79. https://doi.
org/10.1111/j.1574-6968.2009.01657.x
Defraine V, Fauvart M, Michiels J (2018) Fighting bacterial persistence: current and emerging antipersister strategies and therapeutics. Drug Resist Updat 38:12–26. https://doi.org/10.1016/j.
drup.2018.03.002
Dhar N, McKinney JD (2010) Mycobacterium tuberculosis persistence mutants identified by
screening in isoniazid-treated mice. P Natl Acad Sci USA 107(27):12275–12280. https://doi.
org/10.1073/pnas.1003219107
Didelot X, Walker AS, Peto TE, Crook DW, Wilson DJ (2016) Within-host evolution of bacterial
pathogens. Nat Rev Microbiol 14(3):150–162. https://doi.org/10.1038/nrmicro.2015.13
Dorr T, Lewis K, Vulic M (2009) SOS response induces persistence to fluoroquinolones in
Escherichia coli. PLoS Genet 5(12). https://doi.org/10.1371/journal.pgen.1000760
Dorr T, Vulic M, Lewis K (2010) Ciprofloxacin causes persister formation by inducing the TisB
toxin in Escherichia coli. PLoS Biol 8(2). https://doi.org/10.1371/journal.pbio.1000317
Duan XK, Li YS, Du QL, Huang QQ, Guo SY, Xu MM, Lin YP, Liu ZD, Xie JP (2016)
Mycobacterium Lysine epsilon-aminotransferase is a novel alarmone metabolism related
persister gene via dysregulating the intracellular amino acid level. Sci Rep 6. https://doi.
org/10.1038/srep19695
Eng RH, Padberg FT, Smith SM, Tan EN, Cherubin CE (1991) Bactericidal effects of antibiotics
on slowly growing and nongrowing bacteria. Antimicrob Agents Chemother 35(9):1824–1828.
https://doi.org/10.1128/aac.35.9.1824
Figueira R, Watson KG, Holden DW, Helaine S (2013) Identification of salmonella pathogenicity island-2 type III secretion system effectors involved in intramacrophage replication of
S. enterica serovar typhimurium: implications for rational vaccine design. MBio 4(2). https://
doi.org/10.1128/mBio.00065-13
Fisher RA, Gollan B, Helaine S (2017) Persistent bacterial infections and persister cells. Nat Rev
Microbiol 15(8):453–464. https://doi.org/10.1038/nrmicro.2017.42
Fridman O, Goldberg A, Ronin I, Shoresh N, Balaban NQ (2014) Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. Nature 513(7518):418–421. https://
doi.org/10.1038/nature13469
Fu Y, Waldor MK, Mekalanos JJ (2013) Tn-Seq analysis of Vibrio cholerae intestinal colonization reveals a role for T6SS-mediated antibacterial activity in the host. Cell Host Microbe
14(6):652–663. https://doi.org/10.1016/j.chom.2013.11.001
Gallagher LA, Shendure J, Manoil C (2011) Genome-scale identification of resistance functions
in Pseudomonas aeruginosa using Tn-seq. MBio 2(1). https://doi.org/10.1128/mBio.00315-10
5 Molecular and Systems Biology Approaches for Analyzing Drug-Tolerant Bacterial…