{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T04:07:57Z","timestamp":1793678877253,"version":"4.5.1"},"reference-count":63,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,1,21]],"date-time":"2025-01-21T00:00:00Z","timestamp":1737417600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,1,21]],"date-time":"2025-01-21T00:00:00Z","timestamp":1737417600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"DOI":"10.1186\/s12866-025-03771-5","type":"journal-article","created":{"date-parts":[[2025,1,21]],"date-time":"2025-01-21T02:14:28Z","timestamp":1737425668000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Fluoroquinolone-specific resistance trajectories in E. coli and their dependence on the SOS-response"],"prefix":"10.1186","volume":"25","author":[{"given":"Lisa","family":"Teichmann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Luitwieler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johan","family":"Bengtsson-Palme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benno","family":"ter Kuile","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,1,21]]},"reference":[{"issue":"1","key":"3771_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1365-2885.1996.tb00001.x","volume":"19","author":"SA Brown","year":"1996","unstructured":"Brown SA. Fluoroquinolones in animal health. J Vet Pharmacol Ther. 1996;19(1):1\u201314. https:\/\/doi.org\/10.1111\/j.1365-2885.1996.tb00001.x. PMID: 8992019.","journal-title":"J Vet Pharmacol Ther"},{"issue":"4","key":"3771_CR2","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1128\/CMR.2.4.378","volume":"2","author":"JS Wolfson","year":"1989","unstructured":"Wolfson JS, Hooper DC. Fluoroquinolone antimicrobial agents. Clin Microbiol Rev. 1989;2(4):378\u2013424. https:\/\/doi.org\/10.1128\/CMR.2.4.378. PMID: 2680058; PMCID: PMC358131.","journal-title":"Clin Microbiol Rev"},{"key":"3771_CR3","unstructured":"World Health Organization. WHO\/HMP\/HPS\/EML\/2021.04. 2021. 2021 AWaRe classification. Available from: https:\/\/www.who.int\/publications\/i\/item\/2021-aware-classification"},{"key":"3771_CR4","doi-asserted-by":"publisher","unstructured":"Sharland M, Pulcini C, Harbarth S, Zeng M, Gandra S, Mathur S, Magrini N; 21st WHO Expert Committee on Selection and Use of Essential Medicines. Classifying antibiotics in the WHO Essential Medicines List for optimal use-be AWaRe. Lancet Infect Dis. 2018;18(1):18\u201320. https:\/\/doi.org\/10.1016\/S1473-3099(17)30724-7. Epub 2017 Dec 20. PMID: 29303731.","DOI":"10.1016\/S1473-3099(17)30724-7"},{"issue":"Suppl 1","key":"3771_CR5","doi-asserted-by":"publisher","first-page":"S9","DOI":"10.1086\/319370","volume":"32","author":"DC Hooper","year":"2001","unstructured":"Hooper DC. Mechanisms of action of antimicrobials: focus on fluoroquinolones. Clin Infect Dis. 2001;32(Suppl 1):S9\u201315. https:\/\/doi.org\/10.1086\/319370. PMID: 11249823.","journal-title":"Clin Infect Dis"},{"issue":"8","key":"3771_CR6","doi-asserted-by":"publisher","first-page":"4371","DOI":"10.1128\/AAC.02892-14","volume":"58","author":"N H\u00e4ndel","year":"2014","unstructured":"H\u00e4ndel N, Schuurmans JM, Feng Y, Brul S, ter Kuile BH. Interaction between mutations and regulation of gene expression during development of de novo antibiotic resistance. Antimicrob Agents Chemother. 2014;58(8):4371\u20139. https:\/\/doi.org\/10.1128\/AAC.02892-14. Epub 2014 May 19. PMID: 24841263; PMCID: PMC4135992.","journal-title":"Antimicrob Agents Chemother."},{"issue":"2","key":"3771_CR7","doi-asserted-by":"publisher","first-page":"337","DOI":"10.3201\/eid0702.010239","volume":"7","author":"DC Hooper","year":"2001","unstructured":"Hooper DC. Emerging mechanisms of fluoroquinolone resistance. Emerg Infect Dis. 2001;7(2):337\u201341. https:\/\/doi.org\/10.3201\/eid0702.010239. PMID: 11294736; PMCID: PMC2631735.","journal-title":"Emerg Infect Dis"},{"issue":"6","key":"3771_CR8","doi-asserted-by":"publisher","first-page":"e176","DOI":"10.1371\/journal.pbio.0030176","volume":"3","author":"RT Cirz","year":"2005","unstructured":"Cirz RT, Chin JK, Andes DR, de Cr\u00e9cy-Lagard V, Craig WA, Romesberg FE. Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biol. 2005;3(6):e176. https:\/\/doi.org\/10.1371\/journal.pbio.0030176. Epub 2005 May 10. PMID: 15869329; PMCID: PMC1088971.","journal-title":"PLoS Biol."},{"key":"3771_CR9","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1016\/j.csbj.2021.01.003","volume":"19","author":"A Yakimov","year":"2021","unstructured":"Yakimov A, Bakhlanova I, Baitin D. Targeting evolution of antibiotic resistance by SOS response inhibition. Comput Struct Biotechnol J. 2021;19:777\u201383. https:\/\/doi.org\/10.1016\/j.csbj.2021.01.003. PMID: 33552448; PMCID: PMC7843400.","journal-title":"Comput Struct Biotechnol J"},{"issue":"4","key":"3771_CR10","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1002\/em.22267","volume":"60","author":"KH Maslowska","year":"2019","unstructured":"Maslowska KH, Makiela-Dzbenska K, Fijalkowska IJ. The SOS system: A complex and tightly regulated response to DNA damage. Environ Mol Mutagen. 2019;60(4):368\u201384. https:\/\/doi.org\/10.1002\/em.22267. Epub 2019 Jan 7. PMID: 30447030; PMCID: PMC6590174.","journal-title":"Environ Mol Mutagen."},{"key":"3771_CR11","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1146\/annurev.biochem.71.083101.133940","volume":"71","author":"SL Lusetti","year":"2002","unstructured":"Lusetti SL, Cox MM. The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Annu Rev Biochem. 2002;71:71\u2013100. https:\/\/doi.org\/10.1146\/annurev.biochem.71.083101.133940. Epub 2001 Nov 9 PMID: 12045091.","journal-title":"Annu Rev Biochem"},{"issue":"6","key":"3771_CR12","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1111\/j.1574-6976.2007.00082.x","volume":"31","author":"I Erill","year":"2007","unstructured":"Erill I, Campoy S, Barb\u00e9 J. Aeons of distress: an evolutionary perspective on the bacterial SOS response. FEMS Microbiol Rev. 2007;31(6):637\u201356. https:\/\/doi.org\/10.1111\/j.1574-6976.2007.00082.x. Epub 2007 Sep 18 PMID: 17883408.","journal-title":"FEMS Microbiol Rev"},{"issue":"4","key":"3771_CR13","doi-asserted-by":"publisher","first-page":"1515","DOI":"10.1128\/JB.187.4.1515-1518.2005","volume":"187","author":"T P\u00e9rez-Capilla","year":"2005","unstructured":"P\u00e9rez-Capilla T, Baquero MR, G\u00f3mez-G\u00f3mez JM, Ionel A, Mart\u00edn S, Bl\u00e1zquez J. SOS-independent induction of dinB transcription by beta-lactam-mediated inhibition of cell wall synthesis in Escherichia coli. J Bacteriol. 2005;187(4):1515\u20138. https:\/\/doi.org\/10.1128\/JB.187.4.1515-1518.2005. PMID: 15687217; PMCID: PMC545630.","journal-title":"J Bacteriol"},{"issue":"8","key":"3771_CR14","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1016\/j.tim.2014.04.007","volume":"22","author":"LS Redgrave","year":"2014","unstructured":"Redgrave LS, Sutton SB, Webber MA, Piddock LJ. Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success. Trends Microbiol. 2014;22(8):438\u201345. https:\/\/doi.org\/10.1016\/j.tim.2014.04.007. Epub 2014 May 16 PMID: 24842194.","journal-title":"Trends Microbiol"},{"issue":"1","key":"3771_CR15","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1128\/jb.178.1.306-308.1996","volume":"178","author":"H Okusu","year":"1996","unstructured":"Okusu H, Ma D, Nikaido H. AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants. J Bacteriol. 1996;178(1):306\u20138. https:\/\/doi.org\/10.1128\/jb.178.1.306-308.1996. PMID: 8550435; PMCID: PMC177656.","journal-title":"J Bacteriol"},{"issue":"8","key":"3771_CR16","doi-asserted-by":"publisher","first-page":"e1000541","DOI":"10.1371\/journal.ppat.1000541","volume":"5","author":"LL Marcusson","year":"2009","unstructured":"Marcusson LL, Frimodt-M\u00f8ller N, Hughes D. Interplay in the selection of fluoroquinolone resistance and bacterial fitness. PLoS Pathog. 2009;5(8):e1000541. https:\/\/doi.org\/10.1371\/journal.ppat.1000541. Epub 2009 Aug 7. PMID: 19662169; PMCID: PMC2714960.","journal-title":"PLoS Pathog."},{"issue":"6","key":"3771_CR17","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1093\/jac\/44.6.735","volume":"44","author":"MM Tav\u00edo","year":"1999","unstructured":"Tav\u00edo MM, Vila J, Ruiz J, Ruiz J, Mart\u00edn-S\u00e1nchez AM, Jim\u00e9nez de Anta MT. Mechanisms involved in the development of resistance to fluoroquinolones in Escherichia coli isolates. J Antimicrob Chemother. 1999;44(6):735\u201342. https:\/\/doi.org\/10.1093\/jac\/44.6.735. PMID: 10590273.","journal-title":"J Antimicrob Chemother."},{"issue":"3","key":"3771_CR18","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1128\/AAC.02684-15","volume":"60","author":"N H\u00e4ndel","year":"2015","unstructured":"H\u00e4ndel N, Hoeksema M, Freijo Mata M, Brul S, ter Kuile BH. Effects of stress, reactive oxygen species, and the SOS response on de novo acquisition of antibiotic resistance in escherichia coli. Antimicrob Agents Chemother. 2015;60(3):1319\u201327. https:\/\/doi.org\/10.1128\/AAC.02684-15. PMID: 26666928; PMCID: PMC4776001.","journal-title":"Antimicrob Agents Chemother"},{"issue":"12","key":"3771_CR19","doi-asserted-by":"publisher","first-page":"e1000760","DOI":"10.1371\/journal.pgen.1000760","volume":"5","author":"T D\u00f6rr","year":"2009","unstructured":"D\u00f6rr T, Lewis K, Vuli\u0107 M. SOS response induces persistence to fluoroquinolones in Escherichia coli. PLoS Genet. 2009;5(12):e1000760. https:\/\/doi.org\/10.1371\/journal.pgen.1000760. PMID: 20011100; PMCID: PMC2780357.","journal-title":"PLoS Genet."},{"issue":"23","key":"3771_CR20","doi-asserted-by":"publisher","first-page":"7387","DOI":"10.1021\/bi9603175","volume":"35","author":"SE Critchlow","year":"1996","unstructured":"Critchlow SE, Maxwell A. DNA cleavage is not required for the binding of quinolone drugs to the DNA gyrase-DNA complex. Biochemistry. 1996;35(23):7387\u201393. https:\/\/doi.org\/10.1021\/bi9603175. PMID: 8652515.","journal-title":"Biochemistry"},{"issue":"20","key":"3771_CR21","doi-asserted-by":"publisher","first-page":"9671","DOI":"10.1073\/pnas.89.20.9671","volume":"89","author":"G Pal\u00f9","year":"1992","unstructured":"Pal\u00f9 G, Valisena S, Ciarrocchi G, Gatto B, Palumbo M. Quinolone binding to DNA is mediated by magnesium ions. Proc Natl Acad Sci U S A. 1992;89(20):9671\u20135. https:\/\/doi.org\/10.1073\/pnas.89.20.9671. PMID: 1409681; PMCID: PMC50194.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"3771_CR22","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1038\/embor.2009.99","volume":"10","author":"S Da Re","year":"2009","unstructured":"Da Re S, Garnier F, Gu\u00e9rin E, Campoy S, Denis F, Ploy MC. The SOS response promotes qnrB quinolone-resistance determinant expression. EMBO Rep. 2009;10(8):929\u201333. https:\/\/doi.org\/10.1038\/embor.2009.99. Epub 2009 Jun 26. PMID: 19556999; PMCID: PMC2726673.","journal-title":"EMBO Rep."},{"issue":"6079","key":"3771_CR23","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1126\/science.1219192","volume":"336","author":"JJ Foti","year":"2012","unstructured":"Foti JJ, Devadoss B, Winkler JA, Collins JJ, Walker GC. Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science. 2012;336(6079):315\u20139. https:\/\/doi.org\/10.1126\/science.1219192. PMID: 22517853; PMCID: PMC3357493.","journal-title":"Science"},{"issue":"3","key":"3771_CR24","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/j.chembiol.2016.02.010","volume":"23","author":"MK Alam","year":"2016","unstructured":"Alam MK, Alhhazmi A, DeCoteau JF, Luo Y, Geyer CR. RecA inhibitors potentiate antibiotic activity and block evolution of antibiotic resistance. Cell Chem Biol. 2016;23(3):381\u201391. https:\/\/doi.org\/10.1016\/j.chembiol.2016.02.010. PMID: 26991103.","journal-title":"Cell Chem Biol"},{"issue":"5","key":"3771_CR25","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1016\/j.cell.2007.06.049","volume":"130","author":"MA Kohanski","year":"2007","unstructured":"Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA, Collins JJ. A common mechanism of cellular death induced by bactericidal antibiotics. Cell. 2007;130(5):797\u2013810. https:\/\/doi.org\/10.1016\/j.cell.2007.06.049. PMID: 17803904.","journal-title":"Cell"},{"issue":"13","key":"3771_CR26","doi-asserted-by":"publisher","first-page":"2081","DOI":"10.1002\/cbic.200800041","volume":"9","author":"S Madurga","year":"2008","unstructured":"Madurga S, S\u00e1nchez-C\u00e9spedes J, Belda I, Vila J, Giralt E. Mechanism of binding of fluoroquinolones to the quinolone resistance-determining region of DNA gyrase: towards an understanding of the molecular basis of quinolone resistance. ChemBioChem. 2008;9(13):2081\u20136. https:\/\/doi.org\/10.1002\/cbic.200800041. PMID: 18677735.","journal-title":"ChemBioChem"},{"issue":"1","key":"3771_CR27","doi-asserted-by":"publisher","first-page":"1444","DOI":"10.1038\/s41467-017-01405-7","volume":"8","author":"P Sharma","year":"2017","unstructured":"Sharma P, Haycocks JRJ, Middlemiss AD, Kettles RA, Sellars LE, Ricci V, Piddock LJV, Grainger DC. The multiple antibiotic resistance operon of enteric bacteria controls DNA repair and outer membrane integrity. Nat Commun. 2017;8(1):1444. https:\/\/doi.org\/10.1038\/s41467-017-01405-7. PMID: 29133912; PMCID: PMC5684230.","journal-title":"Nat Commun"},{"issue":"8","key":"3771_CR28","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1128\/AAC.33.8.1318","volume":"33","author":"SP Cohen","year":"1989","unstructured":"Cohen SP, McMurry LM, Hooper DC, Wolfson JS, Levy SB. Cross-resistance to fluoroquinolones in multiple-antibiotic-resistant (Mar) Escherichia coli selected by tetracycline or chloramphenicol: decreased drug accumulation associated with membrane changes in addition to OmpF reduction. Antimicrob Agents Chemother. 1989;33(8):1318\u201325. https:\/\/doi.org\/10.1128\/AAC.33.8.1318. PMID: 2679373; PMCID: PMC172647.","journal-title":"Antimicrob Agents Chemother"},{"issue":"4","key":"3771_CR29","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1128\/AAC.44.4.814-820.2000","volume":"44","author":"WV Kern","year":"2000","unstructured":"Kern WV, Oethinger M, Jellen-Ritter AS, Levy SB. Non-target gene mutations in the development of fluoroquinolone resistance in Escherichia coli. Antimicrob Agents Chemother. 2000;44(4):814\u201320. https:\/\/doi.org\/10.1128\/AAC.44.4.814-820.2000. PMID: 10722475; PMCID: PMC89776.","journal-title":"Antimicrob Agents Chemother"},{"issue":"11","key":"3771_CR30","doi-asserted-by":"publisher","first-page":"e1009198","DOI":"10.1371\/journal.pgen.1009198","volume":"16","author":"A Gerstel","year":"2020","unstructured":"Gerstel A, Zamarre\u00f1o Beas J, Duverger Y, Bouveret E, Barras F, Py B. Oxidative stress antagonizes fluoroquinolone drug sensitivity via the SoxR-SUF Fe-S cluster homeostatic axis. PLoS Genet. 2020;16(11):e1009198. https:\/\/doi.org\/10.1371\/journal.pgen.1009198. PMID: 33137124; PMCID: PMC7671543.","journal-title":"PLoS Genet"},{"issue":"5","key":"3771_CR31","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1093\/jac\/45.5.583","volume":"45","author":"E Pestova","year":"2000","unstructured":"Pestova E, Millichap JJ, Noskin GA, Peterson LR. Intracellular targets of moxifloxacin: a comparison with other fluoroquinolones. J Antimicrob Chemother. 2000;45(5):583\u201390. https:\/\/doi.org\/10.1093\/jac\/45.5.583. PMID: 10797078.","journal-title":"J Antimicrob Chemother"},{"key":"3771_CR32","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1093\/jac\/43.suppl_2.31","volume":"43 Suppl B","author":"H Schedletzky","year":"1999","unstructured":"Schedletzky H, Wiedemann B, Heisig P. The effect of moxifloxacin on its target topoisomerases from Escherichia coli and Staphylococcus aureus. J Antimicrob Chemother. 1999;43 Suppl B:31\u20137. https:\/\/doi.org\/10.1093\/jac\/43.suppl_2.31. PMID: 10382873.","journal-title":"J Antimicrob Chemother."},{"issue":"5","key":"3771_CR33","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1093\/molbev\/msx052.PMID:28087782;PMCID:PMC5400412","volume":"34","author":"DL Huseby","year":"2017","unstructured":"Huseby DL, Pietsch F, Brandis G, Garoff L, Tegehall A, Hughes D. Mutation supply and relative fitness shape the genotypes of ciprofloxacin-resistant escherichia coli. Mol Biol Evol. 2017;34(5):1029\u201339. https:\/\/doi.org\/10.1093\/molbev\/msx052.PMID:28087782;PMCID:PMC5400412.","journal-title":"Mol Biol Evol"},{"key":"3771_CR34","doi-asserted-by":"publisher","unstructured":"Johnson JR, Johnston B, Kuskowski MA, Sokurenko EV, Tchesnokova V. Intensity and mechanisms of fluoroquinolone resistance within the h30 and h30rx subclones of escherichia coli sequence type 131 compared with other fluoroquinolone-resistant E. coli. Antimicrob Agents Chemother. 2015 Aug;59(8):4471\u201380. https:\/\/doi.org\/10.1128\/AAC.00673-15. Epub 2015 May 18. Erratum in: Antimicrob Agents Chemother. 2015 Sep;59(9):5871. https:\/\/doi.org\/10.1128\/AAC.01716-15. PMID: 25987621; PMCID: PMC4505254.","DOI":"10.1128\/AAC.00673-15 10.1128\/AAC.01716-15"},{"issue":"11","key":"3771_CR35","doi-asserted-by":"publisher","first-page":"7132","DOI":"10.1128\/AAC.01687-15","volume":"59","author":"JR Johnson","year":"2015","unstructured":"Johnson JR, Porter SB, Thuras P, Johnson TJ, Price LB, Tchesnokova V, Sokurenko EV. Greater ciprofloxacin tolerance as a possible selectable phenotype underlying the pandemic spread of the H30 subclone of Escherichia coli sequence type 131. Antimicrob Agents Chemother. 2015;59(11):7132\u20135. https:\/\/doi.org\/10.1128\/AAC.01687-15. Epub 2015 Aug 31. PMID: 26324269; PMCID: PMC4604381.","journal-title":"Antimicrob Agents Chemother."},{"issue":"1","key":"3771_CR36","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1534\/genetics.109.108803","volume":"184","author":"R Springman","year":"2010","unstructured":"Springman R, Keller T, Molineux IJ, Bull JJ. Evolution at a high imposed mutation rate: adaptation obscures the load in phage T7. Genetics. 2010;184(1):221\u201332. https:\/\/doi.org\/10.1534\/genetics.109.108803. Epub 2009 Oct 26. PMID: 19858285; PMCID: PMC2815918.","journal-title":"Genetics."},{"issue":"6","key":"3771_CR37","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1093\/genetics\/54.6.1337","volume":"54","author":"M Kimura","year":"1966","unstructured":"Kimura M, Maruyama T. The mutational load with epistatic gene interactions in fitness. Genetics. 1966;54(6):1337\u201351. https:\/\/doi.org\/10.1093\/genetics\/54.6.1337. PMID: 17248359; PMCID: PMC1211299.","journal-title":"Genetics"},{"issue":"4","key":"3771_CR38","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1111\/j.1365-2958.2006.05150.x","volume":"60","author":"E Denamur","year":"2006","unstructured":"Denamur E, Matic I. Evolution of mutation rates in bacteria. Mol Microbiol. 2006;60(4):820\u20137. https:\/\/doi.org\/10.1111\/j.1365-2958.2006.05150.x. PMID: 16677295.","journal-title":"Mol Microbiol"},{"issue":"24","key":"3771_CR39","doi-asserted-by":"publisher","first-page":"6881","DOI":"10.1021\/j100335a010","volume":"92","author":"M Eigen","year":"1988","unstructured":"Eigen M, Mccaskill J, Schuster P. Molecular quasi-species. J Phys Chem. 1988;92(24):6881\u201391. https:\/\/doi.org\/10.1021\/j100335a010.","journal-title":"J Phys Chem"},{"issue":"10","key":"3771_CR40","doi-asserted-by":"publisher","first-page":"3222","DOI":"10.1128\/AAC.47.10.3222-3232.2003","volume":"47","author":"P Komp Lindgren","year":"2003","unstructured":"Komp Lindgren P, Karlsson A, Hughes D. Mutation rate and evolution of fluoroquinolone resistance in Escherichia coli isolates from patients with urinary tract infections. Antimicrob Agents Chemother. 2003;47(10):3222\u201332. https:\/\/doi.org\/10.1128\/AAC.47.10.3222-3232.2003. PMID: 14506034; PMCID: PMC201150.","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"3771_CR41","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1093\/genetics\/152.2.485","volume":"152","author":"O Tenaillon","year":"1999","unstructured":"Tenaillon O, Toupance B, Le Nagard H, Taddei F, Godelle B. Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria. Genetics. 1999;152(2):485\u201393. https:\/\/doi.org\/10.1093\/genetics\/152.2.485. PMID: 10353893; PMCID: PMC1460623.","journal-title":"Genetics"},{"issue":"2","key":"3771_CR42","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1534\/genetics.105.045526","volume":"171","author":"E Denamur","year":"2005","unstructured":"Denamur E, Tenaillon O, Deschamps C, Skurnik D, Ronco E, Gaillard JL, Picard B, Branger C, Matic I. Intermediate mutation frequencies favor evolution of multidrug resistance in Escherichia coli. Genetics. 2005;171(2):825\u20137. https:\/\/doi.org\/10.1534\/genetics.105.045526. Epub 2005 Jun 18. PMID: 15965238; PMCID: PMC1456789.","journal-title":"Genetics."},{"key":"3771_CR43","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1093\/jac\/43.suppl_2.43","volume":"43 Suppl B","author":"FJ Boswell","year":"1999","unstructured":"Boswell FJ, Andrews JM, Wise R, Dalhoff A. Bactericidal properties of moxifloxacin and post-antibiotic effect. J Antimicrob Chemother. 1999;43 Suppl B:43\u20139. https:\/\/doi.org\/10.1093\/jac\/43.suppl_2.43. PMID: 10382875.","journal-title":"J Antimicrob Chemother."},{"issue":"8","key":"3771_CR44","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1186\/s13104-015-1735-2","volume":"8","author":"M Vestergaard","year":"2015","unstructured":"Vestergaard M, Paulander W, Ingmer H. Activation of the SOS response increases the frequency of small colony variants. BMC Res Notes. 2015;8(8):749. https:\/\/doi.org\/10.1186\/s13104-015-1735-2. PMID: 26643526; PMCID: PMC4672542.","journal-title":"BMC Res Notes"},{"issue":"5","key":"3771_CR45","doi-asserted-by":"publisher","first-page":"2582","DOI":"10.3390\/ijms25052582","volume":"25","author":"W Qi","year":"2024","unstructured":"Qi W, Jonker MJ, Katsavelis D, de Leeuw W, Wortel M, Ter Kuile BH. The effect of the stringent response and oxidative stress response on fitness costs of de novo acquisition of antibiotic resistance. Int J Mol Sci. 2024;25(5):2582. https:\/\/doi.org\/10.3390\/ijms25052582. PMID: 38473832; PMCID: PMC10932037..","journal-title":"Int J Mol Sci"},{"issue":"1725","key":"3771_CR46","doi-asserted-by":"publisher","first-page":"3617","DOI":"10.1098\/rspb.2011.1537","volume":"278","author":"JA de Visser","year":"2011","unstructured":"de Visser JA, Cooper TF, Elena SF. The causes of epistasis. Proc Biol Sci. 2011;278(1725):3617\u201324. https:\/\/doi.org\/10.1098\/rspb.2011.1537. Epub 2011 Oct 5. PMID: 21976687; PMCID: PMC3203509.","journal-title":"Proc Biol Sci."},{"issue":"4","key":"3771_CR47","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1038\/nrmicro2319","volume":"8","author":"DI Andersson","year":"2010","unstructured":"Andersson DI, Hughes D. Antibiotic resistance and its cost: is it possible to reverse resistance? Nat Rev Microbiol. 2010;8(4):260\u201371. https:\/\/doi.org\/10.1038\/nrmicro2319. Epub 2010 Mar 8 PMID: 20208551.","journal-title":"Nat Rev Microbiol"},{"issue":"5","key":"3771_CR48","doi-asserted-by":"publisher","first-page":"2085","DOI":"10.1128\/AAC.01460-09","volume":"54","author":"P Schulz zurWiesch","year":"2010","unstructured":"Schulz zurWiesch P, Engelst\u00e4dter J, Bonhoeffer S. Compensation of fitness costs and reversibility of antibiotic resistance mutations. Antimicrob Agents Chemother. 2010;54(5):2085\u201395. https:\/\/doi.org\/10.1128\/AAC.01460-09. Epub 2010 Feb 22. PMID: 20176903; PMCID: PMC2863634.","journal-title":"Antimicrob Agents Chemother."},{"issue":"8","key":"3771_CR49","doi-asserted-by":"publisher","first-page":"1370","DOI":"10.3389\/fmicb.2017.01370","volume":"19","author":"J Machuca","year":"2017","unstructured":"Machuca J, Recacha E, Briales A, D\u00edaz-de-Alba P, Blazquez J, Pascual \u00c1, Rodr\u00edguez-Mart\u00ednez JM. Cellular response to ciprofloxacin in low-level quinolone-resistant Escherichia coli. Front Microbiol. 2017;19(8):1370. https:\/\/doi.org\/10.3389\/fmicb.2017.01370. PMID: 28769919; PMCID: PMC5516121.","journal-title":"Front Microbiol"},{"issue":"1","key":"3771_CR50","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1128\/AAC.50.1.220-225.2006","volume":"50","author":"RT Cirz","year":"2006","unstructured":"Cirz RT, Romesberg FE. Induction and inhibition of ciprofloxacin resistance-conferring mutations in hypermutator bacteria. Antimicrob Agents Chemother. 2006;50(1):220\u20135. https:\/\/doi.org\/10.1128\/AAC.50.1.220-225.2006. PMID: 16377689; PMCID: PMC1346780.","journal-title":"Antimicrob Agents Chemother"},{"issue":"27","key":"3771_CR51","doi-asserted-by":"publisher","first-page":"e2407832121","DOI":"10.1073\/pnas.2407832121","volume":"121","author":"TH Sass","year":"2024","unstructured":"Sass TH, Lovett ST. The DNA damage response of\u00a0Escherichia coli, revisited: Differential gene expression after replication inhibition. Proc Natl Acad Sci U S A. 2024;121(27):e2407832121. https:\/\/doi.org\/10.1073\/pnas.2407832121. Epub 2024 Jun 27. PMID: 38935560; PMCID: PMC11228462.","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"2","key":"3771_CR52","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1046\/j.1365-2958.2003.03704.x","volume":"50","author":"JC Layton","year":"2003","unstructured":"Layton JC, Foster PL. Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS. Escherichia coli Mol Microbiol. 2003;50(2):549\u201361. https:\/\/doi.org\/10.1046\/j.1365-2958.2003.03704.x. PMID: 14617178; PMCID: PMC1237112.","journal-title":"Escherichia coli Mol Microbiol"},{"issue":"3","key":"3771_CR53","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1128\/JB.01092-07","volume":"190","author":"T Durfee","year":"2008","unstructured":"Durfee T, Hansen AM, Zhi H, Blattner FR, Jin DJ. Transcription profiling of the stringent response in Escherichia coli. J Bacteriol. 2008;190(3):1084\u201396. https:\/\/doi.org\/10.1128\/JB.01092-07. Epub 2007 Nov 26. PMID: 18039766; PMCID: PMC2223561.","journal-title":"J Bacteriol."},{"issue":"5","key":"3771_CR54","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1016\/j.resmic.2004.01.020","volume":"155","author":"MN Hersh","year":"2004","unstructured":"Hersh MN, Ponder RG, Hastings PJ, Rosenberg SM. Adaptive mutation and amplification in Escherichia coli: two pathways of genome adaptation under stress. Res Microbiol. 2004;155(5):352\u20139. https:\/\/doi.org\/10.1016\/j.resmic.2004.01.020. PMID: 15207867.","journal-title":"Res Microbiol"},{"issue":"4","key":"3771_CR55","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1080\/10409230701507757","volume":"42","author":"PJ Hastings","year":"2007","unstructured":"Hastings PJ. Adaptive amplification. Crit Rev Biochem Mol Biol. 2007;42(4):271\u201383. https:\/\/doi.org\/10.1080\/10409230701507757. PMID: 17687669.","journal-title":"Crit Rev Biochem Mol Biol."},{"issue":"5","key":"3771_CR56","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/j.resmic.2004.01.016","volume":"155","author":"JR Roth","year":"2004","unstructured":"Roth JR, Andersson DI. Amplification-mutagenesis\u2013how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation. Res Microbiol. 2004;155(5):342\u201351. https:\/\/doi.org\/10.1016\/j.resmic.2004.01.016. PMID: 15207866.","journal-title":"Res Microbiol"},{"issue":"8","key":"3771_CR57","doi-asserted-by":"publisher","first-page":"3752","DOI":"10.1128\/AAC.02096-12","volume":"57","author":"N H\u00e4ndel","year":"2013","unstructured":"H\u00e4ndel N, Schuurmans JM, Brul S, ter Kuile BH. Compensation of the metabolic costs of antibiotic resistance by physiological adaptation in Escherichia coli. Antimicrob Agents Chemother. 2013;57(8):3752\u201362. https:\/\/doi.org\/10.1128\/AAC.02096-12. Epub 2013 May 28. PMID: 23716056; PMCID: PMC3719774.","journal-title":"Antimicrob Agents Chemother."},{"issue":"2","key":"3771_CR58","doi-asserted-by":"publisher","first-page":"0008","DOI":"10.1038\/msb4100050","volume":"2006","author":"T Baba","year":"2006","unstructured":"Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006;2006(2):0008. https:\/\/doi.org\/10.1038\/msb4100050. Epub 2006 Feb 21. PMID: 16738554; PMCID: PMC1681482.","journal-title":"Mol Syst Biol."},{"issue":"12","key":"3771_CR59","doi-asserted-by":"publisher","first-page":"6640","DOI":"10.1073\/pnas.120163297","volume":"97","author":"KA Datsenko","year":"2000","unstructured":"Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A. 2000;97(12):6640\u20135. https:\/\/doi.org\/10.1073\/pnas.120163297. PMID: 10829079; PMCID: PMC18686.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"3771_CR60","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.mimet.2009.07.017","volume":"79","author":"JM Schuurmans","year":"2009","unstructured":"Schuurmans JM, Nuri Hayali AS, Koenders BB, ter Kuile BH. Variations in MIC value caused by differences in experimental protocol. J Microbiol Methods. 2009;79(1):44\u20137. https:\/\/doi.org\/10.1016\/j.mimet.2009.07.017. Epub 2009 Jul 25 PMID: 19635505.","journal-title":"J Microbiol Methods"},{"issue":"2","key":"3771_CR61","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1089\/mdr.2010.0101","volume":"17","author":"MA van der Horst","year":"2011","unstructured":"van der Horst MA, Schuurmans JM, Smid MC, Koenders BB, ter Kuile BH. De novo acquisition of resistance to three antibiotics by Escherichia coli. Microb Drug Resist. 2011;17(2):141\u20137. https:\/\/doi.org\/10.1089\/mdr.2010.0101. Epub 2011 Jan 16 PMID: 21235391.","journal-title":"Microb Drug Resist"},{"issue":"19","key":"3771_CR62","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels P, Magnusson M, Lundin S, K\u00e4ller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047\u20138. https:\/\/doi.org\/10.1093\/bioinformatics\/btw354. Epub 2016 Jun 16. PMID: 27312411; PMCID: PMC5039924.","journal-title":"Bioinformatics."},{"key":"3771_CR63","doi-asserted-by":"publisher","unstructured":"Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17(1). https:\/\/doi.org\/10.14806\/ej.17.1.200. ISSN 2226\u20136089.","DOI":"10.14806\/ej.17.1.200"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-025-03771-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-025-03771-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-025-03771-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,21]],"date-time":"2025-01-21T14:03:17Z","timestamp":1737468197000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcmicrobiol.biomedcentral.com\/articles\/10.1186\/s12866-025-03771-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,21]]},"references-count":63,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["3771"],"URL":"https:\/\/doi.org\/10.1186\/s12866-025-03771-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-4939869\/v1","asserted-by":"object"}]},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,21]]},"assertion":[{"value":"19 August 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 January 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 January 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"37"}}