{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T00:47:54Z","timestamp":1793148474486,"version":"4.5.0"},"reference-count":207,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2024,3,14]],"date-time":"2024-03-14T00:00:00Z","timestamp":1710374400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Universidad Cient\u00edfica del Sur"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Life"],"abstract":"<jats:p>Quinolone resistance has been largely related to the presence of specific point mutations in chromosomal targets, with an accessory role of impaired uptake and enhanced pump-out. Meanwhile the relevance of transferable mechanisms of resistance able to protect the target of pump-out or inactivate quinolones has been increasingly reported since 1998. Nevertheless, bacteria have other strategies and mechanisms allowing them to survive and even proliferate in the presence of quinolones, which might be qualified as resistance or resilience mechanisms. These include decreasing levels of quinolone target production, transient amoeba protection, benthonic lifestyle, nutrient-independent slow growth, activation of stringent response, inactivation or degradation of quinolones as well as apparently unrelated or forgotten chromosomal mutations. These mechanisms have been largely overlooked, either because of the use of classical approaches to antibiotic resistance determination or due to the low increase in final minimum inhibitory concentration levels. This article is devoted to a review of a series of these mechanisms.<\/jats:p>","DOI":"10.3390\/life14030383","type":"journal-article","created":{"date-parts":[[2024,3,14]],"date-time":"2024-03-14T05:43:30Z","timestamp":1710395010000},"page":"383","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Unusual and Unconsidered Mechanisms of Bacterial Resilience and Resistance to Quinolones"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4431-2036","authenticated-orcid":false,"given":"Joaquim","family":"Ruiz","sequence":"first","affiliation":[{"name":"Grupo de Investigaci\u00f3n en Din\u00e1micas y Epidemiolog\u00eda de la Resistencia a Antimicrobianos\u2014\u201cOne Health\u201d, Universidad Cient\u00edfica del Sur, Lima 15067, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,3,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e00007-19","DOI":"10.1128\/CMR.00007-19","article-title":"Transferable mechanisms of quinolone resistance from 1998 onward","volume":"32","author":"Ruiz","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1099\/jmm.0.000475","article-title":"Mechanisms of quinolone action and resistance: Where do we stand?","volume":"66","author":"Correia","year":"2017","journal-title":"J. Med. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"a025320","DOI":"10.1101\/cshperspect.a025320","article-title":"Topoisomerase Inhibitors: Fluoroquinolone mechanisms of action and resistance","volume":"6","author":"Hooper","year":"2016","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1111\/j.1365-2958.2005.04638.x","article-title":"Norfloxacin-induced DNA gyrase cleavage complexes block Escherichia coli replication forks, causing double-stranded breaks in vivo","volume":"56","author":"Pohlhaus","year":"2005","journal-title":"Mol. Microbiol."},{"key":"ref_5","unstructured":"Barton, N., Crowther, A.F., Hepworth, W., Richardson, N.D., and Driver, G.W. (1960). New Quinolones and Therapeutic Compositions Containing Them. (830832), British Patent."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"4874","DOI":"10.1021\/jm501881c","article-title":"Origins of the quinolone class of antibacterials: An expanded \u201cdiscovery story\u201d","volume":"58","author":"Bisacchi","year":"2015","journal-title":"J. Med. Chem."},{"key":"ref_7","unstructured":"Hepworth, W. (1959). Manufacture of 1-Methyl-6-nitro-4-quinolone-3-carboxylic Acid. (820295), British Patent."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1021\/jm01240a021","article-title":"1,8-Naphthyridine derivatives: A new class of chemotherapy agents","volume":"5","author":"Lesher","year":"1962","journal-title":"J. Med. Pharm. Chem."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"522","DOI":"10.4269\/ajtmh.2007.76.522","article-title":"Etiology of diarrhea in children younger than 5 years of age admitted in a rural hospital of southern Mozambique","volume":"76","author":"Mandomando","year":"2007","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1016\/S0140-6736(83)91261-8","article-title":"Nalidixic acid for shigellosis","volume":"322","author":"Parry","year":"1983","journal-title":"Lancet"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1016\/S0140-6736(88)92515-9","article-title":"Nalidixic-acid resistant Shigella dysenteriae type 1 in eastern India","volume":"332","author":"Sen","year":"1988","journal-title":"Lancet"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1093\/jac\/dkg208","article-title":"The quinolones: Decades of development and use","volume":"51","author":"Emmerson","year":"2003","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e18243","DOI":"10.1097\/MD.0000000000018243","article-title":"Management of infective corneal ulcers in a high-income developing country","volume":"98","author":"AlMahmoud","year":"2019","journal-title":"Medicine"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1007\/s00404-007-0380-y","article-title":"Salmonella ovarian abscess following travel diarrhoea episode","volume":"276","author":"Alonso","year":"2007","journal-title":"Arch. Gynecol. Obstet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"i41","DOI":"10.1093\/jac\/dku251","article-title":"Current antibiotic management of prosthetic joint infections in Italy: The \u2018Udine strategy\u2019","volume":"69","author":"Bassetti","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/jac\/28.suppl_C.97","article-title":"Review of quinolones in the treatment of infections of the skin and skin structure","volume":"28","author":"Gentry","year":"1991","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Koulenti, D., Xu, E., Mok, I.Y.S., Song, A., Karageorgopoulos, D.E., Armaganidis, A., Lipman, J., and Tsiodras, S. (2019). Novel antibiotics for multidrug-resistant gram-positive microorganisms. Microorganisms, 7.","DOI":"10.3390\/microorganisms7080270"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1007\/BF01643395","article-title":"Ciprofloxacin in the treatment of nosocomial multiply resistant Acinetobacter calcoaceticus bacteremia","volume":"18","author":"Leonov","year":"1990","journal-title":"Infection"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.resinv.2017.11.005","article-title":"Recent trends in practice patterns and impact of corticosteroid use on pediatric Mycoplasma pneumoniae-related respiratory infections","volume":"56","author":"Okubo","year":"2018","journal-title":"Respir. Investig."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1111\/j.1600-0463.2007.apm_567.x","article-title":"Trends in antimicrobial resistance in Campylobacter spp. causing traveler\u2019s diarrhea","volume":"115","author":"Ruiz","year":"2007","journal-title":"APMIS"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1128\/AAC.43.1.161","article-title":"Increase in quinolone resistance in a Haemophilus influenzae strain isolated from a patient with recurrent respiratory infections treated with ofloxacin","volume":"43","author":"Vila","year":"1999","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"559708","DOI":"10.3389\/fphar.2020.559708","article-title":"The use of ozenoxacin in pediatric patients: Clinical evidence, efficacy and safety","volume":"11","author":"Davino","year":"2020","journal-title":"Front. Pharmacol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1080\/14728214.2019.1685494","article-title":"Emerging antibiotics for community-acquired pneumonia","volume":"24","author":"Liapikou","year":"2019","journal-title":"Expert Opin. Emerg. Drugs"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e13145","DOI":"10.1111\/ctr.13145","article-title":"Ciprofloxacin vs levofloxacin for prophylaxis during hematopoietic stem-cell transplantation","volume":"32","author":"Copeland","year":"2018","journal-title":"Clin. Transplant."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e6","DOI":"10.4142\/jvs.23245","article-title":"Intramammary preparation of enrofloxacin hydrochloride-dihydrate for bovine mastitis (biofilm-forming Staphylococcus aureus)","volume":"25","author":"Sumano","year":"2024","journal-title":"J. Vet. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1086\/512369","article-title":"Fluoroquinolone-resistant Campylobacter species and the withdrawal of fluoroquinolones from use in poultry: A public health success story","volume":"44","author":"Nelson","year":"2007","journal-title":"Clin. Infect. Dis."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"40","DOI":"10.4236\/ojvm.2016.62006","article-title":"A review of enrofloxacin for veterinary use","volume":"6","author":"Trouchon","year":"2016","journal-title":"Open J. Vet. Med."},{"key":"ref_28","unstructured":"World Organisation for Animal Health (2018). OIE Annual Report on Antimicrobial Agents Intended for Use in Animals, World Organisation for Animal Health (OIE). [3rd ed.]. Available online: https:\/\/www.oie.int\/fileadmin\/Home\/eng\/Our_scientific_expertise\/docs\/pdf\/AMR\/Annual_Report_AMR_3.pdf."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1007\/s10096-014-2296-3","article-title":"Antiviral, antifungal, and antiparasitic activities of fluoroquinolones optimized for treatment of bacterial infections: A puzzling paradox or a logical consequence of their mode of action?","volume":"34","author":"Dalhoff","year":"2015","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1645\/GE-3489.1","article-title":"Selective action of fluoroquinolones against intracellular amastigotes of Leishmania (Viannia) panamensis in vitro","volume":"91","author":"Romero","year":"2005","journal-title":"J. Parasitol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1093\/jac\/dkn473","article-title":"Comparative pharmacodynamic interaction analysis between ciprofloxacin, moxifloxacin and levofloxacin and antifungal agents against Candida albicans and Aspergillus fumigatus","volume":"63","author":"Stergiopoulou","year":"2009","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"4052","DOI":"10.1128\/AAC.00259-12","article-title":"Levofloxacin inhibits rhinovirus infection in primary cultures of human tracheal epithelial cells","volume":"56","author":"Yamaya","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/S0022-5347(17)64441-0","article-title":"Neggram (nalidixic acid): A new antimicrobial chemotherapeutic agent","volume":"90","author":"Carroll","year":"1963","journal-title":"J. Urol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1128\/AAC.33.6.886","article-title":"Cloning and characterization of a DNA gyrase A gene from Escherichia coli that confers clinical resistance to 4-quinolones","volume":"33","author":"Cullen","year":"1989","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Guibert, F., Espinoza, K., Taboada-Blanco, C., Alonso, C.A., Oporto, R., Castillo, A.K., Rojo-Bezares, B., L\u00f3pez, M., S\u00e1enz, Y., and Pons, M.J. (Int. Microbiol., 2024). Traditional marketed meats as a reservoir of multidrug-resistant Escherichia coli, Int. Microbiol., in press.","DOI":"10.1007\/s10123-023-00445-y"},{"key":"ref_36","first-page":"12","article-title":"Mechanisms of action of and resistance to ciprofloxacin","volume":"82","author":"Hooper","year":"1987","journal-title":"Am. J. Med."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"41","DOI":"10.3109\/inf.1973.5.issue-1.08","article-title":"Antibiotic resistance and R factors in gram-negative bacteria isolated in a hospital for infectious diseases. III. The effect of antibacterial treatment on the incidence of R factor-mediated antibiotic resistance","volume":"5","author":"Jonsson","year":"1973","journal-title":"Scand. J. Infect. Dis."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1111\/j.1464-410X.1963.tb02602.x","article-title":"Studies of a new antibacterial agent, nalidixic acid","volume":"35","author":"Lishman","year":"1963","journal-title":"Br. J. Urol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1016\/S0140-6736(97)07322-4","article-title":"Quinolone resistance from a transferable plasmid","volume":"351","author":"Pascual","year":"1998","journal-title":"Lancet"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"183","DOI":"10.47665\/tb.40.2.009","article-title":"Transferable mechanisms of quinolone resistance are more frequent among enterotoxigenic Escherichia coli isolates displaying low-level quinolone resistance","volume":"40","author":"Medina","year":"2023","journal-title":"Trop. Biomed."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1093\/jac\/dkn068","article-title":"Surveillance for plasmid-mediated quinolone resistance determinants in Enterobacteriaceae within the Calgary Health Region, Canada: The emergence of aac(6\u2032)-Ib-cr","volume":"61","author":"Pitout","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/trstmh\/trt106","article-title":"Analysis of quinolone-resistance in commensal and diarrheagenic Escherichia coli isolates from infants in Lima, Peru","volume":"108","author":"Pons","year":"2014","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1128\/AAC.50.1.38-42.2006","article-title":"Ciprofloxacin-resistant Salmonella enterica serovar Typhimurium strains are difficult to select in the absence of AcrB and TolC","volume":"50","author":"Ricci","year":"2006","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1093\/jac\/dkr548","article-title":"qnr, aac(6\u2032)-Ib-cr and qepA genes in Escherichia coli and Klebsiella spp.: Genetic environments and plasmid and chromosomal location","volume":"67","author":"Ruiz","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1093\/jac\/44.6.735","article-title":"Mechanisms involved in the development of resistance to fluoroquinolones in Escherichia coli isolates","volume":"44","author":"Vila","year":"1999","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2477","DOI":"10.1128\/AAC.38.10.2477","article-title":"Association between double mutation in gyrA gene of ciprofloxacin-resistant clinical isolates of Escherichia coli and minimal inhibitory concentration","volume":"38","author":"Vila","year":"1994","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/j.ijantimicag.2018.01.012","article-title":"Chromosomal mutations that accompany qnr in clinical isolates of Escherichia coli","volume":"51","author":"Hooper","year":"2018","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"4772","DOI":"10.1073\/pnas.74.11.4772","article-title":"Nalidixic acid resistance: A second genetic character involved in DNA gyrase activity","volume":"74","author":"Gellert","year":"1977","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2380","DOI":"10.1128\/AAC.40.10.2380","article-title":"Contributions of individual mechanisms to fluoroquinolone resistance in 36 Escherichia coli strains isolated from humans and animals","volume":"40","author":"Everett","year":"1996","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2084","DOI":"10.1128\/AAC.42.8.2084","article-title":"Correlation between quinolone susceptibility patterns and sequences in the A and B subunits of DNA gyrase in Mycobacteria","volume":"42","author":"Guillemin","year":"1998","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"33584","DOI":"10.1038\/srep33584","article-title":"Development and characterisation of highly antibiotic resistant Bartonella bacilliformis mutants","volume":"6","author":"Gomes","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"2081","DOI":"10.1002\/cbic.200800041","article-title":"Mechanism of binding of fluoroquinolones to the quinolone resistance-determining region of DNA gyrase: Towards an understanding of the molecular basis of quinolone resistance","volume":"9","author":"Madurga","year":"2008","journal-title":"ChemBioChem"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Mendoza-Mujica, G., Flores-Leon, D., and Ruiz, J. (2021). Molecular characterization of fluoroquinolone-resistant Bartonella bacilliformis. Pathogens, 10.","DOI":"10.3390\/pathogens10070876"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1016\/0966-842X(93)90138-H","article-title":"On the mechanism of action of quinolone drugs","volume":"1","author":"Palumbo","year":"1993","journal-title":"Trends Microbiol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1093\/jac\/dkg222","article-title":"Mechanisms of resistance to quinolones: Target alterations, decreased accumulation and DNA Gyrase protection","volume":"51","author":"Ruiz","year":"2003","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1046\/j.1469-0691.2002.00400.x","article-title":"Correlation between the activity of different fluoroquinolones and the presence of mechanisms of quinolone resistance in epidemiologically related and unrelated strains of methicillin-susceptible and -resistant Staphylococcus aureus","volume":"8","author":"Sierra","year":"2002","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1093\/jac\/dki139","article-title":"Brevundimonas diminuta infections and its resistance to fluoroquinolones","volume":"55","author":"Han","year":"2005","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"e506","DOI":"10.1016\/j.ijid.2009.07.025","article-title":"Bartonella bacilliformis, endemic pathogen of the Andean region, is intrinsically resistant to quinolones","volume":"14","author":"Flores","year":"2010","journal-title":"Int. J. Infect. Dis."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1128\/AAC.30.2.248","article-title":"Isolation and characterization of norfloxacin-resistant mutants of Escherichia coli K-12","volume":"30","author":"Hirai","year":"1986","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.jgar.2017.06.011","article-title":"Resistance to quinolones, cephalosporins and macrolides in Escherichia coli causing bacteraemia in Peruvian children","volume":"11","author":"Palma","year":"2017","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1016\/j.tim.2014.04.007","article-title":"Fluoroquinolone resistance: Mechanisms, impact on bacteria, and role in evolutionary success","volume":"22","author":"Redgrave","year":"2014","journal-title":"Trends Microbiol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1093\/jac\/dkh117","article-title":"Effect of the efflux pump inhibitor Phe-Arg-beta-naphthylamide on the MIC values of the quinolones, tetracycline and chloramphenicol, in Escherichia coli isolates of different origin","volume":"53","author":"Ruiz","year":"2004","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/j.cmi.2015.01.007","article-title":"High-level quinolone resistance is associated with the overexpression of smeVWX in Stenotrophomonas maltophilia clinical isolates","volume":"21","year":"2015","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1093\/jac\/dki182","article-title":"Preservation of topoisomerase genetic sequences during in vivo and in vitro development of high-level resistance to ciprofloxacin in isogenic Stenotrophomonas maltophilia strains","volume":"56","author":"Valdezate","year":"2005","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1089\/10766290260469499","article-title":"Mutations in gyrA and parC QRDRs are not relevant for quinolone resistance in epidemiological unrelated Stenotrophomonas maltophilia clinical isolates","volume":"8","author":"Ribera","year":"2002","journal-title":"Microb. Drug Resist."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/S0732-8893(01)00335-2","article-title":"In vitro activity of clinafloxacin in comparison with other quinolones against Stenotrophomonas maltophilia clinical isolates in the presence and absence of reserpine","volume":"42","author":"Ribera","year":"2002","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1128\/am.25.1.21-23.1973","article-title":"R-factors of Escherichia coli from dressed beef and humans","volume":"25","author":"Babcock","year":"1973","journal-title":"Appl. Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1128\/AAC.34.5.681","article-title":"Plasmid-mediated 4-quinolone resistance: A real or apparent absence?","volume":"34","author":"Courvalin","year":"1990","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_69","first-page":"1015","article-title":"Medizinische aspekte der infekti\u00f6sen antibiotika-resistenz gram-negativer darmbakterien","volume":"30","author":"Lebek","year":"1967","journal-title":"Pathol. Microbiol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1016\/S0140-6736(87)90957-3","article-title":"Plasmid-mediated resistance to nalidixic acid in Shigella dysenteriae type 1","volume":"330","author":"Munshi","year":"1987","journal-title":"Lancet"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1016\/S0140-6736(85)91310-8","article-title":"Nalidixic-acid-resistant Shigella dysenteriae I","volume":"325","author":"Panhotra","year":"1985","journal-title":"Lancet"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.eimc.2012.09.008","article-title":"QnrVC, a new transferable Qnr-like family","volume":"31","author":"Pons","year":"2013","journal-title":"Enferm. Infecc. Microbiol. Clin."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/nm1347","article-title":"Fluoroquinolone-modifying enzyme: A new adaptation of a common aminoglycoside acetyltransferase","volume":"12","author":"Robicsek","year":"2006","journal-title":"Nat. Med."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1093\/jac\/dky025","article-title":"Analysis of the presence of erroneous Qnr sequences in GenBank","volume":"73","author":"Ruiz","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_75","first-page":"537","article-title":"In silico analysis of transferable QepA variants and related chromosomal efflux pumps","volume":"31","author":"Ruiz","year":"2018","journal-title":"Rev. Esp. Quimioterap."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"3397","DOI":"10.1093\/jac\/dkz316","article-title":"CrpP, a passenger or a hidden stowaway in the Pseudomonas aeruginosa genome?","volume":"74","author":"Ruiz","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"e0077321","DOI":"10.1128\/AAC.00773-21","article-title":"CrpP is not a fluoroquinolone-inactivating enzyme","volume":"65","author":"Zubyk","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.diagmicrobio.2012.02.011","article-title":"Intrahospitalary dissemination of Klebsiella pneumoniae carrying blaDHA-1 and qnrB4 genes within a novel complex class 1 integron","volume":"73","author":"Estepa","year":"2012","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.meegid.2013.06.029","article-title":"Distribution and functional identification of complex class 1 integrons","volume":"19","author":"Quiroga","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1093\/jac\/48.4.545","article-title":"Frequency of selection of fluoroquinolone-resistant mutants of Neisseria gonorrhoeae exposed to gemifloxacin and four other quinolones","volume":"48","author":"Ruiz","year":"2001","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/S0924-8579(01)00366-1","article-title":"Characterization of sparfloxacin-resistant mutants of Staphylococcus aureus obtained in vitro","volume":"18","author":"Ruiz","year":"2001","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/S0924-8579(03)00241-3","article-title":"In vitro fluoroquinolone-resistant mutants of Salmonella enterica serotype Enteritidis: Analysis of mechanisms involved in resistance","volume":"22","author":"Soto","year":"2003","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_83","first-page":"251","article-title":"Mecanismos de resistencia a betalact\u00e1micos y \u00e1cido nalid\u00edxico en aislados cl\u00ednicos de Salmonella enterica serotipo hadar y bsilla","volume":"22","author":"Navia","year":"2004","journal-title":"Enferm. Infecc. Microbiol. Clin."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1128\/AAC.39.11.2478","article-title":"Incidence and mechanisms of resistance to the combination of amoxicillin and clavulanate in Escherichia coli","volume":"39","author":"Stapleton","year":"1995","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1128\/AAC.38.3.494","article-title":"Effect of hyperproduction of TEM-1 \u03b2-lactamase on in vitro susceptibility of Escherichia coli to \u03b2-lactam antibiotics","volume":"38","author":"Wu","year":"1994","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"6883","DOI":"10.1128\/JB.185.23.6883-6892.2003","article-title":"Quinolone resistance due to reduced target enzyme expression","volume":"185","author":"Ince","year":"2003","journal-title":"J. Bacteriol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"5999","DOI":"10.1128\/jb.176.19.5999-6006.1994","article-title":"Mutations in the -10 TATAAT sequence of the gyrA promoter affect both promoter strength and sensitivity to DNA supercoiling","volume":"176","author":"Straney","year":"1994","journal-title":"J. Bacteriol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1128\/AAC.35.1.20","article-title":"Effects of ciprofloxacin on plasmid DNA supercoiling of Escherichia coli topoisomerase I and gyrase mutants","volume":"35","author":"Aleixandre","year":"1991","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"14759","DOI":"10.1038\/s41598-018-33089-4","article-title":"Inhibition of the gyrA promoter by transcription-coupled DNA supercoiling in Escherichia coli","volume":"8","author":"Dages","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1128\/AAC.46.8.2498-2506.2002","article-title":"Small-colony mutants of Staphylococcus aureus allow selection of gyrase-mediated resistance to dual-target fluoroquinolones","volume":"46","author":"Pan","year":"2002","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"3615","DOI":"10.1093\/nar\/gkx070","article-title":"Measurements of translation initiation from all 64 codons in E. coli","volume":"45","author":"Hecht","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1093\/femsre\/fuz011","article-title":"Free-living amoebae and squatters in the wild: Ecological and molecular features","volume":"43","author":"Delafont","year":"2019","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"3254","DOI":"10.1128\/iai.62.8.3254-3261.1994","article-title":"Growth of Legionella pneumophila in Acanthamoeba castellanii enhances invasion","volume":"62","author":"Cirillo","year":"1994","journal-title":"Infect. Immun."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1128\/AEM.71.1.20-28.2005","article-title":"Amoebae as training grounds for intracellular bacterial pathogens","volume":"71","author":"Molmeret","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Saisongkorh, W., Robert, C., La Scola, B., Raoult, D., and Rolain, J.M. (2010). Evidence of transfer by conjugation of type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0012666"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1590\/S0036-46652015000100012","article-title":"identification of Pseudomonas spp. as amoeba-resistant microorganisms in isolates of Acanthamoeba","volume":"57","author":"Maschio","year":"2015","journal-title":"Rev. Inst. Med. Trop. Sao Paulo"},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Judy, B.M., Whitlock, G.C., Torres, A.G., and Estes, D.M. (2009). Comparison of the in vitro and in vivo susceptibilities of Burkholderia mallei to ceftazidime and levofloxacin. BMC Microbiol., 9.","DOI":"10.1186\/1471-2180-9-88"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"11","DOI":"10.3354\/dao02696","article-title":"Antibiotic uptake by cultured Atlantic cod leucocytes and effect on intracellular Francisella noatunensis subsp. noatunensis replication","volume":"108","author":"Kaldestad","year":"2014","journal-title":"Dis. Aquat. Organ."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.ijantimicag.2017.03.033","article-title":"In-vitro development of an effective treatment for Acanthamoeba keratitis","volume":"50","author":"Belloc","year":"2017","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.1128\/AAC.49.6.2429-2437.2005","article-title":"Influence of efflux transporters on the accumulation and efflux of four quinolones (ciprofloxacin, levofloxacin, garenoxacin, and moxifloxacin) in J774 macrophages","volume":"49","author":"Michot","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"3040","DOI":"10.1128\/AAC.00105-08","article-title":"Cooperation between prokaryotic (Lde) and eukaryotic (MRP) efflux transporters in J774 macrophages infected with Listeria monocytogenes: Studies with ciprofloxacin and moxifloxacin","volume":"52","author":"Lismond","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.molbiopara.2016.03.009","article-title":"Characterisation and expression analysis of trophozoite and cyst proteins of Acanthamoeba spp. isolated from Acanthamoeba keratitis (AK) patient","volume":"205","author":"Behera","year":"2016","journal-title":"Mol. Biochem. Parasitol."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1128\/EC.05301-11","article-title":"Cellular, biochemical, and molecular changes during encystment of free-living amoebae","volume":"11","author":"Fouque","year":"2012","journal-title":"Eukaryot. Cell"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.micinf.2011.10.004","article-title":"The Pseudomonas aeruginosa toxin L-2-amino-4-methoxy-trans-3-butenoic acid inhibits growth and induces encystment in Acanthamoeba castellanii","volume":"14","author":"Lee","year":"2012","journal-title":"Microbes Infect."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.exppara.2019.03.011","article-title":"Fate of internalized Campylobacter jejuni and Mycobacterium avium from encysted and excysted Acanthamoeba polyphaga","volume":"199","author":"Dixon","year":"2019","journal-title":"Exp. Parasitol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"2684","DOI":"10.1128\/AAC.39.12.2684","article-title":"Intraphagocytic growth induces an antibiotic-resistant phenotype of Legionella pneumophila","volume":"39","author":"Barker","year":"1995","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_107","doi-asserted-by":"crossref","unstructured":"Dubois, V., Pawlik, A., Bories, A., Le Moigne, V., Sismeiro, O., Legendre, R., Varet, H., Rodr\u00edguez-Ord\u00f3\u00f1ez, M.D.P., Gaillard, J.L., and Copp\u00e9e, J.Y. (2019). Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages. PLoS Pathog., 15.","DOI":"10.1101\/529057"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/S0923-2508(01)01240-2","article-title":"Bacterial infections of free-living amoebae","volume":"152","author":"Linder","year":"2001","journal-title":"Res. Microbiol."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"e01600-17","DOI":"10.1128\/AEM.01600-17","article-title":"CmeABC Multidrug efflux pump contributes to antibiotic resistance and promotes Campylobacter jejuni survival and multiplication in Acanthamoeba polyphaga","volume":"83","author":"Vieira","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Grinnage-Pulley, T., and Zhang, Q. (2015). Genetic basis and functional consequences of differential expression of the CmeABC efflux pump in Campylobacter jejuni isolates. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0131534"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1093\/jac\/dkl412","article-title":"Role of the CmeABC efflux pump in the emergence of fluoroquinolone-resistant Campylobacter under selection pressure","volume":"58","author":"Yan","year":"2006","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"1913","DOI":"10.1111\/j.1462-2920.2011.02657.x","article-title":"The Pel and Psl polysaccharides provide Pseudomonas aeruginosa structural redundancy within the biofilm matrix","volume":"14","author":"Colvin","year":"2012","journal-title":"Environ. Microbiol."},{"key":"ref_113","doi-asserted-by":"crossref","unstructured":"Oliveira, F., Lima, C.A., Br\u00e1s, S., Fran\u00e7a, \u00c2., and Cerca, N. (2015). Evidence for inter- and intraspecies biofilm formation variability among a small group of coagulase-negative staphylococci. FEMS Microbiol. Lett., 362.","DOI":"10.1093\/femsle\/fnv175"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1093\/femsre\/fux010","article-title":"Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria","volume":"41","author":"Hall","year":"2017","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1016\/j.ijantimicag.2009.12.011","article-title":"Antibiotic resistance of bacterial biofilms","volume":"35","author":"Bjarnsholt","year":"2010","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.mib.2016.01.004","article-title":"Escaping the biofilm in more than one way: Desorption, detachment or dispersion","volume":"30","author":"Petrova","year":"2016","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-3-319-11038-7_1","article-title":"Biofilm formation by clinical isolates and its relevance to clinical infections","volume":"830","author":"Akers","year":"2015","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1080\/14787210.2018.1417036","article-title":"Biofilm-related disease","volume":"16","year":"2018","journal-title":"Expert Rev. Anti Infect. Ther."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.ajic.2003.08.005","article-title":"Role of biofilm in catheter-associated urinary tract infection","volume":"32","author":"Trautner","year":"2004","journal-title":"Am. J. Infect. Control"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1093\/femsre\/fuw002","article-title":"Experimental evolution in biofilm populations","volume":"40","author":"Steenackers","year":"2016","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_121","doi-asserted-by":"crossref","unstructured":"Taghizadeh, L., Karimi, A., Presterl, E., and Heitzinger, C. (2020). Bayesian inversion for a biofilm model including quorum sensing. Comput. Biol. Med., 117.","DOI":"10.1016\/j.compbiomed.2019.103582"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"2613","DOI":"10.2147\/IDR.S310081","article-title":"Phenotypic and genotypic characteristics of biofilm formation in clinical isolates of Acinetobacter baumannii","volume":"14","author":"Li","year":"2021","journal-title":"Infect. Drug Resist."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1556\/avet.2013.054","article-title":"Characterisation of Pseudomonas aeruginosa related to bovine mastitis","volume":"62","author":"Park","year":"2014","journal-title":"Acta Vet. Hung."},{"key":"ref_124","doi-asserted-by":"crossref","unstructured":"Ciofu, O., and Tolker-Nielsen, T. (2019). Tolerance and resistance of Pseudomonas aeruginosa biofilms to antimicrobial agents-How P. aeruginosa can escape antibiotics. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00913"},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"1818","DOI":"10.1128\/AAC.44.7.1818-1824.2000","article-title":"Role of antibiotic penetration limitation in Klebsiella pneumoniae biofilm resistance to ampicillin and ciprofloxacin","volume":"44","author":"Anderl","year":"2000","journal-title":"Antimicrob. Agents Chemoter."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1128\/AAC.38.9.2125","article-title":"Investigation of ciprofloxacin penetration into Pseudomonas aeruginosa biofilms","volume":"38","author":"Suci","year":"1994","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Billings, N., Millan, M., Caldara, M., Rusconi, R., Tarasova, Y., Stocker, R., and Ribbeck, K. (2013). The extracellular matrix component Psl provides fast-acting antibiotic defense in Pseudomonas aeruginosa biofilms. PLoS Pathog., 9.","DOI":"10.1371\/journal.ppat.1003526"},{"key":"ref_128","doi-asserted-by":"crossref","unstructured":"Colvin, K.M., Gordon, V.D., Murakami, K., Borlee, B.R., Wozniak, D.J., Wong, G.C., and Parsek, M.R. (2011). The Pel polysaccharide can serve a structural and protective role in the biofilm matrix of Pseudomonas aeruginosa. PLoS Pathog., 7.","DOI":"10.1371\/journal.ppat.1001264"},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"2958","DOI":"10.1128\/AEM.67.7.2958-2965.2001","article-title":"Detection of differential gene expression in biofilm-forming versus planktonic populations of Staphylococcus aureus using micro-representational-difference analysis","volume":"67","author":"Becker","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"3190","DOI":"10.1021\/pr2002353","article-title":"Differences in metabolism between the biofilm and planktonic response to metal stress","volume":"10","author":"Booth","year":"2011","journal-title":"J. Proteome Res."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1128\/AAC.8.3.251","article-title":"Nalidixic acid: An antibacterial paradox","volume":"8","author":"Crumplin","year":"1975","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_132","doi-asserted-by":"crossref","unstructured":"Uru\u00e9n, C., Chopo-Escuin, G., Tommassen, J., Mainar-Jaime, R.C., and Arenas, J. (2020). Biofilms as promoters of bacterial antibiotic resistance and tolerance. Antibiotics, 10.","DOI":"10.3390\/antibiotics10010003"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"e01024-17","DOI":"10.1128\/AAC.01024-17","article-title":"Hyperbaric oxygen sensitizes anoxic Pseudomonas aeruginosa biofilm to ciprofloxacin","volume":"61","author":"Kolpen","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_134","doi-asserted-by":"crossref","unstructured":"Soares, A., Roussel, V., Pestel-Caron, M., Barreau, M., Caron, F., Bouffartigues, E., Chevalier, S., and Etienne, M. (2019). Understanding ciprofloxacin failure in Pseudomonas aeruginosa biofilm: Persister cells survive matrix disruption. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.02603"},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"5568","DOI":"10.1128\/jb.178.19.5568-5572.1996","article-title":"Identification of a pKM101 region which confers a slow growth rate and interferes with susceptibility to quinolone in Escherichia coli AB1157","volume":"178","author":"Clerch","year":"1996","journal-title":"J. Bacteriol."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1016\/j.ejmech.2013.01.057","article-title":"Antibacterial action of quinolones: From target to network","volume":"66","author":"Cheng","year":"2013","journal-title":"Eur. J. Med. Chem."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1128\/AAC.01617-06","article-title":"Quinolone-mediated bacterial death","volume":"52","author":"Drlica","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"e01283-20","DOI":"10.1128\/AAC.01283-20","article-title":"(p)ppGpp and its role in bacterial persistence: New challenges","volume":"64","author":"Pacios","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"e14220","DOI":"10.1016\/j.heliyon.2023.e14220","article-title":"Toxin-antitoxin systems in bacterial pathogenesis","volume":"9","author":"Sonika","year":"2023","journal-title":"Heliyon"},{"key":"ref_140","doi-asserted-by":"crossref","unstructured":"Ma, Z., King, K., Alqahtani, M., Worden, M., Muthuraman, P., Cioffi, C.L., Bakshi, C.S., and Malik, M. (2019). Stringent response governs the oxidative stress resistance and virulence of Francisella tularensis. PLoS ONE, 14.","DOI":"10.1101\/653790"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1146\/annurev.micro.62.081307.162903","article-title":"(p)ppGpp: Still magical?","volume":"62","author":"Potrykus","year":"2008","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_142","doi-asserted-by":"crossref","unstructured":"Pan, X., Liu, W., Du, Q., Zhang, H., and Han, D. (2023). Recent advances in bacterial persistence mechanisms. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241814311"},{"key":"ref_143","doi-asserted-by":"crossref","unstructured":"Das, B., and Bhadra, R.K. (2020). (p)ppGpp Metabolism and antimicrobial resistance in bacterial pathogens. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.563944"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1111\/j.1348-0421.2006.tb03793.x","article-title":"Functional analysis of spoT, relA and dksA genes on quinolone tolerance in Pseudomonas aeruginosa under nongrowing condition","volume":"50","author":"Viducic","year":"2006","journal-title":"Microbiol. Immunol."},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"D\u00f6rr, T., Vuli\u0107, M., and Lewis, K. (2010). Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol., 8.","DOI":"10.1371\/journal.pbio.1000317"},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1111\/mmi.14165","article-title":"The toxin from a ParDE toxin-antitoxin system found in Pseudomonas aeruginosa offers protection to cells challenged with anti-gyrase antibiotics","volume":"111","author":"Muthuramalingam","year":"2019","journal-title":"Mol. Microbiol."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"9872","DOI":"10.1038\/s41598-019-46318-1","article-title":"A ParDE-family toxin antitoxin system in major resistance plasmids of Enterobacteriaceae confers antibiotic and heat tolerance","volume":"9","author":"Kamruzzaman","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"Kang, S.M., Kim, D.H., Jin, C., and Lee, B.J. (2018). A systematic overview of type II and III toxin-antitoxin systems with a focus on druggability. Toxins, 10.","DOI":"10.3390\/toxins10120515"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/j.chom.2013.05.012","article-title":"The normalcy of dormancy: Common themes in microbial quiescence","volume":"13","author":"Rittershaus","year":"2013","journal-title":"Cell Host Microbe"},{"key":"ref_150","doi-asserted-by":"crossref","unstructured":"Bush, N.G., Evans-Roberts, K., and Maxwell, A. (2015). DNA Topoisomerases. EcoSal Plus, 6.","DOI":"10.1128\/ecosalplus.esp-0010-2014"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"4573","DOI":"10.1128\/AAC.02463-14","article-title":"Antagonism between bacteriostatic and bactericidal antibiotics is prevalent","volume":"58","author":"Ocampo","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/ismej.2017.168","article-title":"Polymorphism of antibiotic-inactivating enzyme driven by ecology expands the environmental resistome","volume":"12","author":"Kim","year":"2018","journal-title":"ISME J."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"e02629-17","DOI":"10.1128\/AAC.02629-17","article-title":"CrpP is a novel ciprofloxacin-modifying enzyme encoded by the Pseudomonas aeruginosa pUM505 plasmid","volume":"62","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"4206","DOI":"10.1128\/aem.62.11.4206-4209.1996","article-title":"Degradation of the fluoroquinolone enrofloxacin by wood-rotting fungi","volume":"62","author":"Martens","year":"1996","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_155","doi-asserted-by":"crossref","unstructured":"Ben Ayed, A., Akrout, I., Albert, Q., Greff, S., Simmler, C., Armengaud, J., Kielbasa, M., Turb\u00e9-Doan, A., Chaduli, D., and Navarro, D. (2022). Biotransformation of the fluoroquinolone, levofloxacin, by the white-rot fungus Coriolopsis gallica. J. Fungi, 8.","DOI":"10.3390\/jof8090965"},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.chemosphere.2014.12.012","article-title":"Biotransformation of fluoroquinolone antibiotics by ligninolytic fungi\u2014Metabolites, enzymes and residual antibacterial activity","volume":"136","author":"Moeder","year":"2015","journal-title":"Chemosphere"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"6897","DOI":"10.1021\/acs.jafc.5b02343","article-title":"Biotransformation of the antibiotic danofloxacin by Xylaria longipes leads to an efficient reduction of its antibacterial activity","volume":"63","author":"Rusch","year":"2015","journal-title":"J. Agric. Food Chem."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"1556","DOI":"10.1128\/AEM.65.4.1556-1563.1999","article-title":"Degradation of ciprofloxacin by basidiomycetes and identification of metabolites generated by the brown rot fungus Gloeophyllum striatum","volume":"65","author":"Wetzstein","year":"1999","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.chemosphere.2017.12.062","article-title":"Simultaneous removal of ciprofloxacin, norfloxacin, sulfamethoxazole by co-producing oxidative enzymes system of Phanerochaete chrysosporium and Pycnoporus sanguineus","volume":"195","author":"Gao","year":"2018","journal-title":"Chemosphere"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"e08865","DOI":"10.1016\/j.heliyon.2022.e08865","article-title":"Biodelignification of lignocellulose using ligninolytic enzymes from white-rot fungi","volume":"8","author":"Suryadi","year":"2022","journal-title":"Heliyon"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1007\/s00449-017-1786-y","article-title":"Efficient enzymatic degradation used as pre-stage treatment for norfloxacin removal by activated sludge","volume":"40","author":"Zhao","year":"2017","journal-title":"Bioprocess. Biosyst. Eng."},{"key":"ref_162","doi-asserted-by":"crossref","unstructured":"Chen, Z., Li, N., Lan, Q., Zhang, X., Wu, L., Liu, J., and Yang, R. (2021). Laccase inducer Mn2+ inhibited the intracellular degradation of norfloxacin by Phanerochaete chrysosporium. Int. Biodeterior. Biodegrad., 164.","DOI":"10.1016\/j.ibiod.2021.105300"},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"5790","DOI":"10.1128\/AEM.03032-05","article-title":"Transformation of the antibacterial agent norfloxacin by environmental mycobacteria","volume":"72","author":"Adjei","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"3181","DOI":"10.1007\/s00253-013-5333-8","article-title":"Biodegradation of ofloxacin, norfloxacin, and ciprofloxacin as single and mixed substrates by Labrys portucalensis F11","volume":"98","author":"Amorim","year":"2014","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"6100","DOI":"10.1128\/AEM.00545-11","article-title":"Modification of norfloxacin by a Microbacterium sp. strain isolated from a wastewater treatment plant","volume":"77","author":"Kim","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.jhazmat.2017.09.009","article-title":"Study of ciprofloxacin biodegradation by a Thermus sp. isolated from pharmaceutical sludge","volume":"343","author":"Pan","year":"2018","journal-title":"J. Hazard. Mater."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1038\/sj.jim.2900409","article-title":"Microbial models of soil metabolism: Biotransformations of danofloxacin","volume":"19","author":"Chen","year":"1997","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1128\/AEM.02347-12","article-title":"Identification of the enzyme responsible for N-acetylation of norfloxacin by Microbacterium sp. strain 4N2-2","volume":"79","author":"Kim","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_169","doi-asserted-by":"crossref","unstructured":"Millanao, A.R., Mora, A.Y., Saavedra, C., Villagra, N.A., Mora, G.C., and Hidalgo, A.A. (2020). Inactivation of glutamine synthetase-coding gene glnA increases susceptibility to quinolones through increasing outer membrane protein F in Salmonella enterica Serovar Typhi. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00428"},{"key":"ref_170","doi-asserted-by":"crossref","unstructured":"Bl\u00e1nquez, A., Guill\u00e9n, F., Rodr\u00edguez, J., Arias, M.E., and Hern\u00e1ndez, M. (2016). The degradation of two fluoroquinolone based antimicrobials by SilA, an alkaline laccase from Streptomyces ipomoeae. World J. Microbiol. Biotechnol., 32.","DOI":"10.1007\/s11274-016-2032-5"},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1080\/07391102.2023.2197074","article-title":"Comparative analysis of SilA-laccase mediated degradation of ciprofloxacin, norfloxacin and ofloxacin and interpretation of the possible catalytic mechanism","volume":"42","author":"Bhatt","year":"2024","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"4979","DOI":"10.1128\/AAC.05187-11","article-title":"Citrobacter spp. as a source of qnrB alleles","volume":"55","author":"Jacoby","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1093\/jac\/dks086","article-title":"Prevalence of the oqxAB gene complex in Klebsiella pneumoniae and Escherichia coli clinical isolates","volume":"67","author":"Yuan","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1093\/jac\/45.4.521","article-title":"In vitro selected fluoroquinolone-resistant mutants of Citrobacter freundii: Analysis of the quinolone resistance acquisition","volume":"45","author":"Vila","year":"2000","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.ijantimicag.2008.03.012","article-title":"In vitro-selected resistance to fluoroquinolones in two Brucella strains associated with mutational changes in gyrA","volume":"32","author":"Turkmani","year":"2008","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/S0924-8579(00)00117-5","article-title":"Decreased permeability and enhanced proton-dependent active efflux in the development of resistance to quinolones in Morganella morganii","volume":"14","author":"Vila","year":"2000","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_177","first-page":"537","article-title":"Mutations that enhance the ciprofloxacin resistance of Escherichia coli with qnrA1","volume":"60","author":"Corcoran","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"3699","DOI":"10.1128\/JB.184.13.3699-3703.2002","article-title":"Toxic waste disposal in Escherichia coli","volume":"184","author":"Helling","year":"2002","journal-title":"J. Bacteriol."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"2241","DOI":"10.1093\/jac\/dkv109","article-title":"Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure","volume":"70","author":"Webber","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/jac\/dkw364","article-title":"Ciprofloxacin selects for RNA polymerase mutations with pleiotropic antibiotic resistance effects","volume":"72","author":"Pietsch","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_181","first-page":"3285","article-title":"Effect of aminoacyl-tRNA synthetase mutations on susceptibility to ciprofloxacin in Escherichia coli","volume":"73","author":"Garoff","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1093\/jac\/dkn077","article-title":"Low selection of topoisomerase mutants from strains of Escherichia coli harbouring plasmid-borne qnr genes","volume":"61","author":"Cesaro","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"196","DOI":"10.7883\/yoken.JJID.2014.153","article-title":"Contribution of QnrA, a plasmid mediated quinolone resistance peptide, to survival of Escherichia coli exposed to a lethal ciprofloxacin concentration","volume":"68","author":"Goto","year":"2015","journal-title":"Jpn. J. Infect. Dis."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1128\/jb.104.2.1027-1029.1970","article-title":"Nalidixic acid-resistant auxotrophs of Escherichia coli","volume":"104","author":"Helling","year":"1970","journal-title":"J. Bacteriol."},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"e02769-19","DOI":"10.1128\/AEM.02769-19","article-title":"Dissemination of quinolone-resistant Escherichia coli in the Norwegian broiler and pig production chains and possible persistence in the broiler production environment","volume":"86","author":"Kaspersen","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1007\/s00203-019-01693-1","article-title":"Proteomics-based discrimination of differentially expressed proteins in antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium, Klebsiella pneumoniae, and Staphylococcus aureus","volume":"201","author":"Uddin","year":"2019","journal-title":"Arch. Microbiol."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"18261","DOI":"10.1073\/pnas.0810357105","article-title":"Revisiting the mechanism of macrolide-antibiotic resistance mediated by ribosomal protein L22","volume":"105","author":"Moore","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1111\/j.1574-6968.1993.tb06458.x","article-title":"Correlation between umuC induction and Salmonella mutagenicity assay for quinolone antimicrobial agents","volume":"112","author":"Power","year":"1993","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1093\/mutage\/5.1.63","article-title":"Induction of SOS genes in Escherichia coli and mutagenesis in Salmonella typhimurium by fluoroquinolones","volume":"5","author":"Ysern","year":"1990","journal-title":"Mutagenesis"},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"4486","DOI":"10.1128\/AAC.00222-08","article-title":"Complex ciprofloxacin resistome revealed by screening a Pseudomonas aeruginosa mutant library for altered susceptibility","volume":"52","author":"Breidenstein","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_191","doi-asserted-by":"crossref","unstructured":"Agnello, M., Finkel, S.E., and Wong-Beringer, A. (2016). Fitness cost of fluoroquinolone resistance in clinical isolates of Pseudomonas aeruginosa differs by type III secretion genotype. Front. Microbiol., 7.","DOI":"10.3389\/fmicb.2016.01591"},{"key":"ref_192","doi-asserted-by":"crossref","unstructured":"Agnello, M., and Wong-Beringer, A. (2012). Differentiation in quinolone resistance by virulence genotype in Pseudomonas aeruginosa. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0042973"},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"10874","DOI":"10.1038\/s41598-019-47303-4","article-title":"High frequency of the exoU+\/exoS+ genotype associated with multidrug-resistant \u201chigh-risk clones\u201d of Pseudomonas aeruginosa clinical isolates from Peruvian hospitals","volume":"9","author":"Horna","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_194","doi-asserted-by":"crossref","unstructured":"Lim, W.S., Phang, K.K., Tan, A.H., Li, S.F., and Ow, D.S. (2016). Small colony variants and single nucleotide variations in Pf1 region of PB1 phage-resistant Pseudomonas aeruginosa. Front. Microbiol., 7.","DOI":"10.3389\/fmicb.2016.00282"},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1111\/eva.12397","article-title":"Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity","volume":"9","author":"Ramiro","year":"2016","journal-title":"Evol. Appl."},{"key":"ref_196","doi-asserted-by":"crossref","unstructured":"Curtis, T.D., Gram, L., and Knudsen, G.M. (2016). The small colony variant of Listeria monocytogenes is more tolerant to antibiotics and has altered survival in RAW 264.7 murine macrophages. Front. Microbiol., 7.","DOI":"10.3389\/fmicb.2016.01056"},{"key":"ref_197","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1093\/jac\/39.6.697","article-title":"Characteristics of quinolone-induced small colony variants in Staphylococcus aureus","volume":"39","author":"Mitsuyama","year":"1997","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.ygeno.2019.04.002","article-title":"Transcriptome analysis of Burkholderia pseudomallei SCV reveals an association with virulence, stress resistance and intracellular persistence","volume":"112","author":"Vellasamy","year":"2020","journal-title":"Genomics"},{"key":"ref_199","doi-asserted-by":"crossref","unstructured":"Sandoz, K.M., Popham, D.L., Beare, P.A., Sturdevant, D.E., Hansen, B., Nair, V., and Heinzen, R.A. (2016). Transcriptional profiling of Coxiella burnetii reveals extensive cell wall remodeling in the small cell variant developmental form. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0149957"},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.femsim.2003.12.007","article-title":"Persistence of a Staphylococcus aureus small-colony variant under antibiotic pressure in vivo","volume":"41","author":"Brouillette","year":"2004","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1128\/IAI.01487-13","article-title":"Identification of point mutations in clinical Staphylococcus aureus strains that produce small-colony variants auxotrophic for menadione","volume":"82","author":"Dean","year":"2014","journal-title":"Infect. Immun."},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1002\/ppul.24730","article-title":"Thymidine-auxotrophic Staphylococcus aureus small-colony variant bacteremia in a patient with cystic fibrosis","volume":"55","author":"Cogo","year":"2020","journal-title":"Pediatr. Pulmonol."},{"key":"ref_203","doi-asserted-by":"crossref","unstructured":"Hubbard, A.T.M., Bulgasim, I., and Roberts, A.P. (2021). A novel hemA mutation is responsible for a small-colony-variant phenotype in Escherichia coli. Microbiology, 167.","DOI":"10.1099\/mic.0.000962"},{"key":"ref_204","first-page":"e000262","article-title":"Genomic and transcriptomic characterization of Pseudomonas aeruginosa small colony variants derived from a chronic infection model","volume":"5","author":"Irvine","year":"2019","journal-title":"Microb. Genom."},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1128\/AAC.02330-15","article-title":"Optimized in vitro antibiotic susceptibility testing method for small-colony variant Staphylococcus aureus","volume":"60","author":"Precit","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_206","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1128\/mr.52.3.354-374.1988","article-title":"Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli","volume":"52","author":"Eggertsson","year":"1988","journal-title":"Microbiol. Rev."},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1590\/S1517-83822012000400010","article-title":"Mutations in the quinolone resistance-determining regions of gyrA and parC in Enterobacteriaceae isolates from Brazil","volume":"43","author":"Minarini","year":"2012","journal-title":"Braz. J. Microbiol."}],"container-title":["Life"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2075-1729\/14\/3\/383\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:13:26Z","timestamp":1760105606000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2075-1729\/14\/3\/383"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,14]]},"references-count":207,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2024,3]]}},"alternative-id":["life14030383"],"URL":"https:\/\/doi.org\/10.3390\/life14030383","relation":{},"ISSN":["2075-1729"],"issn-type":[{"value":"2075-1729","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,14]]}}}