{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T02:53:59Z","timestamp":1790650439787,"version":"4.1.0"},"reference-count":64,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T00:00:00Z","timestamp":1697068800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001505","name":"Health Research Council of New Zealand","doi-asserted-by":"publisher","award":["17\/372"],"award-info":[{"award-number":["17\/372"]}],"id":[{"id":"10.13039\/501100001505","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p><jats:italic>Pseudomonas aeruginosa<\/jats:italic> is an opportunistic pathogen that causes a wide range of problematic infections in individuals with predisposing conditions. Infections can be treated with colistin but some isolates are resistant to this antibiotic. To better understand the genetic basis of resistance, we experimentally evolved 19 independent resistant mutants from the susceptible laboratory strain PAO1. Whole genome sequencing identified mutations in multiple genes including <jats:italic>phoQ<\/jats:italic> and <jats:italic>pmrB<\/jats:italic> that have previously been associated with resistance, <jats:italic>pitA<\/jats:italic> that encodes a phosphate transporter, and <jats:italic>carB<\/jats:italic> and <jats:italic>eno<\/jats:italic> that encode enzymes of metabolism. Individual mutations were engineered into the genome of strain PAO1. Mutations in <jats:italic>pitA<\/jats:italic>, <jats:italic>pmrB<\/jats:italic> and <jats:italic>phoQ<\/jats:italic> increased the minimum inhibitory concentration (MIC) for colistin 8-fold, making the bacteria resistant. Engineered <jats:italic>pitA\/phoQ<\/jats:italic> and <jats:italic>pitA\/pmrB<\/jats:italic> double mutants had higher MICs than single mutants, demonstrating additive effects on colistin susceptibility. Single <jats:italic>carB<\/jats:italic> and <jats:italic>eno<\/jats:italic> mutations did not increase the MIC suggesting that their effect is dependent on the presence of other mutations. Many of the resistant mutants had increased susceptibility to \u03b2-lactams and lower growth rates than the parental strain demonstrating that colistin resistance can impose a fitness cost. Two hundred and fourteen <jats:italic>P<\/jats:italic>. <jats:italic>aeruginosa<\/jats:italic> isolates from a range of sources were tested and 18 (7.8%) were colistin resistant. Sequence variants in genes identified by experimental evolution were present in the 18 resistant isolates and may contribute to resistance. Overall our results identify <jats:italic>pitA<\/jats:italic> mutations as novel contributors to colistin resistance and demonstrate that resistance can reduce fitness of the bacteria.<\/jats:p>","DOI":"10.1371\/journal.pone.0292818","type":"journal-article","created":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T17:44:52Z","timestamp":1697132692000},"page":"e0292818","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["The PitA protein contributes to colistin susceptibility in Pseudomonas aeruginosa"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6173-8306","authenticated-orcid":true,"given":"Mareike B.","family":"Erdmann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7808-1213","authenticated-orcid":true,"given":"Paul P.","family":"Gardner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7601-6354","authenticated-orcid":true,"given":"Iain L.","family":"Lamont","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,10,12]]},"reference":[{"issue":"18","key":"pone.0292818.ref001","doi-asserted-by":"crossref","first-page":"2117","DOI":"10.1007\/s40265-021-01635-6","article-title":"The Epidemiology and Pathogenesis and Treatment of Pseudomonas aeruginosa Infections: An Update","volume":"81","author":"D Reynolds","year":"2021","journal-title":"Drugs"},{"issue":"3","key":"pone.0292818.ref002","first-page":"e00181","article-title":"Antimicrobial Resistance in ESKAPE Pathogens","volume":"33","author":"DMP De Oliveira","year":"2020","journal-title":"Clin Microbiol Rev"},{"issue":"3","key":"pone.0292818.ref003","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1586\/eri.13.12","article-title":"Clinical relevance of the ESKAPE pathogens","volume":"11","author":"JN Pendleton","year":"2013","journal-title":"Expert Rev Anti Infect Ther"},{"issue":"1","key":"pone.0292818.ref004","doi-asserted-by":"crossref","first-page":"115557","DOI":"10.1016\/j.diagmicrobio.2021.115557","article-title":"Antimicrobial susceptibility of Gram-negative bacteria from intensive care unit and non-intensive care unit patients from United States hospitals (2018\u20132020)","volume":"102","author":"HS Sader","year":"2022","journal-title":"Diagn Microbiol Infect Dis"},{"issue":"2","key":"pone.0292818.ref005","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.gendis.2019.04.001","article-title":"Emergence of antibiotic resistance Pseudomonas aeruginosa in intensive care unit; a critical review","volume":"6","author":"P Pachori","year":"2019","journal-title":"Genes Dis"},{"key":"pone.0292818.ref006","doi-asserted-by":"crossref","first-page":"212527","DOI":"10.7573\/dic.212527","article-title":"How to manage Pseudomonas aeruginosa infections","volume":"7","author":"M Bassetti","year":"2018","journal-title":"Drugs Context"},{"issue":"1","key":"pone.0292818.ref007","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1080\/22221751.2020.1754133","article-title":"Colistin and its role in the Era of antibiotic resistance: an extended review (2000\u20132019)","volume":"9","author":"MAE El-Sayed Ahmed","year":"2020","journal-title":"Emerg Microbes Infect"},{"key":"pone.0292818.ref008","volume-title":"Critically important antimicrobials for human medicine","author":"World Health Organisation","year":"2019"},{"key":"pone.0292818.ref009","first-page":"123","article-title":"Polymyxins: \u201cLast Resort\u201d for MDR and\/or XDR Gram-negative infections","volume":"2","author":"MME Ahmed","year":"2021","journal-title":"Journal of Scientific Research in Medical and BIological Sciences"},{"issue":"4","key":"pone.0292818.ref010","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.idc.2020.08.003","article-title":"Agents of Last Resort: An Update on Polymyxin Resistance","volume":"34","author":"Q Yang","year":"2020","journal-title":"Infect Dis Clin North Am"},{"key":"pone.0292818.ref011","doi-asserted-by":"crossref","first-page":"7271","DOI":"10.2147\/IDR.S318173","article-title":"Inhaled Colistimethate Sodium in the Management of Patients with Bronchiectasis Infected by Pseudomonas aeruginosa: A Narrative Review of Current Evidence","volume":"15","author":"D de la Rosa-Carrillo","year":"2022","journal-title":"Infect Drug Resist"},{"issue":"6","key":"pone.0292818.ref012","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1016\/j.ijantimicag.2017.01.023","article-title":"Emergence of colistin resistance in Pseudomonas aeruginosa ST235 clone in South Korea","volume":"49","author":"YM Wi","year":"2017","journal-title":"Int J Antimicrob Agents"},{"issue":"7","key":"pone.0292818.ref013","doi-asserted-by":"crossref","first-page":"1825","DOI":"10.1093\/jac\/dkz147","article-title":"Spanish nationwide survey on Pseudomonas aeruginosa antimicrobial resistance mechanisms and epidemiology","volume":"74","author":"E Del Barrio-Tofino","year":"2019","journal-title":"J Antimicrob Chemother"},{"issue":"7","key":"pone.0292818.ref014","doi-asserted-by":"crossref","first-page":"e00355","DOI":"10.1128\/AAC.00355-19","article-title":"The Microbiology of Bloodstream Infection: 20-Year Trends from the SENTRY Antimicrobial Surveillance Program","volume":"63","author":"DJ Diekema","year":"2019","journal-title":"Antimicrob Agents Chemother"},{"issue":"4","key":"pone.0292818.ref015","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1007\/s10123-022-00256-7","article-title":"Antimicrobial resistance, virulence factors, and genotypes of Pseudomonas aeruginosa clinical isolates from Gorgan, northern Iran","volume":"25","author":"FN Shahri","year":"2022","journal-title":"Int Microbiol"},{"issue":"4","key":"pone.0292818.ref016","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1038\/nrmicro2319","article-title":"Antibiotic resistance and its cost: is it possible to reverse resistance?","volume":"8","author":"DI Andersson","year":"2010","journal-title":"Nat Rev Microbiol"},{"issue":"6268","key":"pone.0292818.ref017","doi-asserted-by":"crossref","DOI":"10.1126\/science.aad3292","article-title":"Multidrug evolutionary strategies to reverse antibiotic resistance","volume":"351","author":"M Baym","year":"2016","journal-title":"Science"},{"issue":"1\u20132","key":"pone.0292818.ref018","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.cell.2017.12.012","article-title":"Drug-Driven Phenotypic Convergence Supports Rational Treatment Strategies of Chronic Infections","volume":"172","author":"L Imamovic","year":"2018","journal-title":"Cell"},{"key":"pone.0292818.ref019","doi-asserted-by":"crossref","first-page":"643","DOI":"10.3389\/fmicb.2014.00643","article-title":"Mechanisms of polymyxin resistance: acquired and intrinsic resistance in bacteria","volume":"5","author":"AO Olaitan","year":"2014","journal-title":"Front Microbiol"},{"key":"pone.0292818.ref020","doi-asserted-by":"crossref","first-page":"e65836","DOI":"10.7554\/eLife.65836","article-title":"Colistin kills bacteria by targeting lipopolysaccharide in the cytoplasmic membrane","volume":"10","author":"A Sabnis","year":"2021","journal-title":"Elife"},{"key":"pone.0292818.ref021","doi-asserted-by":"crossref","first-page":"677720","DOI":"10.3389\/fmed.2021.677720","article-title":"Current Update on Intrinsic and Acquired Colistin Resistance Mechanisms in Bacteria","volume":"8","author":"FA Gogry","year":"2021","journal-title":"Front Med (Lausanne)"},{"issue":"3","key":"pone.0292818.ref022","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.01820-17","article-title":"Aminoarabinosylation of Lipid A Is Critical for the Development of Colistin Resistance in Pseudomonas aeruginosa","volume":"62","author":"A Lo Sciuto","year":"2018","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"pone.0292818.ref023","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1016\/j.ijantimicag.2016.11.029","article-title":"Resistance to polymyxins in Gram-negative organisms","volume":"49","author":"K Jeannot","year":"2017","journal-title":"Int J Antimicrob Agents"},{"key":"pone.0292818.ref024","doi-asserted-by":"crossref","first-page":"778968","DOI":"10.3389\/fmicb.2021.778968","article-title":"Exogenous and Endogenous Phosphoethanolamine Transferases Differently Affect Colistin Resistance and Fitness in Pseudomonas aeruginosa","volume":"12","author":"M Cervoni","year":"2021","journal-title":"Front Microbiol"},{"issue":"3","key":"pone.0292818.ref025","doi-asserted-by":"crossref","first-page":"2897","DOI":"10.1007\/s11033-021-06307-y","article-title":"Mobilized colistin resistance (mcr) genes from 1 to 10: a comprehensive review","volume":"48","author":"NH Hussein","year":"2021","journal-title":"Mol Biol Rep"},{"key":"pone.0292818.ref026","doi-asserted-by":"crossref","first-page":"13002","DOI":"10.1038\/ncomms13002","article-title":"The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is shaped by strong epistatic interactions","volume":"7","author":"N Jochumsen","year":"2016","journal-title":"Nat Commun"},{"issue":"9","key":"pone.0292818.ref027","doi-asserted-by":"crossref","first-page":"e00043","DOI":"10.1128\/AAC.00043-17","article-title":"Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture","volume":"61","author":"B Dosselmann","year":"2017","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0292818.ref028","unstructured":"European Committee on Antimicrobial Susceptibility Testing. Clinical breakpoints \u2010 bacteria (v 12.0). 2022."},{"key":"pone.0292818.ref029","doi-asserted-by":"crossref","first-page":"153","DOI":"10.3389\/fmicb.2018.00153","article-title":"Growth Rate and Biofilm Formation Ability of Clinical and Laboratory-Evolved Colistin-Resistant Strains of Acinetobacter baumannii","volume":"9","author":"Z Farshadzadeh","year":"2018","journal-title":"Front Microbiol"},{"issue":"6","key":"pone.0292818.ref030","doi-asserted-by":"crossref","first-page":"2298","DOI":"10.1128\/AAC.01016-08","article-title":"Genetic analysis of colistin resistance in Salmonella enterica serovar Typhimurium","volume":"53","author":"S Sun","year":"2009","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"pone.0292818.ref031","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1128\/AAC.05829-11","article-title":"PmrB mutations promote polymyxin resistance of Pseudomonas aeruginosa isolated from colistin-treated cystic fibrosis patients","volume":"56","author":"SM Moskowitz","year":"2012","journal-title":"Antimicrob Agents Chemother"},{"issue":"3","key":"pone.0292818.ref032","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.diagmicrobio.2013.11.027","article-title":"Mutations and expression of PmrAB and PhoPQ related with colistin resistance in Pseudomonas aeruginosa clinical isolates","volume":"78","author":"JY Lee","year":"2014","journal-title":"Diagn Microbiol Infect Dis"},{"key":"pone.0292818.ref033","article-title":"Pseudomonas aeruginosa Phosphate Transporter PitA (PA4292) Controls Susceptibility to Aminoglycoside Antibiotics by Regulating the Proton Motive Force","author":"X Zhao","year":"2022","journal-title":"Antimicrob Agents Chemother"},{"issue":"4","key":"pone.0292818.ref034","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1128\/JB.05230-11","article-title":"Surface-localized spermidine protects the Pseudomonas aeruginosa outer membrane from antibiotic treatment and oxidative stress","volume":"194","author":"L Johnson","year":"2012","journal-title":"J Bacteriol"},{"issue":"23","key":"pone.0292818.ref035","doi-asserted-by":"crossref","first-page":"6387","DOI":"10.1128\/JB.01479-12","article-title":"Sequence-verified two-allele transposon mutant library for Pseudomonas aeruginosa PAO1","volume":"194","author":"K Held","year":"2012","journal-title":"J Bacteriol"},{"key":"pone.0292818.ref036","article-title":"High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality","author":"FA Ghomi","journal-title":"BioRxiv"},{"issue":"1","key":"pone.0292818.ref037","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1046\/j.1365-2958.2003.03673.x","article-title":"Cationic antimicrobial peptides activate a two-component regulatory system, PmrA-PmrB, that regulates resistance to polymyxin B and cationic antimicrobial peptides in Pseudomonas aeruginosa","volume":"50","author":"JB McPhee","year":"2003","journal-title":"Mol Microbiol"},{"issue":"1","key":"pone.0292818.ref038","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1111\/mmi.13018","article-title":"Extracellular zinc induces phosphoethanolamine addition to Pseudomonas aeruginosa lipid A via the ColRS two-component system","volume":"97","author":"Nowicki EM","year":"2015","journal-title":"Mol Microbiol"},{"issue":"5","key":"pone.0292818.ref039","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1177\/1753425909106436","article-title":"Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa","volume":"15","author":"JD King","year":"2009","journal-title":"Innate Immun"},{"issue":"3","key":"pone.0292818.ref040","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1111\/j.1432-1033.1983.tb07105.x","article-title":"Carbamoylphosphate synthetase from Pseudomonas aeruginosa. Subunit composition, kinetic analysis and regulation","volume":"129","author":"AT Abdelal","year":"1983","journal-title":"Eur J Biochem"},{"issue":"1","key":"pone.0292818.ref041","doi-asserted-by":"crossref","DOI":"10.4236\/aim.2012.21005","article-title":"Differential Role of Two-Component Regulatory Systems (phoPQ and pmrAB) in Polymyxin B Susceptibility of Pseudomonas aeruginosa","volume":"2","author":"D Owusu-Anim","year":"2012","journal-title":"Adv Microbiol"},{"issue":"11","key":"pone.0292818.ref042","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1016\/j.cmi.2021.05.011","article-title":"Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence resistome analysis","volume":"27","author":"S Cortes-Lara","year":"2021","journal-title":"Clin Microbiol Infect"},{"key":"pone.0292818.ref043","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.3389\/fmicb.2020.01013","article-title":"Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data","volume":"11","author":"PJ Van Camp","year":"2020","journal-title":"Front Microbiol"},{"issue":"10","key":"pone.0292818.ref044","doi-asserted-by":"crossref","first-page":"e01044","DOI":"10.1128\/AAC.01044-19","article-title":"Production of Norspermidine Contributes to Aminoglycoside Resistance in pmrAB Mutants of Pseudomonas aeruginosa","volume":"63","author":"A Bolard","year":"2019","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0292818.ref045","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/s12859-016-1016-7","article-title":"Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves","volume":"17","author":"K Sprouffske","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"pone.0292818.ref046","first-page":"e01619","article-title":"A large-scale whole-genome comparison shows that experimental evolution in response to antibiotics predicts changes in naturally evolved clinical Pseudomonas aeruginosa","volume":"63","author":"SJT Wardell","year":"2019","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"pone.0292818.ref047","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/nprot.2007.521","article-title":"Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances","volume":"3","author":"I Wiegand","year":"2008","journal-title":"Nat Protoc"},{"key":"pone.0292818.ref048","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/S0378-1119(98)00130-9","article-title":"A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants","volume":"212","author":"TT Hoang","year":"1998","journal-title":"Gene"},{"issue":"11","key":"pone.0292818.ref049","doi-asserted-by":"crossref","first-page":"1820","DOI":"10.1038\/nprot.2015.115","article-title":"Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange","volume":"10","author":"LR Hmelo","year":"2015","journal-title":"Nat Protoc"},{"issue":"2","key":"pone.0292818.ref050","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1111\/j.1574-6968.2009.01556.x","article-title":"An improved Escherichia coli donor strain for diparental mating","volume":"294","author":"S Thoma","year":"2009","journal-title":"FEMS Microbiol Lett"},{"issue":"7","key":"pone.0292818.ref051","doi-asserted-by":"crossref","first-page":"e0269620","DOI":"10.1128\/AAC.02696-20","article-title":"Gene-Gene Interactions Dictate Ciprofloxacin Resistance in Pseudomonas aeruginosa and Facilitate Prediction of Resistance Phenotype from Genome Sequence Data","volume":"65","author":"A Rehman","year":"2021","journal-title":"Antimicrob Agents Chemother"},{"issue":"14","key":"pone.0292818.ref052","doi-asserted-by":"crossref","DOI":"10.1093\/femsle\/fny120","article-title":"Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools","volume":"365","author":"L Freschi","year":"2018","journal-title":"FEMS Microbiol Lett"},{"issue":"1","key":"pone.0292818.ref053","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1093\/gbe\/evy259","article-title":"The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity","volume":"11","author":"L Freschi","year":"2019","journal-title":"Genome Biol Evol"},{"issue":"11","key":"pone.0292818.ref054","first-page":"000681","article-title":"Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection","volume":"7","author":"SJT Wardell","year":"2021","journal-title":"Microb Genom"},{"issue":"1","key":"pone.0292818.ref055","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"DE Wood","year":"2019","journal-title":"Genome Biol"},{"issue":"15","key":"pone.0292818.ref056","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"5","key":"pone.0292818.ref057","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"pone.0292818.ref058","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.3389\/fmicb.2015.01036","article-title":"Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium","volume":"6","author":"L Freschi","year":"2015","journal-title":"Front Microbiol"},{"issue":"7","key":"pone.0292818.ref059","doi-asserted-by":"crossref","first-page":"884","DOI":"10.3390\/antibiotics11070884","article-title":"Aminoglycoside-Modifying Enzymes Are Sufficient to Make Pseudomonas aeruginosa Clinically Resistant to Key Antibiotics","volume":"11","author":"A Thacharodi","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"pone.0292818.ref060","doi-asserted-by":"crossref","unstructured":"Deatherage DE, Barrick JE. Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq. In: Sun L, Shou W, editors. Engineering and Analyzing Multicellular Systems: Methods and Protocols. New York, NY: Springer New York; 2014. p. 165\u201388.","DOI":"10.1007\/978-1-4939-0554-6_12"},{"issue":"14","key":"pone.0292818.ref061","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T. Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"10","key":"pone.0292818.ref062","doi-asserted-by":"crossref","first-page":"e46688","DOI":"10.1371\/journal.pone.0046688","article-title":"Predicting the functional effect of amino acid substitutions and indels","volume":"7","author":"Y Choi","year":"2012","journal-title":"PLoS One"},{"issue":"D1","key":"pone.0292818.ref063","doi-asserted-by":"crossref","first-page":"D646","DOI":"10.1093\/nar\/gkv1227","article-title":"Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database","volume":"44","author":"GL Winsor","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"17","key":"pone.0292818.ref064","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"SF Altschul","year":"1997","journal-title":"Nucleic Acids Res"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0292818","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T17:45:31Z","timestamp":1697132731000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0292818"}},"subtitle":[],"editor":[{"given":"Iddya","family":"Karunasagar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,10,12]]},"references-count":64,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2023,10,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0292818","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,12]]}}}