{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T14:42:23Z","timestamp":1792852943837,"version":"4.5.0"},"reference-count":250,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,4,10]],"date-time":"2025-04-10T00:00:00Z","timestamp":1744243200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    More than three decades ago multidrug-resistant (MDR) clones of the pathogens:\n                    <jats:italic>Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Clostridioides difficile, Enterococcus faecium, Pseudomonas aeruginosa and Acinetobacter baumannii<\/jats:italic>\n                    have started to disseminate across wide geographical areas. A characteristic feature of all these MDR lineages is the carriage of some mutations in the quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV which besides conferring resistance to fluoroquinolones are associated with a fitness benefit. Several lines of evidence strongly suggest that extra fitness conferred by these mutations facilitated the dissemination of the international MDR lineages. MDR pathogens require extra energy to cover the fitness cost conferred by the excess antibiotic resistance gene cargo. However, extra energy generated by upgraded metabolic activity was demonstrated to increase the uptake of antibiotics enhancing susceptibility. Accordingly, MDR bacteria need additional positive fitness schemes which, similarly to the QRDR advantage, will not compromise resistance. Some of these, not clone-specific effects are large genomes, the carriage of low-cost plasmids, the transfer of plasmid genes to the chromosome, the application of weak promoters in integrons and various techniques for the economic control of the activity of the integrase enzyme including a highly sophisticated system in\n                    <jats:italic>A. baumannii.<\/jats:italic>\n                    These impacts \u2013 among others \u2013 will confer a fitness advantage promoting the spread of MDR pathogens. However, even the potential of extra fitness generated by the combined effect of various schemes is not without limit and virulence-related genes or less relevant antibiotic resistance gene cargoes will often be sacrificed to permit the acquisition of high-priority resistance determinants. Accordingly major MDR clone strains are usually less virulent than susceptible isolates. In summary, a fitness approach to the research of antibiotic resistance is very useful since the fitness status of MDR bacteria seem to profoundly impact the capacity to disseminate in the healthcare setting.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2025.1556656","type":"journal-article","created":{"date-parts":[[2025,4,10]],"date-time":"2025-04-10T09:48:01Z","timestamp":1744278481000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":23,"title":["The fitness connection of antibiotic resistance"],"prefix":"10.3389","volume":"16","author":[{"given":"Miklos","family":"Fuzi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,4,10]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"15","DOI":"10.20506\/rst.31.1.2093","article-title":"Antimicrobial resistance in animal and public health: introduction and classification of antimicrobial agents","volume":"31","author":"Acar","year":"2012","journal-title":"Rev. Sci. Tech."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"425","DOI":"10.18388\/abp.2003_3696","article-title":"Spread and survival of promiscuous IncP-1 plasmids","volume":"50","author":"Adamczyk","year":"2003","journal-title":"Acta Biochim. Pol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1526","DOI":"10.1093\/molbev\/msu111","article-title":"High fitness costs and instability of gene duplications reduce rates of evolution of new genes by duplication-divergence mechanisms","volume":"31","author":"Adler","year":"2014","journal-title":"Mol. Biol. Evol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"1591","DOI":"10.3389\/fmicb.2016.01591","article-title":"Fitness cost of fluoroquinolone resistance in clinical isolates of Pseudomonas aeruginosa differs by type III secretion genotype","volume":"7","author":"Agnello","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"e42973","DOI":"10.1371\/journal.pone.0042973","article-title":"Differentiation in quinolone resistance by virulence genotype in Pseudomonas aeruginosa","volume":"7","author":"Agnello","year":"2012","journal-title":"PLoS One"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"2912","DOI":"10.1128\/JCM.00692-08","article-title":"Changing patterns in frequency of recovery of five methicillin-resistant Staphylococcus aureus clones in Portuguese hospitals: surveillance over a 16-year period","volume":"46","author":"Aires-De-Sousa","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1250","DOI":"10.3390\/antibiotics11091250","article-title":"A threshold logistic modelling approach for identifying thresholds between antibiotic use and methicillin-resistant Staphylococcus aureus incidence rates in hospitals","volume":"11","author":"Aldeyab","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"2881","DOI":"10.1128\/JCM.00603-07","article-title":"Changes in the clonal nature and antibiotic resistance profiles of methicillin-resistant Staphylococcus aureus isolates associated with spread of the EMRSA-15 clone in a tertiary care Portuguese hospital","volume":"45","author":"Amorim","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1038\/nrmicro2319","article-title":"Antibiotic resistance and its cost: is it possible to reverse resistance?","volume":"8","author":"Andersson","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"5577","DOI":"10.1128\/JB.00853-13","article-title":"Identification of a DNA-damage-inducible regulon in Acinetobacter baumannii","volume":"195","author":"Aranda","year":"2013","journal-title":"J. Bacteriol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"e0018422","DOI":"10.1128\/msphere.00184-22","article-title":"Genomics, transcriptomics, and metabolomics reveal that minimal modifications in the host are crucial for the compensatory evolution of ColE1-like plasmids","volume":"7","author":"Ares-Arroyo","year":"2022","journal-title":"mSphere"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"108","DOI":"10.3390\/antibiotics12010108","article-title":"Antimicrobial resistance, virulence factors, and genotypes of Enterococcus faecalis and Enterococcus faecium clinical isolates in northern Japan: identification of optrA in ST480 E. faecalis","volume":"12","author":"Aung","year":"2023","journal-title":"Antibiotics (Basel)"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1016\/j.cmi.2023.05.015","article-title":"Markers of epidemiological success of methicillin-resistant Staphylococcus aureus isolates in European populations","volume":"29","author":"Baede","year":"2023","journal-title":"Clin. Microbiol. Infect."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"e01229","DOI":"10.7554\/eLife.01229","article-title":"Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure","volume":"2","author":"Baker","year":"2013","journal-title":"eLife"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.7754\/Clin.Lab.2018.180709","article-title":"Molecular study of Klebsiella pneumoniae virulence genes from patients with hospital acquired sepsis","volume":"65","author":"Bakr","year":"2019","journal-title":"Clin. Lab."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"2575","DOI":"10.1128\/JCM.00533-15","article-title":"Clostridium difficile PCR ribotype 018, a successful epidemic genotype","volume":"53","author":"Baldan","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/j.eimc.2013.01.004","article-title":"Escherichia coli ST131: variations on a theme of clonal expansion","volume":"31","author":"Banerjee","year":"2013","journal-title":"Enferm. Infecc. Microbiol. Clin."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"e0005019","DOI":"10.1128\/CMR.00050-19","article-title":"Evolutionary pathways and trajectories in antibiotic resistance","volume":"34","author":"Baquero","year":"2021","journal-title":"Clin. Microbiol. Rev."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1472","DOI":"10.1093\/molbev\/msaa307","article-title":"Genetic architecture and fitness of bacterial interspecies hybrids","volume":"38","author":"Bartke","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/S0140-6736(10)61266-4","article-title":"Clostridium difficile infection in Europe: a hospital-based survey","volume":"377","author":"Bauer","year":"2011","journal-title":"Lancet"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/j.medmal.2019.11.008","article-title":"Example of antimicrobial stewardship program in a community hospital in Italy","volume":"50","author":"Bolla","year":"2020","journal-title":"Med. Mal. Infect."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"e0133727","DOI":"10.1371\/journal.pone.0133727","article-title":"Genomic analysis of the emergence and rapid global dissemination of the clonal group Klebsiella pneumoniae pandemic","volume":"10","author":"Bowers","year":"2015","journal-title":"PLoS One"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"1852","DOI":"10.1093\/gbe\/evy139","article-title":"Comparative genomics of nonoutbreak Pseudomonas aeruginosa strains underlines genome plasticity and geographic relatedness of the global clone ST235","volume":"10","author":"Br\u00fcggemann","year":"2018","journal-title":"Genome Biol. Evol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"100224","DOI":"10.1016\/j.coesh.2020.10.012","article-title":"Aspects of excessive antibiotic consumption and environmental influences correlated with the occurrence of resistance to antimicrobial agents","volume":"19","author":"Bungau","year":"2021","journal-title":"Curr Opin Environ Sci Health"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"6349","DOI":"10.1128\/AAC.01388-12","article-title":"Genetic markers of widespread extensively drug-resistant Pseudomonas aeruginosa high-risk clones","volume":"56","author":"Cabot","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.001583","article-title":"Molecular patterns of clinically important fluoroquinolone resistance in multidrug-resistant Klebsiella pneumoniae isolates during nosocomial outbreaks in Shanghai, PR China","volume":"71","author":"Cai","year":"2022","journal-title":"J. Med. Microbiol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1759-8753-2-6","article-title":"Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons","volume":"2","author":"Cambray","year":"2011","journal-title":"Mob. DNA"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1016\/j.anaerobe.2009.09.009","article-title":"Diversity of moxifloxacin resistance during a nosocomial outbreak of a predominantly ribotype ARU 027 Clostridium difficile diarrhea","volume":"15","author":"Carman","year":"2009","journal-title":"Anaerobe"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"e0071322","DOI":"10.1128\/msystems.00713-22","article-title":"Evolutionary responses to acquiring a multidrug resistance plasmid are dominated by metabolic functions across diverse Escherichia coli lineages","volume":"8","author":"Carrilero","year":"2023","journal-title":"mSystems"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"e0252023","DOI":"10.1128\/mbio.02520-23","article-title":"Genomic epidemiology of Acinetobacter baumannii goes global","volume":"14","author":"Castillo-Ram\u00edrez","year":"2023","journal-title":"MBio"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1093\/jac\/dks469","article-title":"Twenty-five years of shared life with vancomycin-resistant enterococci: is it time to divorce?","volume":"68","author":"Cattoir","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"e02016","DOI":"10.1128\/mBio.02016-17","article-title":"Range expansion and the origin of USA300 north American epidemic methicillin-resistant Staphylococcus aureus","volume":"9","author":"Challagundla","year":"2018","journal-title":"MBio"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1556\/030.2024.02230","article-title":"Carbapenem-resistant Klebsiella pneumoniae in the Balkans: clonal distribution and associated resistance determinants","volume":"71","author":"Chatzidimitriou","year":"2024","journal-title":"Acta Microbiol. Immunol. Hung."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e31702","DOI":"10.1097\/MD.0000000000031702","article-title":"The association between antibiotics and community-associated Staphylococcus aureus colonization in the United States population: analysis of the National Health and nutrition examination survey (NHANES)","volume":"101","author":"Chen","year":"2022","journal-title":"Medicine (Baltimore)"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"e01355","DOI":"10.1128\/mBio.01355-14","article-title":"Epidemic Klebsiella pneumoniae ST258 is a hybrid strain","volume":"5","author":"Chen","year":"2014","journal-title":"MBio"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"e0369223","DOI":"10.1128\/spectrum.03692","article-title":"CRISPR-Cas9-mediated IncF plasmid curing in extraintestinal pathogenic Escherichia coli","volume":"12","author":"Chen","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"2311","DOI":"10.1128\/AAC.37.11.2311","article-title":"Characterization of glycopeptide-resistant enterococci from U.S. hospitals","volume":"37","author":"Clark","year":"1993","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"1256","DOI":"10.1093\/cid\/cit503","article-title":"Escherichia coli sequence type 131 (ST131) subclone H30 as an emergent multidrug-resistant pathogen among US veterans","volume":"57","author":"Colpan","year":"2013","journal-title":"Clin. Infect. Dis."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"msad217","DOI":"10.1093\/molbev\/msad217","article-title":"Chance favors the prepared genomes: horizontal transfer shapes the emergence of antibiotic resistance mutations in core genes","volume":"40","author":"Coluzzi","year":"2023","journal-title":"Mol. Biol. Evol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"971","DOI":"10.1111\/j.1469-0691.2007.01794.x","article-title":"Replacement of methicillin-resistant Staphylococcus aureus clones in Hungary over time: a 10-year surveillance study","volume":"13","author":"Concei\u00e7\u00e3o","year":"2007","journal-title":"Clin. Microbiol. Infect."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1016\/j.jare.2019.10.005","article-title":"Vancomycin resistant Staphylococcus aureus infections: a review of case updating and clinical features","volume":"21","author":"Cong","year":"2019","journal-title":"J. Adv. Res."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"47","DOI":"10.33321\/cdi.2023.47.67","article-title":"Australian Staphylococcus aureus surveillance outcome program (ASSOP) bloodstream infection annual report 2022","volume":"47","author":"Coombs","year":"2023","journal-title":"Commun. Dis. Intell."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"100187","DOI":"10.1016\/j.infpip.2021.100187","article-title":"Impact of an empiric antimicrobial therapy manual on antimicrobial usage and multidrug resistant organism trends in a large Italian teaching hospital","volume":"4","author":"Corcione","year":"2021","journal-title":"Infect. Prev. Pract."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1093\/cid\/ciu236","article-title":"Fluoroquinolone use is a risk factor for methicillin-resistant Staphylococcus aureus acquisition in long-term care facilities: a nested case-case-control study","volume":"59","author":"Couderc","year":"2014","journal-title":"Clin. Infect. Dis."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"e99","DOI":"10.1017\/ash.2024.95","article-title":"The changing epidemiology of Clostridioides difficile infection and the NAP1\/027 strain in two Quebec hospitals: a 17-year time-series study","volume":"4","author":"Couture","year":"2024","journal-title":"Antimicrob Steward Healthc. Epidemiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1016\/j.ijantimicag.2018.11.012","article-title":"Class 1 integrons in Acinetobacter baumannii: a weak expression of gene cassettes to counterbalance the lack of LexA-driven integrase repression","volume":"53","author":"Couv\u00e9-Deacon","year":"2019","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-021-04359-3","article-title":"The role of potentiating mutations in the evolution of pandemic Escherichia coli clones","volume":"17","author":"Cummins","year":"2021","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"4539","DOI":"10.1093\/nar\/gkw319","article-title":"Identification and analysis of integrons and cassette arrays in bacterial genomes","volume":"44","author":"Cury","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1007\/s10096-006-0120-4","article-title":"Nationwide spread of clonally related CTX-M-15-producing multidrug-resistant Klebsiella pneumoniae strains in Hungary","volume":"25","author":"Damjanova","year":"2006","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1093\/jac\/dkn287","article-title":"Expansion and countrywide dissemination of ST11, ST15 and ST147 ciprofloxacin-resistant CTX-M-15-type \u03b2-lactamase-producing Klebsiella pneumoniae epidemic clones in Hungary in 2005\u2013the new\u2018MRSAs?\u2019","volume":"62","author":"Damjanova","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"3454","DOI":"10.1128\/JCM.01050-08","article-title":"Epidemiology of invasive methicillin-resistant Staphylococcus aureus clones collected in France in 2006 and 2007","volume":"46","author":"Dauwalder","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1574","DOI":"10.1093\/jac\/dkx043","article-title":"Ecological impact of ciprofloxacin on commensal enterococci in healthy volunteers","volume":"72","author":"De Lastours","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"e00418","DOI":"10.1128\/mBio.00440-18","article-title":"Genomic analysis of a pan-resistant isolate of Klebsiella pneumoniae, United States 2016","volume":"9","author":"De Man","year":"2016","journal-title":"MBio"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1016\/j.jgar.2019.05.026","article-title":"Genetic mutations in the quinolone resistance-determining region are related to changes in the epidemiological profile of methicillin-resistant Staphylococcus aureus isolates","volume":"19","author":"De Oliveira","year":"2019","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"e01589","DOI":"10.1128\/AAC.01589-17","article-title":"Genomics and susceptibility profiles of extensively drug-resistant Pseudomonas aeruginosa isolates from Spain","volume":"61","author":"Del Barrio-Tofi\u00f1o","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1093\/labmed\/lmw030","article-title":"Association between presence of virulence genes and antibiotic resistance in clinical Klebsiella pneumoniae isolates","volume":"47","author":"Derakhshan","year":"2016","journal-title":"Lab. Med."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1016\/S1473-3099(16)30514-X","article-title":"Effects of control interventions on Clostridium difficile infection in England: an observational study","volume":"17","author":"Dingle","year":"2017","journal-title":"Lancet Infect. Dis."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"e0024323","DOI":"10.1128\/mbio.00243-23","article-title":"Penicillin binding protein substitutions cooccur with fluoroquinolone resistance in epidemic lineages of multidrug-resistant Clostridioides difficile","volume":"14","author":"Dingle","year":"2023","journal-title":"MBio"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"e1010020","DOI":"10.1371\/journal.pgen.1010020","article-title":"Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex","volume":"18","author":"Djahanschiri","year":"2022","journal-title":"PLoS Genet."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"3418","DOI":"10.1128\/AAC.46.11.3418-3421.2002","article-title":"GyrA and gyrB mutations are implicated in cross-resistance to ciprofloxacin and moxifloxacin in Clostridium difficile","volume":"46","author":"Dridi","year":"2002","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"e0220723","DOI":"10.1128\/spectrum.02207-23","article-title":"Nosocomial surveillance of multidrug-resistant Acinetobacter baumannii: a genomic epidemiological study","volume":"12","author":"Duan","year":"2024","journal-title":"Microbiol Spectr"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"e00021","DOI":"10.1128\/mSystems.00083-21","article-title":"Limited and strain-specific transcriptional and growth responses to acquisition of a multidrug resistance plasmid in genetically diverse Escherichia coli lineages","volume":"6","author":"Dunn","year":"2021","journal-title":"mSystems"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"e00520","DOI":"10.1128\/IAI.00576-20","article-title":"Success of Escherichia coli O25b:H4 sequence type 131 clade C associated with a decrease in virulence","volume":"88","author":"Duprilot","year":"2020","journal-title":"Infect. Immun."},{"key":"ref64","doi-asserted-by":"publisher","DOI":"10.1101\/2024.02.05.579024","article-title":"Evolution of a plasmid regulatory circuit ameliorates plasmid fitness cost","author":"Elg","year":"2024","journal-title":"bioRxiv"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"e59960","DOI":"10.1371\/journal.pone.0059960","article-title":"Extensive dissemination of methicillin-resistant Staphylococcus aureus (MRSA) between the hospital and the community in a country with a high prevalence of nosocomial MRSA","volume":"8","author":"Espadinha","year":"2013","journal-title":"PLoS One"},{"key":"ref66","doi-asserted-by":"publisher","first-page":"1278819","DOI":"10.3389\/fcimb.2023.1278819","article-title":"Pandrug-resistant Acinetobacter baumannii from different clones and regions in Mexico have a similar plasmid carrying the Bla(OXA-72) gene","volume":"13","author":"Fern\u00e1ndez-V\u00e1zquez","year":"2023","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"224","DOI":"10.3390\/microorganisms10020224","article-title":"Integron functionality and genome innovation: an update on the subtle and smart strategy of integrase and gene cassette expression regulation","volume":"10","author":"Fonseca","year":"2022","journal-title":"Microorganisms"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"e0176779","DOI":"10.1371\/journal.pone.0176779","article-title":"Carbapenem-resistant Klebsiella pneumoniae in Barbados: driving change in practice at the national level","volume":"12","author":"Forde","year":"2017","journal-title":"PLoS One"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/s13756-015-0064-5","article-title":"Non-linear significant relationship between use of glycopeptides and isolation of vancomycin-resistant Enterococcus species in a university hospital setting","volume":"4","author":"Forstner","year":"2015","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1590\/S1984-82502011000100004","article-title":"Environmental contamination by fluoroquinolones","volume":"50","author":"Frade","year":"2014","journal-title":"Braz. J. Pharm. Sci."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"248.e9","DOI":"10.1016\/j.cmi.2014.09.017","article-title":"Pan-european longitudinal surveillance of antibiotic resistance among prevalent Clostridium difficile ribotypes","volume":"21","author":"Freeman","year":"2015","journal-title":"Clin. Microbiol. Infect."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"3351","DOI":"10.1093\/jac\/dkw312","article-title":"Multilevel population genetic analysis of vanA and vanB Enterococcus faecium causing nosocomial outbreaks in 27 countries (1986-2012)","volume":"71","author":"Freitas","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.3389\/fmicb.2016.01017","article-title":"Dissimilar fitness associated with resistance to fluoroquinolones influences clonal dynamics of various multiresistant bacteria","volume":"7","author":"Fuzi","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"271","DOI":"10.3389\/fmicb.2020.00271","article-title":"Global evolution of pathogenic bacteria with extensive use of fluoroquinolone agents","volume":"11","author":"Fuzi","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"1150","DOI":"10.3390\/pathogens12091150","article-title":"Commensal fitness advantage may contribute to the global dissemination of multidrug-resistant lineages of bacteria. The case of uropathogenic E. coli","volume":"12","author":"Fuzi","year":"2023","journal-title":"Pathogens"},{"key":"ref76","doi-asserted-by":"publisher","first-page":"2261","DOI":"10.3389\/fmicb.2017.02261","article-title":"Double-serine fluoroquinolone resistance mutations advance major international clones and lineages of various multi-drug resistant bacteria","volume":"8","author":"Fuzi","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1099\/jmm.0.05178-0","article-title":"Fitness cost of fluoroquinolone resistance in Salmonella enterica serovar Typhimurium","volume":"52","author":"Giraud","year":"2003","journal-title":"J. Med. Microbiol."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"e02115","DOI":"10.1128\/mBio.02183-15","article-title":"Demography and intercontinental spread of the USA300 community-acquired methicillin-resistant Staphylococcus aureus lineage","volume":"7","author":"Glaser","year":"2016","journal-title":"MBio"},{"key":"ref79","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1086\/592257","article-title":"Emergence of Clostridium difficile infection due to a new hypervirulent strain, polymerase chain reaction ribotype 078","volume":"47","author":"Goorhuis","year":"2008","journal-title":"Clin. Infect. Dis."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"e000353","DOI":"10.1099\/mgen.0.000353","article-title":"Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli","volume":"6","author":"Goswami","year":"2020","journal-title":"Microb Genom"},{"key":"ref81","doi-asserted-by":"publisher","first-page":"e0022022","DOI":"10.1128\/jb.00220-22","article-title":"Locking down SOS mutagenesis repression in a dynamic pathogen","volume":"204","author":"Gregg-Jolly","year":"2022","journal-title":"J. Bacteriol."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"20987","DOI":"10.2807\/1560-7917.ES2014.19.49.20987","article-title":"The dynamic changes of dominant clones of Staphylococcus aureus causing bloodstream infections in the European region: results of a second structured survey","volume":"19","author":"Grundmann","year":"2014","journal-title":"Euro Surveill."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"1320","DOI":"10.1056\/NEJMoa1910215","article-title":"Trends in U.S. burden of Clostridioides difficile infection and outcomes","volume":"382","author":"Guh","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"ref84","doi-asserted-by":"publisher","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":"ref85","doi-asserted-by":"publisher","first-page":"2045","DOI":"10.1093\/cid\/ciy825","article-title":"Fluoroquinolone prophylaxis selects for meropenem-nonsusceptible Pseudomonas aeruginosa in patients with hematologic malignancies and hematopoietic cell transplant recipients","volume":"68","author":"Hakki","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"e3001225","DOI":"10.1371\/journal.pbio.3001225","article-title":"Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation","volume":"19","author":"Hall","year":"2021","journal-title":"PLoS Biol."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"e000306","DOI":"10.1099\/mgen.0.000306","article-title":"Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii","volume":"5","author":"Hamidian","year":"2019","journal-title":"Microb Genom"},{"key":"ref88","doi-asserted-by":"publisher","first-page":"i3","DOI":"10.1093\/jac\/dkp256","article-title":"The changing epidemiology of resistance","volume":"64","author":"Hawkey","year":"2009","journal-title":"Antimicrob Chemother"},{"key":"ref89","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1038\/ng.2478","article-title":"Emergence and global spread of epidemic healthcare-associated Clostridium difficile","volume":"45","author":"He","year":"2013","journal-title":"Nat. Genet."},{"key":"ref90","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/j.ijantimicag.2012.02.007","article-title":"Curing bacteria of antibiotic resistance: reverse antibiotics, a novel class of antibiotics in nature","volume":"39","author":"Hiramatsu","year":"2012","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref91","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1101\/gr.147710.112","article-title":"A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic","volume":"23","author":"Holden","year":"2013","journal-title":"Genome Res."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"828","DOI":"10.3389\/fmicb.2020.00828","article-title":"MarA, RamA, and SoxS as mediators of the stress response: survival at a cost","volume":"11","author":"Holden","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"7216","DOI":"10.1128\/AAC.01601-16","article-title":"Clonal dissemination of Pseudomonas aeruginosa sequence type 235 isolates carrying blaIMP-6 and emergence of blaGES-24 and blaIMP-10 on novel genomic islands PAGI-15 and -16 in South Korea","volume":"60","author":"Hong","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"2029","DOI":"10.1007\/s10096-011-1536-z","article-title":"Varying fitness cost associated with resistance to fluoroquinolones governs clonal dynamic of methicillin-resistant Staphylococcus aureus","volume":"31","author":"Horvath","year":"2012","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1186\/s13059-015-0643-z","article-title":"Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system","volume":"16","author":"Hsu","year":"2015","journal-title":"Genome Biol."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"e00121","DOI":"10.1128\/mSystems.00154-21","article-title":"Emergence and expansion of a carbapenem-resistant Pseudomonas aeruginosa clone are associated with plasmid-borne Bla (KPC-2) and virulence-related genes","volume":"6","author":"Hu","year":"2021","journal-title":"mSystems"},{"key":"ref97","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1093\/molbev\/msx052","article-title":"Mutation supply and relative fitness shape the genotypes of ciprofloxacin-resistant Escherichia coli","volume":"34","author":"Huseby","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref98","doi-asserted-by":"publisher","first-page":"000696","DOI":"10.1099\/mgen.0.000696","article-title":"A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile","volume":"7","author":"Imwattana","year":"2021","journal-title":"Microb. Genom."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"E5616","DOI":"10.1073\/pnas.1704925114","article-title":"Disentangling the effects of selection and loss bias on gene dynamics","volume":"114","author":"Iranzo","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref100","doi-asserted-by":"publisher","first-page":"101137","DOI":"10.1016\/j.drup.2024.101137","article-title":"The key role of iroBCDN-lacking pLVPK-like plasmid in the evolution of the most prevalent hypervirulent carbapenem-resistant ST11-KL64 Klebsiella pneumoniae in China","volume":"77","author":"Jia","year":"2024","journal-title":"Drug Resist Update"},{"key":"ref101","doi-asserted-by":"publisher","first-page":"4471","DOI":"10.1128\/AAC.00673-15","article-title":"Intensity and mechanisms of fuoroquinolone resistance within the H30 and H30Rx subclones of Escherichia coli sequence type 131 compared with other fluoroquinolone resistant E. coli","volume":"59","author":"Johnson","year":"","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref102","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1128\/JCM.01664-18","article-title":"Rapid emergence, subsidence, and molecular detection of Escherichia coli sequence type 1193-fimH64, a new disseminated multidrug-resistant commensal and extraintestinal pathogen","volume":"57","author":"Johnson","year":"2019","journal-title":"J. Clin. Microbiol."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"7132","DOI":"10.1128\/AAC.01687-15","article-title":"Greater ciprofloxacin tolerance as a possible selectable phenotype underlying the pandemic spread of the H30 subclone of Escherichia coli sequence type 131","volume":"59","author":"Johnson","year":"","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref104","doi-asserted-by":"publisher","first-page":"981","DOI":"10.1038\/s41564-021-00930-y","article-title":"Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response","volume":"6","author":"Jones","year":"2021","journal-title":"Nat. Microbiol."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"26","DOI":"10.21315\/mjms2023.30.2.3","article-title":"Dissemination pattern of hospital-acquired methicillin-resistant Staphylococcus aureus and community-acquired MRSA isolates from Malaysian hospitals: a review from a molecular perspective","volume":"30","author":"Junaidi","year":"2023","journal-title":"Malays J. Med. Sci."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1007\/s10096-024-04763-5","article-title":"Genomic epidemiology and molecular characteristics of Bla(NDM-1)-positive carbapenem-resistant Pseudomonas aeruginosa belonging to international high-risk clone ST773 in the Gauteng region, South Africa","volume":"43","author":"Jung","year":"2024","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref107","doi-asserted-by":"publisher","first-page":"e1003269","DOI":"10.1371\/journal.ppat.1003269","article-title":"Mobile genetic element SCCmec-encoded psm-mec RNA suppresses translation of agrA and attenuates MRSA virulence","volume":"9","author":"Kaito","year":"2013","journal-title":"PLoS Pathog."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/j.drup.2012.06.001","article-title":"Insights into the global molecular epidemiology of carbapenem non-susceptible clones of Acinetobacter baumannii","volume":"15","author":"Karah","year":"2012","journal-title":"Drug Resist. Updat."},{"key":"ref109","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1093\/cid\/ciz169","article-title":"Association between antibiotic use and hospital-onset Clostridioides difficile infection in US acute care hospitals, 2006\u20132012: an ecologic analysis","volume":"70","author":"Kazakova","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref110","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/s41429-024-00715-5","article-title":"Correlation between the spread of IMP-producing bacteria and the promoter strength of blaIMP gene","volume":"77","author":"Kikuchi","year":"2024","journal-title":"J. Antibiot. (Tokyo)"},{"key":"ref111","doi-asserted-by":"publisher","first-page":"835403","DOI":"10.3389\/fmicb.2022.835403","article-title":"Genetic diversity, distribution, and genomic characterization of antibiotic resistance and virulence of clinical Pseudomonas aeruginosa strains in Kenya","volume":"13","author":"Kiyaga","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref112","doi-asserted-by":"publisher","first-page":"3188","DOI":"10.1093\/molbev\/msab091","article-title":"Piggybacking on niche adaptation improves the maintenance of multidrug-resistance plasmids","volume":"38","author":"Kloos","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref113","doi-asserted-by":"publisher","first-page":"2514","DOI":"10.1093\/jac\/dks245","article-title":"Shift in dominant hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) clones over time","volume":"67","author":"Knight","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref114","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1099\/jmm.0.000927","article-title":"Acquired qnrVC1 and blaNDM-1 resistance markers in an international high-risk Pseudomonas aeruginosa ST773 clone","volume":"68","author":"Kocsis","year":"2019","journal-title":"J. Med. Microbiol."},{"key":"ref115","doi-asserted-by":"publisher","first-page":"2343","DOI":"10.1128\/AAC.49.6.2343-2351.2005","article-title":"Biological cost of single and multiple norfloxacin resistance mutations in Escherichia coli implicated in urinary tract infections","volume":"49","author":"Komp Lindgren","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref116","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1128\/AAC.03954-14","article-title":"The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility","volume":"59","author":"Kos","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref117","doi-asserted-by":"publisher","first-page":"e00718","DOI":"10.1128\/mSphere.00718-20","article-title":"The parameter-fitness landscape of lexA autoregulation in Escherichia coli","volume":"5","author":"Kozuch","year":"2020","journal-title":"mSphere"},{"key":"ref118","doi-asserted-by":"publisher","first-page":"1264492","DOI":"10.3389\/fmed.2023.1264492","article-title":"Case report: azithromycin-meropenem combination therapy as a low-cost approach to combat PDR gram-negative infections of war wounds in Ukraine","volume":"10","author":"Kryzhevskyi","year":"2023","journal-title":"Front. Med. (Lausanne)"},{"key":"ref119","doi-asserted-by":"publisher","first-page":"997897","DOI":"10.3389\/fcimb.2022.997897","article-title":"Diversity of resistant determinants, virulence factors, and mobile genetic elements in Acinetobacter baumannii from India: a comprehensive in silico genome analysis","volume":"12","author":"Kumkar","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref120","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1007\/s10096-014-2290-9","article-title":"Molecular epidemiology and antimicrobial susceptibility of Clostridium difficile isolated from a university teaching hospital in Japan","volume":"34","author":"Kuwata","year":"2015","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref121","doi-asserted-by":"publisher","first-page":"860436","DOI":"10.3389\/fmicb.2022.860436","article-title":"A 6-year update on the diversity of methicillin-resistant Staphylococcus aureus clones in Africa: a systematic review","volume":"13","author":"Lawal","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref122","doi-asserted-by":"publisher","first-page":"e006596","DOI":"10.1136\/bmjopen-2014-006596","article-title":"Turning the tide or riding the waves? Impacts of antibiotic stewardship and infection control on MRSA strain dynamics in a Scottish region over 16 years: non-linear time series analysis","volume":"5","author":"Lawes","year":"2015","journal-title":"Br. Med. J. Open"},{"key":"ref123","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.1128\/JCM.44.3.1059-1064.2006","article-title":"Highlevel ciprofloxacin resistance from point mutations in gyrA and parC confined to global hospital-adapted clonal lineage CC17 of Enterococcus faecium","volume":"44","author":"Leavis","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"ref124","doi-asserted-by":"publisher","first-page":"1398","DOI":"10.3201\/eid1209.060397","article-title":"Fluoroquinolones and risk for methicillin-resistant Staphylococcus aureus, Canada","volume":"12","author":"LeBlanc","year":"2006","journal-title":"Emerg. Infect. Dis."},{"key":"ref125","doi-asserted-by":"publisher","first-page":"15209","DOI":"10.3390\/ijms242015209","article-title":"Prioritization of critical factors for surveillance of the dissemination of antibiotic resistance in Pseudomonas aeruginosa: a systematic review","volume":"24","author":"Lee","year":"2023","journal-title":"Int. J. Mol. Sci."},{"key":"ref126","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1099\/jmm.0.072082-0","article-title":"The changes of PCR ribotype and antimicrobial resistance of Clostridium difficile in a tertiary care hospital over 10 years","volume":"63","author":"Lee","year":"2014","journal-title":"J. Med. Microbiol."},{"key":"ref127","doi-asserted-by":"publisher","first-page":"mgen000475","DOI":"10.1099\/mgen.0.000475","article-title":"Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections","volume":"6","author":"Li","year":"2020","journal-title":"Microb Genom"},{"key":"ref128","doi-asserted-by":"publisher","first-page":"000721","DOI":"10.1099\/mgen.0.000721","article-title":"Genomic comparisons of Escherichia coli ST131 from Australia","volume":"7","author":"Li","year":"2021","journal-title":"Microb Genom"},{"key":"ref129","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1016\/j.jmii.2013.02.001","article-title":"Comparison of methicillin-resistant Staphylococcus aureus strains isolated in 2003 and 2008 with an emergence of multidrug resistant ST22: SCCmec IV clone in a tertiary hospital, Malaysia","volume":"46","author":"Lim","year":"2013","journal-title":"J. Microbiol. Immunol. Infect."},{"key":"ref130","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1128\/AAC.01440-10","article-title":"Antimicrobial susceptibilities and molecular epidemiology of clinical isolates of Clostridium difficile in Taiwan","volume":"55","author":"Lin","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref131","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/j.amjmed.2004.09.015","article-title":"Fluoroquinolone prescribing in the United States: 1995 to 2002","volume":"118","author":"Linder","year":"2005","journal-title":"Am. J. Med."},{"key":"ref132","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.3390\/antibiotics12071141","article-title":"Insights into the evolving epidemiology of Clostridioides difficile infection and treatment: a global perspective","volume":"12","author":"Liu","year":"2023","journal-title":"Antibiotics (Basel)."},{"key":"ref133","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1097\/INF.0000000000002176","article-title":"A multi-centered case-control study of factors associated with Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae infections in children and young adults","volume":"38","author":"Logan","year":"2019","journal-title":"Pediatr. Infect. Dis. J."},{"key":"ref134","doi-asserted-by":"publisher","first-page":"eaba0862","DOI":"10.1126\/science.aba0862","article-title":"Clinically relevant mutations in core metabolic genes confer antibiotic resistance","volume":"371","author":"Lopatkin","year":"2021","journal-title":"Science"},{"key":"ref135","doi-asserted-by":"publisher","first-page":"e00720","DOI":"10.1128\/mBio.00766-20","article-title":"Codon usage optimization in the prokaryotic tree of life: how synonymous codons are differentially selected in sequence domains with different expression levels and degrees of conservation","volume":"11","author":"L\u00f3pez","year":"2020","journal-title":"MBio"},{"key":"ref136","doi-asserted-by":"publisher","first-page":"e00505","DOI":"10.1128\/mBio.00505-19","article-title":"Codon usage heterogeneity in the multipartite prokaryote genome: selection-based coding bias associated with gene location, expression level, and ancestry","volume":"10","author":"L\u00f3pez","year":"2019","journal-title":"MBio"},{"key":"ref138","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1179\/joc.2011.23.2.87","article-title":"Characterization of the mechanisms of fluoroquinolone resistance in vancomycin-resistant enterococci of different origins","volume":"23","author":"L\u00f3pez","year":"2011","journal-title":"J. Chemother."},{"key":"ref139","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1073\/pnas.0408966102","article-title":"Enhanced in vivo fitness of fluoroquinolone-resistant Campylobacter jejuni in the absence of antibiotic selection pressure","volume":"102","author":"Luo","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref140","doi-asserted-by":"publisher","first-page":"4515","DOI":"10.1128\/JCM.00985-06","article-title":"Predominance of clones carrying Panton-valentine leukocidin genes among methicillin-resistant Staphylococcus aureus strains isolated in Japanese hospitals from 1979 to 1985","volume":"44","author":"Ma","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"ref141","doi-asserted-by":"publisher","first-page":"3203","DOI":"10.1093\/jac\/dku308","article-title":"Interplay between plasmid mediated and chromosomalmediated fluoroquinolone resistance and bacterial fitness in Escherichia coli","volume":"69","author":"Machuca","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref142","doi-asserted-by":"publisher","first-page":"e1000541","DOI":"10.1371\/journal.ppat.1000541","article-title":"Interplay in the selection of fluoroquinolone resistance and bacterial fitness","volume":"5","author":"Marcusson","year":"2009","journal-title":"PLoS Pathog."},{"key":"ref143","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1128\/CMR.15.4.647-679.2002","article-title":"Interactions among strategies associated with bacterial infection: pathogenicity, epidemicity, and antibiotic resistance","volume":"15","author":"Mart\u00ednez","year":"2002","journal-title":"Clin. Microbiol. Rev."},{"key":"ref144","doi-asserted-by":"publisher","first-page":"10893","DOI":"10.3390\/ijms231810893","article-title":"Plasmids as key players in Acinetobacter adaptation","volume":"23","author":"Maslova","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"ref145","doi-asserted-by":"publisher","first-page":"e01823","DOI":"10.1128\/AAC.01823-16","article-title":"Chromosomal integration of the Klebsiella pneumoniae carbapenemase gene, Bla(KPC), in Klebsiella species is elusive but not rare","volume":"61","author":"Mathers","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref146","doi-asserted-by":"publisher","first-page":"e02190","DOI":"10.1128\/AAC.02190-17","article-title":"Distribution and molecular characterization of Acinetobacter baumannii international clone II lineage in Japan","volume":"62","author":"Matsui","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref147","doi-asserted-by":"publisher","first-page":"2098","DOI":"10.1128\/AAC.45.7.2098-2105.2001","article-title":"DNA gyrase-mediated natural resistance to fluoroquinolones in Ehrlichia spp","volume":"45","author":"Maurin","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref148","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fcimb.2015.00001","article-title":"Methicillin resistance and the biofilm phenotype in Staphylococcus aureus","volume":"5","author":"McCarthy","year":"2015","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref149","doi-asserted-by":"publisher","first-page":"2433","DOI":"10.1056\/NEJMoa051590","article-title":"An epidemic, toxin gene-variant strain of Clostridium difficile","volume":"353","author":"McDonald","year":"2005","journal-title":"N. Engl. J. Med."},{"key":"ref150","doi-asserted-by":"publisher","first-page":"3078","DOI":"10.3748\/wjg.v22.i11.3078","article-title":"Comparison of pediatric and adult antibiotic-associated diarrhea and Clostridium difficile infections","volume":"22","author":"McFarland","year":"2016","journal-title":"World J. Gastroenterol."},{"key":"ref151","first-page":"269","article-title":"Vancomycin resistance in Staphylococcus aureus","volume":"90","author":"McGuinness","year":"2017","journal-title":"Yale J. Biol. Med."},{"key":"ref152","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1111\/eva.12196","article-title":"The fitness costs of antibiotic resistance mutations","volume":"8","author":"Melnyk","year":"2015","journal-title":"Evol. Appl."},{"key":"ref154","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1111\/j.1558-5646.1991.tb04336.x","article-title":"Coevolution in bacterial-plasmid populations","volume":"45","author":"Modi","year":"1991","journal-title":"Evolution"},{"key":"ref155","doi-asserted-by":"publisher","first-page":"1725","DOI":"10.1038\/s41598-023-28859-8","article-title":"CID12261165, a flavonoid compound as antibacterial agents against quinolone-resistant Staphylococcus aureus","volume":"13","author":"Morimoto","year":"2023","journal-title":"Sci. Rep."},{"key":"ref156","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1016\/j.ijantimicag.2015.09.006","article-title":"Apigenin as an anti-quinolone-resistance antibiotic","volume":"46","author":"Morimoto","year":"2015","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref157","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1128\/CMR.00125-13","article-title":"Escherichia coli ST131, an intriguing clonal group","volume":"27","author":"Nicolas-Chanoine","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"ref158","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1093\/jac\/dkm464","article-title":"Intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15","volume":"61","author":"Nicolas-Chanoine","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref159","doi-asserted-by":"publisher","first-page":"584603","DOI":"10.3389\/fmicb.2020.584603","article-title":"Genomic analysis of carbapenem-resistant Acinetobacter baumannii isolates belonging to major endemic clones in South America","volume":"11","author":"Nodari","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref160","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1111\/nyas.14918","article-title":"Mobile genetic elements in Acinetobacter antibiotic-resistance acquisition and dissemination","volume":"1518","author":"Noel","year":"2022","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref161","doi-asserted-by":"publisher","first-page":"1335","DOI":"10.1128\/JB.02176-12","article-title":"Antibiotic resistance acquired through a DNA damage-inducible response in Acinetobacter baumannii","volume":"195","author":"Norton","year":"2013","journal-title":"J. Bacteriol."},{"key":"ref162","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1016\/j.ijmm.2011.09.007","article-title":"From types to trees: reconstructing the spatial spread of Staphylococcus aureus based on DNA variation","volume":"301","author":"N\u00fcbel","year":"2011","journal-title":"Int. J. Med. Microbiol."},{"key":"ref163","doi-asserted-by":"publisher","first-page":"1817","DOI":"10.3390\/antibiotics11121817","article-title":"Molecular enetic epidemiology of an emerging antimicrobial-resistant Klebsiella pneumoniae clone (ST307) obtained from clinical isolates in Central Panama","volume":"11","author":"N\u00fa\u00f1ez-Samudio","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"ref164","doi-asserted-by":"publisher","first-page":"2058","DOI":"10.1038\/s41396-023-01509-7","article-title":"Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings","volume":"17","author":"Ogunlana","year":"2023","journal-title":"ISME J."},{"key":"ref165","doi-asserted-by":"publisher","first-page":"12865","DOI":"10.1021\/acsomega.9b00077","article-title":"Antimicrobial activity of a new class of phosphorylated and modified flavonoids","volume":"4","author":"Osonga","year":"2019","journal-title":"ACS Omega"},{"key":"ref166","doi-asserted-by":"publisher","first-page":"2960","DOI":"10.1093\/jac\/dkac250","article-title":"Fitness effects of blaCTX-M-15-harbouring F2:A1:B- plasmids on their native Escherichia coli ST131 H30Rx hosts","volume":"77","author":"Palkovicova","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref167","doi-asserted-by":"publisher","first-page":"1884","DOI":"10.3390\/microorganisms8121884","article-title":"Unravelling the features of success of VIM-producing ST111 and ST235 Pseudomonas aeruginosa in a Greek hospital","volume":"8","author":"Papagiannitsis","year":"2020","journal-title":"Microorganisms"},{"key":"ref168","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1016\/j.anaerobe.2017.02.004","article-title":"Exposure to beta-lactams results in the alteration of penicillin-binding proteins in Clostridium perfringens","volume":"45","author":"Park","year":"2017","journal-title":"Anaerobe"},{"key":"ref169","doi-asserted-by":"publisher","first-page":"19536","DOI":"10.1038\/s41598-023-46985-1","article-title":"Molecular and virulence characteristics of carbapenem-resistant Acinetobacter baumannii isolates: a prospective cohort study","volume":"13","author":"Park","year":"2023","journal-title":"Sci. Rep."},{"key":"ref170","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1089\/mdr.2015.0001","article-title":"Genotypes of ciprofloxacin-resistant Klebsiella pneumoniae in Korea and their characteristics according to the genetic lineages","volume":"21","author":"Park","year":"2015","journal-title":"Microb. Drug Resist."},{"key":"ref171","doi-asserted-by":"publisher","first-page":"e01148","DOI":"10.1128\/AAC.01148-20","article-title":"Emerging antimicrobial-resistant high-risk Klebsiella pneumoniae clones ST307 and ST147","volume":"64","author":"Peirano","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref172","doi-asserted-by":"publisher","first-page":"e0151524","DOI":"10.1128\/jcm.01515-24","article-title":"Rapidly spreading Enterobacterales with OXA-48-like carbapenemases","volume":"63","author":"Peirano","year":"2025","journal-title":"J. Clin. Microbiol."},{"key":"ref173","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1093\/cid\/ciu866","article-title":"Influence of virulence genotype and resistance profile in the mortality of Pseudomonas aeruginosa bloodstream infections","volume":"60","author":"Pe\u00f1a","year":"2015","journal-title":"Clin. Infect. Dis."},{"key":"ref174","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1503\/cmaj.1041104","article-title":"Clostridium difficile-associated diarrhea in a region of Quebec from 1991 to 2003: a changing pattern of disease severity","volume":"171","author":"Pepin","year":"2004","journal-title":"CMAI"},{"key":"ref175","doi-asserted-by":"publisher","first-page":"1244","DOI":"10.1093\/jac\/dkz030","article-title":"High incidence of MDR and XDR Pseudomonas aeruginosa isolates obtained from patients with ventilator-associated pneumonia in Greece, Italy and Spain as part of the MagicBullet clinical trial","volume":"74","author":"P\u00e9rez","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref176","doi-asserted-by":"publisher","first-page":"104265","DOI":"10.1016\/j.meegid.2020.104265","article-title":"The evolutionary puzzle of Escherichia coli ST131","volume":"81","author":"Pitout","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref177","doi-asserted-by":"publisher","first-page":"e0051122","DOI":"10.1128\/aac.00511-22","article-title":"Escherichia coli ST1193: following in the footsteps of E. coli ST131","volume":"66","author":"Pitout","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref178","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1080\/14787210.2023.2184348","article-title":"The contributions of multidrug resistant clones to the success of pandemic extra-intestinal pathogenic Escherichia coli","volume":"21","author":"Pitout","year":"2023","journal-title":"Expert Rev. Anti-Infect. Ther."},{"key":"ref179","doi-asserted-by":"publisher","first-page":"e0133923","DOI":"10.1128\/aac.01339-23","article-title":"Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance","volume":"68","author":"Pitout","year":"2024","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref180","doi-asserted-by":"publisher","first-page":"S71","DOI":"10.1093\/infdis\/jiw444","article-title":"Life after USA300: the rise and fall of a superbug","volume":"215","author":"Planet","year":"2017","journal-title":"J. Infect. Dis."},{"key":"ref181","doi-asserted-by":"publisher","first-page":"106824","DOI":"10.1016\/j.ijantimicag.2023.106824","article-title":"Clostridioides difficile infections were predominantly driven by fluoroquinolone-resistant Clostridioides difficile ribotypes 176 and 001 in Slovakia in 2018-2019","volume":"62","author":"Plankaova","year":"2023","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref182","doi-asserted-by":"publisher","first-page":"1201","DOI":"10.1128\/AAC.00799-07","article-title":"Fluoroquinolone-resistant mutants of Burkholderia cepacia","volume":"52","author":"Pope","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref183","doi-asserted-by":"publisher","first-page":"e00377","DOI":"10.1128\/mBio.00377-13","article-title":"The epidemic of extended-spectrum-beta-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx","volume":"4","author":"Price","year":"2013","journal-title":"MBio"},{"key":"ref184","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1128\/AAC.01370-06","article-title":"(Genome) size matters","volume":"51","author":"Projan","year":"2007","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref185","doi-asserted-by":"publisher","first-page":"e0355221","DOI":"10.1128\/mbio.03552-21","article-title":"The role of antibiotic resistance genes in the fitness cost of multiresistance plasmids","volume":"13","author":"Rajer","year":"2022","journal-title":"MBio"},{"key":"ref186","doi-asserted-by":"publisher","first-page":"106450","DOI":"10.1016\/j.ijantimicag.2021.106450","article-title":"Clinical and bacterial characteristics of Pseudomonas aeruginosa affecting the outcome of patients with bacteraemic pneumonia","volume":"58","author":"Recio","year":"2021","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref187","doi-asserted-by":"publisher","first-page":"251","DOI":"10.20411\/pai.v4i2.327","article-title":"Impact of reduced fluoroquinolone use on Clostridioides difficile infections resulting from the fluoroquinolone-resistant ribotype 027 strain in a veterans affairs medical center","volume":"4","author":"Redmond","year":"2019","journal-title":"Pathog. Immun."},{"key":"ref188","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1017\/ice.2019.135","article-title":"Reduction in Clostridium difficile infection rates following a multifacility prevention initiative in Orange County, California: a controlled interrupted time series evaluation","volume":"40","author":"Rizzo","year":"2019","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref189","doi-asserted-by":"publisher","first-page":"2303","DOI":"10.3389\/fmicb.2017.02303","article-title":"Daptomycin resistance in clinical MRSA strains is associated with a high biological fitness cost","volume":"8","author":"Roch","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref190","doi-asserted-by":"publisher","first-page":"000737","DOI":"10.1099\/mgen.0.000737","article-title":"Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147","volume":"8","author":"Rodrigues","year":"2022","journal-title":"Microb Genom"},{"key":"ref191","doi-asserted-by":"publisher","first-page":"e0339522","DOI":"10.1128\/spectrum.03395-22","article-title":"Phylogenomics of globally spread clonal groups 14 and 15 of Klebsiella pneumoniae","volume":"11","author":"Rodrigues","year":"2023","journal-title":"Microbiol Spectr"},{"key":"ref192","doi-asserted-by":"publisher","first-page":"542","DOI":"10.3389\/fmicb.2019.00542","article-title":"Diversity, virulence, and antimicrobial resistance in isolates from the newly emerging Klebsiella pneumoniae ST101 lineage","volume":"10","author":"Roe","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref193","doi-asserted-by":"publisher","first-page":"e00337","DOI":"10.1128\/mSphere.00337-18","article-title":"Escherichia coli sequence type 410 is causing new international high-risk clones","volume":"3","author":"Roer","year":"2018","journal-title":"mSphere"},{"key":"ref194","doi-asserted-by":"publisher","DOI":"10.1128\/microbiolspec.MTBP-0016-2017","article-title":"Fitness costs of plasmids: a limit to plasmid transmission","volume":"5","author":"San Millan","year":"2017","journal-title":"Microbiol. Spectr."},{"key":"ref195","doi-asserted-by":"publisher","first-page":"e01586","DOI":"10.1128\/AAC.01586-17","article-title":"Interplay among resistance profiles, high-risk clones, and virulence in the Caenorhabditis elegans, Pseudomonas aeruginosa infection model","volume":"61","author":"S\u00e1nchez-Diener","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref196","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1093\/jac\/dkr405","article-title":"Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak","volume":"67","author":"Sandegren","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref197","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/j.jhin.2015.05.013","article-title":"Effects of fluoroquinolone restriction (from 2007 to 2012) on Clostridium difficile infections: interrupted time-series analysis","volume":"91","author":"Sarma","year":"2015","journal-title":"J. Hosp. Infect."},{"key":"ref198","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1128\/AAC.00306-08","article-title":"Effects of exposure of Clostridium difficile PCR ribotypes 027 and 001 to fluoroquinolones in a human gut model","volume":"53","author":"Saxton","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref199","doi-asserted-by":"publisher","first-page":"56","DOI":"10.20510\/ukjpb\/4\/i6\/134666","article-title":"Apigenin naturally occurring flavonoids: occurrence and bioactivity","volume":"4","author":"Sen","year":"2016","journal-title":"UK J Pharmac Biosci"},{"key":"ref200","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1016\/j.diagmicrobio.2015.10.009","article-title":"Coexistence of blaOXA-23 with armA in quinolone-resistant Acinetobacter baumannii from a Chinese university hospital","volume":"84","author":"Shen","year":"2016","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref201","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.ijantimicag.2015.04.012","article-title":"Effect of plasmids harbouring blaCTX-M on the virulence and fitness of Escherichia coli ST131 isolates","volume":"46","author":"Shin","year":"2015","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref202","doi-asserted-by":"publisher","first-page":"e00777","DOI":"10.1128\/AAC.00777-20","article-title":"Nybomycin inhibits both types of E. coli DNA gyrase\u2014fluoroquinolone-sensitive and fluoroquinolone-resistant","volume":"95","author":"Shiriaev","year":"2023","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref203","doi-asserted-by":"publisher","first-page":"3379","DOI":"10.2147\/IDR.S407497","article-title":"Genomic epidemiology and antimicrobial resistance profiles of Clostridioides difficile from multi-hospitals in a city in eastern China","volume":"16","author":"Shu","year":"2023","journal-title":"Infect Drug Resist"},{"key":"ref204","doi-asserted-by":"publisher","first-page":"1248","DOI":"10.3390\/antibiotics12081248","article-title":"Antimicrobial resistance, genetic lineages, and biofilm formation in Pseudomonas aeruginosa isolated from human infections: an emerging one health concern","volume":"12","author":"Silva","year":"2023","journal-title":"Antibiotics (Basel)"},{"key":"ref205","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1186\/s12864-020-6650-9","article-title":"Exploring the success of Brazilian endemic clone Pseudomonas aeruginosa ST277 and its association with the CRISPR-Cas system type I-C","volume":"21","author":"Silveira","year":"2020","journal-title":"BMC Genomics"},{"key":"ref206","doi-asserted-by":"publisher","first-page":"1676","DOI":"10.1093\/jac\/dkab091","article-title":"Antibiotics and healthcare facility-associated Clostridioides difficile infection: systematic review and meta-analysis 2020 update","volume":"76","author":"Slimings","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref207","doi-asserted-by":"publisher","first-page":"1976","DOI":"10.1093\/jac\/dkr275","article-title":"PCR ribotype prevalence and molecular basis of macrolide-lincosamide-streptogramin B (MLSB) and fluoroquinolone resistance in Irish clinical Clostridium difficile isolates","volume":"66","author":"Solomon","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"ref208","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1177\/2049936115622891","article-title":"Recent advances in the understanding of antibiotic resistance in Clostridium difficile infection","volume":"3","author":"Spigaglia","year":"2016","journal-title":"Ther. Adv. Infect. Dis."},{"key":"ref209","doi-asserted-by":"publisher","first-page":"2892","DOI":"10.1128\/JCM.02482-09","article-title":"Clostridium difficile isolates resistant to fluoroquinolones in Italy: emergence of PCR ribotype 018","volume":"48","author":"Spigaglia","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"ref210","doi-asserted-by":"publisher","first-page":"e02162","DOI":"10.1128\/mBio.02162-15","article-title":"Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131","volume":"7","author":"Stoesser","year":"2016","journal-title":"MBio"},{"key":"ref211","doi-asserted-by":"publisher","first-page":"2270","DOI":"10.3390\/microorganisms11092270","article-title":"Genomic haracterization of IMP-producing Pseudomonas aeruginosa in Bulgaria reveals the emergence of IMP-100, a novel plasmid-mediated variant coexisting with a chromosomal VIM-4","volume":"11","author":"Stoikov","year":"2023","journal-title":"Microorganisms"},{"key":"ref212","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.cmet.2019.06.009","article-title":"Bacterial metabolism and antibiotic efficacy","volume":"30","author":"Stokes","year":"2019","journal-title":"Cell Metab."},{"key":"ref213","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1556\/AMicr.57.2010.1.4","article-title":"Investigation of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae outbreaks in Hungary between 2005 and 2008","volume":"57","author":"Szilagyi","year":"2010","journal-title":"Acta Microbiol. Immunol. Hung."},{"key":"ref214","doi-asserted-by":"publisher","first-page":"3106","DOI":"10.1038\/s41598-022-07142-2","article-title":"Correlation between antibiotic consumption and the occurrence of multidrug-resistant organisms in a Malaysian tertiary hospital: a 3-year observational study","volume":"12","author":"Tan","year":"2022","journal-title":"Sci. Rep."},{"key":"ref215","doi-asserted-by":"publisher","first-page":"1276954","DOI":"10.3389\/fmicb.2023.1276954","article-title":"Pts promoter influences antibiotic resistance via proton motive force and ROS in Escherichia coli","volume":"14","author":"Tao","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref216","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1038\/s43856-023-00337-2","article-title":"Increase in the community carriage of fluoroquinolone-resistant Escherichia coli despite a reduction in antibiotic prescriptions","volume":"3","author":"Tchesnokova","year":"2023","journal-title":"Commun. Med."},{"key":"ref217","doi-asserted-by":"publisher","first-page":"14740","DOI":"10.1073\/pnas.1903002116","article-title":"Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci","volume":"116","author":"Tchesnokova","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref218","doi-asserted-by":"publisher","first-page":"4214","DOI":"10.1128\/AAC.02775-13","article-title":"Strain types and antimicrobial resistance patterns of Clostridium difficile isolates from the United States, 2011 to 2013","volume":"58","author":"Tickler","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref219","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1111\/j.1469-0691.2006.01631.x","article-title":"Ecological replacement of Enterococcus faecalis by multiresistant clonal complex 17 Enterococcus faecium","volume":"13","author":"Top","year":"2007","journal-title":"Clin. Microbiol. Infect."},{"key":"ref220","doi-asserted-by":"publisher","first-page":"1862","DOI":"10.1093\/jac\/dkac122","article-title":"Susceptibility profiles and resistance genomics of Pseudomonas aeruginosa isolates from European ICUs participating in the ASPIRE-ICU trial","volume":"77","author":"Torrens","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref221","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1007\/s10096-013-2022-6","article-title":"Fitness cost associated with resistance to fluoroquinolones is diverse across clones of Klebsiella pneumoniae and may select for CTX-M-15 type extendedspectrum \u03b2-lactamase","volume":"33","author":"Toth","year":"2014","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref222","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1016\/j.cmi.2017.06.018","article-title":"Global emergence of the widespread Pseudomonas aeruginosa ST235 clone","volume":"24","author":"Treepong","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref223","doi-asserted-by":"publisher","first-page":"103925","DOI":"10.1016\/j.resmic.2022.103925","article-title":"Comparative characteristics of sequence types, genotypes and virulence of multidrug-resistant Enterococcus faecium isolated from various hosts in eastern Poland. Spread of clonal complex 17 in humans and animals","volume":"173","author":"Troscianczyk","year":"2022","journal-title":"Res. Microbiol."},{"key":"ref224","doi-asserted-by":"publisher","first-page":"e0089222","DOI":"10.1128\/aac.00892-22","article-title":"Genomic analysis of a strain collection containing multidrug-, extensively drug-, pandrug-, and carbapenem-resistant modern clinical isolates of Acinetobacter baumannii","volume":"66","author":"Valcek","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref225","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1093\/jac\/dkr545","article-title":"Clonal outbreak of ST17 multidrug-resistant Enterococcus faecium harbouring an Inc18-like::Tn1546 plasmid in a haemo-oncology ward of a Spanish hospital","volume":"67","author":"Valdezate","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref226","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1093\/jac\/40.3.454","article-title":"High prevalence of colonization with vancomycin- and pristinamycin-resistant enterococci in healthy humans and pigs in the Netherlands: is the addition of antibiotics to animal feeds to blame?","volume":"40","author":"Van den Bogaard","year":"1997","journal-title":"J. Antimicrob. Chemother."},{"key":"ref227","doi-asserted-by":"publisher","first-page":"1927","DOI":"10.1128\/JCM.36.7.1927-1932.1998","article-title":"Molecular characterization of vancomycin-resistant enterococci from hospitalized patients and poultry products in the Netherlands","volume":"36","author":"Van den Braak","year":"1998","journal-title":"J. Clin. Microbiol."},{"key":"ref228","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.2217\/fmb.13.61","article-title":"Prevalence and spread of multidrug-resistant Escherichia coli including ST131 in different patient populations in the Euroregion Meuse-Rhine","volume":"8","author":"Van der Donk","year":"2013","journal-title":"Future Microbiol."},{"key":"ref229","doi-asserted-by":"publisher","first-page":"1186920","DOI":"10.3389\/fmicb.2023.1186920","article-title":"The fitness cost of horizontally transferred and mutational antimicrobial resistance in Escherichia coli","volume":"14","author":"Vanacker","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref230","doi-asserted-by":"publisher","first-page":"3877","DOI":"10.1128\/JCM.42.8.3877-3880.2004","article-title":"Surveillance of methicillin-resistant Staphylococcus aureus in a pediatric hospital in Mexico City during a 7-year period (1997 to 2003): clonal evolution and impact of infection control","volume":"42","author":"Velazquez-Meza","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"ref231","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1093\/jac\/dky535","article-title":"Effect of fluoroquinolone resistance mutation Thr-82Ile on Clostridioides difficile fitness","volume":"74","author":"Vernon","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref232","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1016\/j.ijantimicag.2011.07.007","article-title":"Diversity of class 1 integron gene cassette pc promoter variants in clinical Escherichia coli strains and description of a new P2 promoter variant","volume":"38","author":"Vinu\u00e9","year":"2011","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref233","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1111\/eva.12202","article-title":"The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach","volume":"8","author":"Vogwill","year":"2015","journal-title":"Evol. Appl."},{"key":"ref234","doi-asserted-by":"publisher","first-page":"101083","DOI":"10.1016\/j.drup.2024.101083","article-title":"Expansion and transmission dynamics of high risk carbapenem-resistant Klebsiella pneumoniae subclones in China: an epidemiological, spatial, genomic analysis","volume":"74","author":"Wang","year":"2024","journal-title":"Drug Resist. Updat."},{"key":"ref235","doi-asserted-by":"publisher","first-page":"e0050124","DOI":"10.1128\/spectrum.00501-24","article-title":"Whole genome sequencing insight into carbapenem-resistant and multidrug-resistant Acinetobacter baumannii harboring chromosome-borne Bla(OXA-23)","volume":"12","author":"Wang","year":"2024","journal-title":"Microbiol Spectr"},{"key":"ref236","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.2147\/TCRM.S210872","article-title":"Trends and correlation of antibiotic susceptibility and antibiotic consumption at a large teaching hospital in China (2007-2016): a surveillance study","volume":"15","author":"Wang","year":"2019","journal-title":"Ther. Clin. Risk Manag."},{"key":"ref237","doi-asserted-by":"publisher","first-page":"106051","DOI":"10.1016\/j.micpath.2023.106051","article-title":"Molecular characterization of class 1 integrons in carbapenem-resistant Enterobacterales isolates","volume":"177","author":"Wang","year":"2023","journal-title":"Microb. Pathog."},{"key":"ref238","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1186\/s12879-016-1526-y","article-title":"Molecular characterization and antimicrobial susceptibility of Acinetobacter baumannii isolates obtained from two hospital outbreaks in Los Angeles County, California, USA","volume":"16","author":"Warner","year":"2016","journal-title":"BMC Infect. Dis."},{"key":"ref239","doi-asserted-by":"publisher","first-page":"1794","DOI":"10.1128\/AAC.04503-14","article-title":"Fluoroquinolone resistance does not impose a cost on the fitness of Clostridium difficile in vitro","volume":"59","author":"Wasels","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref240","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1007\/s00284-013-0399-1","article-title":"Diversity of gene cassette promoter variants of class 1 integrons in uropathogenic Escherichia coli","volume":"67","author":"Wei","year":"2013","journal-title":"Curr. Microbiol."},{"key":"ref241","doi-asserted-by":"publisher","first-page":"2595","DOI":"10.1038\/s41467-019-10600-7","article-title":"Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance","volume":"10","author":"Wein","year":"2019","journal-title":"Nat. Commun."},{"key":"ref242","doi-asserted-by":"publisher","first-page":"821","DOI":"10.3201\/1106.041204","article-title":"Global spread of vancomycin-resistant Enterococcus faecium from distinct nosocomial genetic complex","volume":"11","author":"Willems","year":"2005","journal-title":"Emerg. Infect. Dis."},{"key":"ref243","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1186\/s12864-023-09734-2","article-title":"Comparative genotypic characterization related to antibiotic resistance phenotypes of clinical carbapenem-resistant Acinetobacter baumannii MTC1106 (ST2) and MTC0619 (ST25)","volume":"24","author":"Wiradiputra","year":"2023","journal-title":"BMC Genomics"},{"key":"ref244","doi-asserted-by":"publisher","first-page":"e0222423","DOI":"10.1128\/spectrum.02224-23","article-title":"The type III secretion system facilitates systemic infections of Pseudomonas aeruginosa in the clinic","volume":"12","author":"Wu","year":"2024","journal-title":"Microbiol Spectr"},{"key":"ref245","doi-asserted-by":"publisher","first-page":"e0255422","DOI":"10.1128\/spectrum.02554","article-title":"Global phylogeny and F virulence plasmid carriage in pandemic Escherichia coli ST1193","volume":"10","author":"Wyrsch","year":"2022","journal-title":"Microbiol Spectr"},{"key":"ref246","doi-asserted-by":"publisher","first-page":"790","DOI":"10.3389\/fmicb.2019.00790","article-title":"Polymorphisms of gene cassette promoters of the class 1 integron in clinical Proteus isolates","volume":"10","author":"Xiao","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref247","doi-asserted-by":"publisher","first-page":"189","DOI":"10.33073\/pjm-2024-017","article-title":"Analysis of the class 1 integrons, carbapenemase genes and biofilm formation genes occurrence in Acinetobacter baumannii clinical isolates","volume":"73","author":"Xiu","year":"2024","journal-title":"Pol. J. Microbiol."},{"key":"ref249","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1111\/mmi.13407","article-title":"Evolved plasmid-host interactions reduce plasmid interference cost","volume":"101","author":"Yano","year":"2016","journal-title":"Mol. Microbiol."},{"key":"ref250","doi-asserted-by":"publisher","first-page":"815600","DOI":"10.3389\/fmicb.2022.815600","article-title":"Acquisition of daptomycin resistance by Enterococcus faecium confers collateral sensitivity to glycopeptides","volume":"13","author":"Zeng","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref251","doi-asserted-by":"publisher","first-page":"104319","DOI":"10.1016\/j.meegid.2020.104319","article-title":"The determination of gyrA and parC mutations and the prevalence of plasmid-mediated quinolone resistance genes in carbapenem resistant Klebsiella pneumonia ST11 and ST76 strains isolated from patients in Heilongjiang Province, China","volume":"82","author":"Zeng","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref252","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.jgar.2023.01.011","article-title":"Characteristics of rare ST463 carbapenem-resistant Pseudomonas aeruginosa clinical isolates from blood","volume":"32","author":"Zhang","year":"2023","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref253","doi-asserted-by":"publisher","first-page":"e0124222","DOI":"10.1128\/msystems.01242-22","article-title":"Phenotypic and genomic analysis of the hypervirulent ST22 methicillin-resistant Staphylococcus aureus in China","volume":"8","author":"Zhao","year":"2023","journal-title":"Msystems"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1556656\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,10]],"date-time":"2025-04-10T09:48:04Z","timestamp":1744278484000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1556656\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,10]]},"references-count":250,"alternative-id":["10.3389\/fmicb.2025.1556656"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1556656","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,10]]},"article-number":"1556656"}}