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Bott","year":"1997","journal-title":"Arch Microbiol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1007\/s00203-002-0420-8","article-title":"Characterization of the citrate\/acetate antiporter CitW of <italic>Klebsiella pneumoniae<\/italic>.","volume":"177","author":"CN K\u00e4stner","year":"2002","journal-title":"Arch Microbiol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"31113","DOI":"10.1074\/jbc.M404283200","article-title":"Alternating access and a pore-loop structure in the Na<sup>+<\/sup>-citrate transporter CitS of <italic>Klebsiella pneumoniae<\/italic>.","volume":"279","author":"I Sobczak","year":"2004","journal-title":"J Biol Chem"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1128\/MMBR.62.2.379-433.1998","article-title":"Type III protein secretion systems in bacterial pathogens of animals and plants.","volume":"62","author":"CJ Hueck","year":"1998","journal-title":"Microbiol Mol Biol 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its NADH-oxidizing redox partner.","volume":"280","author":"JB Vicente","year":"2005","journal-title":"J Biol Chem"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1094\/MPMI.2004.17.1.43","article-title":"The phytoalexin-inducible multidrug efflux pump AcrAB contributes to virulence in the fire blight pathogen, <italic>Erwinia amylovora<\/italic>.","volume":"17","author":"A Burse","year":"2004","journal-title":"Mol Plant Microbe Interact"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1099\/mic.0.25833-0","article-title":"Application of a novel multi-screening signature-tagged mutagenesis assay for identification of <italic>Klebsiella pneumoniae<\/italic> genes essential in colonization and infection.","volume":"149","author":"C Struve","year":"2003","journal-title":"Microbiology"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1111\/j.1365-2958.2005.04918.x","article-title":"Identification of <italic>Klebsiella pneumoniae<\/italic> virulence determinants using an intranasal infection model.","volume":"58","author":"MS Lawlor","year":"2005","journal-title":"Mol Microbiol"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"7140","DOI":"10.1128\/IAI.69.11.7140-7145.2001","article-title":"Identification of genes induced <italic>in vivo<\/italic> during <italic>Klebsiella pneumoniae<\/italic> CG43 infection.","volume":"69","author":"YC Lai","year":"2001","journal-title":"Infect Immun"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"2831","DOI":"10.1128\/AAC.47.9.2831-2837.2003","article-title":"Role of AcrR and RamA in fluoroquinolone resistance in clinical <italic>Klebsiella pneumoniae<\/italic> isolates from Singapore.","volume":"47","author":"T Schneiders","year":"2003","journal-title":"Antimicrob Agents Chemother"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"2856","DOI":"10.1128\/AAC.45.10.2856-2861.2001","article-title":"SHV-1 beta-lactamase is mainly a chromosomally encoded species-specific enzyme in <italic>Klebsiella pneumoniae<\/italic>.","volume":"45","author":"J Chaves","year":"2001","journal-title":"Antimicrob Agents Chemother"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"1909","DOI":"10.1099\/13500872-141-8-1909","article-title":"Multidrug resistance in <italic>Klebsiella pneumoniae<\/italic>: a novel gene, <italic>ramA<\/italic>, confers a multidrug resistance phenotype in <italic>Escherichia coli<\/italic>.","volume":"141 ( Pt 8)","author":"AM George","year":"1995","journal-title":"Microbiology"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"4082","DOI":"10.1128\/jb.172.7.4082-4089.1990","article-title":"Molecular characterization of an <italic>Enterobacter cloacae<\/italic> gene (<italic>romA<\/italic>) which pleiotropically inhibits the expression of <italic>Escherichia coli<\/italic> outer membrane proteins.","volume":"172","author":"T Komatsu","year":"1990","journal-title":"J Bacteriol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"2155","DOI":"10.1128\/AAC.35.10.2155","article-title":"Increased resistance to multiple drugs by introduction of the <italic>Enterobacter cloacae romA<\/italic> gene into OmpF porin-deficient mutants of <italic>Escherichia coli<\/italic> K-12.","volume":"35","author":"T Komatsu","year":"1991","journal-title":"Antimicrob Agents Chemother"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1128\/AAC.49.3.1017-1022.2005","article-title":"Influence of transcriptional activator RamA on expression of multidrug efflux pump AcrAB and tigecycline susceptibility in <italic>Klebsiella pneumoniae<\/italic>.","volume":"49","author":"A Ruzin","year":"2005","journal-title":"Antimicrob Agents Chemother"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"3894","DOI":"10.1128\/JB.187.11.3894-3897.2005","article-title":"The <italic>eefABC<\/italic> multidrug efflux pump operon is repressed by H-NS in <italic>Enterobacter aerogenes<\/italic>.","volume":"187","author":"M Masi","year":"2005","journal-title":"J Bacteriol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"3332","DOI":"10.1128\/AAC.48.9.3332-3337.2004","article-title":"Plasmid-encoded multidrug efflux pump conferring resistance to olaquindox in <italic>Escherichia coli<\/italic>.","volume":"48","author":"LH Hansen","year":"2004","journal-title":"Antimicrob Agents Chemother"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"4168","DOI":"10.1128\/JB.184.15.4168-4176.2002","article-title":"The <italic>baeSR<\/italic> two-component regulatory system activates transcription of the <italic>yegMNOB<\/italic> (<italic>mdtABCD<\/italic>) transporter gene cluster in <italic>Escherichia coli<\/italic> and increases its resistance to novobiocin and deoxycholate.","volume":"184","author":"N Baranova","year":"2002","journal-title":"J Bacteriol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"5639","DOI":"10.1128\/JB.183.19.5639-5644.2001","article-title":"Novel macrolide-specific ABC-type efflux transporter in <italic>Escherichia coli<\/italic>.","volume":"183","author":"N Kobayashi","year":"2001","journal-title":"J Bacteriol"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"33324","DOI":"10.1074\/jbc.M506500200","article-title":"The EAL domain protein VieA is a cyclic diguanylate phosphodiesterase.","volume":"280","author":"R Tamayo","year":"2005","journal-title":"J Biol Chem"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1128\/AEM.51.2.323-327.1986","article-title":"Generation and Characterization of <italic>Tn<\/italic>5 Insertion Mutations in <italic>Pseudomonas syringae<\/italic> pv. <italic>tomato<\/italic>.","volume":"51","author":"DA Cuppels","year":"1986","journal-title":"Appl Environ Microbiol"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1111\/j.1462-2920.2005.00940.x","article-title":"A two-partner secretion system is involved in seed and root colonization and iron uptake by <italic>Pseudomonas putida<\/italic> KT2440.","volume":"8","author":"MA Molina","year":"2006","journal-title":"Environ Microbiol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"8285","DOI":"10.1074\/jbc.270.14.8285","article-title":"Transcriptional activation of the <italic>Escherichia coli<\/italic> adaptive response gene <italic>aidB<\/italic> is mediated by binding of methylated Ada protein. Evidence for a new consensus sequence for Ada-binding sites.","volume":"270","author":"P Landini","year":"1995","journal-title":"J Biol Chem"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"6297","DOI":"10.1073\/pnas.83.17.6297","article-title":"Regulatory mechanisms for induction of synthesis of repair enzymes in response to alkylating agents: Ada protein acts as a transcriptional regulator.","volume":"83","author":"Y Nakabeppu","year":"1986","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1007\/s11177-005-0115-8","article-title":"Quasi-adaptive response to alkylating agents in <italic>Escherichia coli<\/italic>: A new phenomenon.","volume":"41","author":"SV Vasilieva","year":"2005","journal-title":"Russ J Genet"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1007\/BF01577443","article-title":"Hydrogen-peroxide induces the repair of UV-damaged DNA in <italic>Escherichia coli<\/italic>-a LexA-independent but UvrA-dependent and RecA-dependent mechanism.","volume":"29","author":"LMBO Asad","year":"1994","journal-title":"Curr Microbiol"},{"key":"ref88","first-page":"275","article-title":"Genotoxic effects of the hydroxycinnamic acid derivatives-caffeic, chlorogenic and cichoric acids.","volume":"60","author":"M Mikulasova","year":"2005","journal-title":"Biologia"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/S0300-9084(82)80094-1","article-title":"Properties and regulation of the UvrABC endonuclease.","volume":"64","author":"WD Rupp","year":"1982","journal-title":"Biochimie"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"6255","DOI":"10.1128\/jb.177.21.6255-6262.1995","article-title":"Oxygen, iron, carbon, and superoxide control of the fumarase <italic>fumA<\/italic> and <italic>fumC<\/italic> genes of <italic>Escherichia coli<\/italic>: role of the <italic>arcA<\/italic>, <italic>fnr<\/italic>, and <italic>soxR<\/italic> gene products.","volume":"177","author":"SJ Park","year":"1995","journal-title":"J Bacteriol"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1093\/oxfordjournals.jbchem.a123448","article-title":"Purification and characterization of two types of fumarase from <italic>Escherichia coli<\/italic>.","volume":"109","author":"Y Ueda","year":"1991","journal-title":"J Biochem"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"3699","DOI":"10.1128\/JB.184.13.3699-3703.2002","article-title":"Toxic waste disposal in <italic>Escherichia coli<\/italic>.","volume":"184","author":"RB Helling","year":"2002","journal-title":"J Bacteriol"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1111\/j.1365-2958.1995.tb02390.x","article-title":"Genes <italic>acrA<\/italic> and <italic>acrB<\/italic> encode a stress-induced efflux system of <italic>Escherichia coli<\/italic>.","volume":"16","author":"D Ma","year":"1995","journal-title":"Mol Microbiol"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1093\/jac\/41.1.111","article-title":"Association of organic solvent tolerance and fluoroquinolone resistance in clinical isolates of <italic>Escherichia coli<\/italic>.","volume":"41","author":"M Oethinger","year":"1998","journal-title":"J Antimicrob Chemother"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"7856","DOI":"10.1128\/jb.175.24.7856-7862.1993","article-title":"Salicylate induction of antibiotic resistance in <italic>Escherichia coli<\/italic>: activation of the <italic>mar<\/italic> operon and a <italic>mar<\/italic>-independent pathway.","volume":"175","author":"SP Cohen","year":"1993","journal-title":"J Bacteriol"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1093\/jac\/46.2.279","article-title":"Salicylate induction of phenotypic resistance to quinolones in <italic>Serratia marcescens<\/italic>.","volume":"46","author":"M Berlanga","year":"2000","journal-title":"J Antimicrob Chemother"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1093\/jac\/25.6.903","article-title":"Potentiation of aminoglycoside inhibition and reduction of capsular polysaccharide production in <italic>Klebsiella pneumoniae<\/italic> by sodium salicylate.","volume":"25","author":"P Domenico","year":"1990","journal-title":"J Antimicrob Chemother"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1093\/jac\/26.3.343","article-title":"The effect of sodium salicylate on antibiotic susceptibility and synergy in <italic>Klebsiella pneumoniae<\/italic>.","volume":"26","author":"P Domenico","year":"1990","journal-title":"J Antimicrob Chemother"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1104\/pp.99.3.799","article-title":"Salicylate, A New Plant Hormone.","volume":"99","author":"I Raskin","year":"1992","journal-title":"Plant Physiol"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1099\/ijs.0.64089-0","article-title":"<italic>Aquitalea magnusonii<\/italic> gen. nov., sp. nov., a novel Gram-negative bacterium isolated from a humic lake.","volume":"56","author":"HT Lau","year":"2006","journal-title":"Int J Syst Evol Microbiol"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"2950","DOI":"10.1128\/IAI.65.7.2950-2958.1997","article-title":"Invasion of cultured human epithelial cells by <italic>Klebsiella pneumoniae<\/italic> isolated from the urinary tract.","volume":"65","author":"TA Oelschlaeger","year":"1997","journal-title":"Infect Immun"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1111\/j.1574-6968.2003.tb11511.x","article-title":"Role of capsule in <italic>Klebsiella pneumoniae<\/italic> virulence: lack of correlation between <italic>in vitro<\/italic> and <italic>in vivo<\/italic> studies.","volume":"218","author":"C Struve","year":"2003","journal-title":"FEMS Microbiol Lett"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1371\/journal.pbio.0030015","article-title":"Major structural differences and novel potential virulence mechanisms from the genomes of multiple <italic>Campylobacter<\/italic> species.","volume":"3","author":"DE Fouts","year":"2005","journal-title":"PLoS Biol"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1126\/science.287.5461.2196","article-title":"A whole-genome assembly of <italic>Drosophila<\/italic>.","volume":"287","author":"EW Myers","year":"2000","journal-title":"Science"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1101\/gr.1536204","article-title":"Hierarchical scaffolding with Bambus.","volume":"14","author":"M Pop","year":"2004","journal-title":"Genome Res"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"4636","DOI":"10.1093\/nar\/27.23.4636","article-title":"Improved microbial gene identification with GLIMMER.","volume":"27","author":"AL Delcher","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"ref107","first-page":"743","article-title":"Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the <italic>E. coli<\/italic> chromosome.","volume":"52","author":"D Bramhill","year":"1988"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/20601","article-title":"Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of <italic>Thermotoga maritima<\/italic>.","volume":"399","author":"KE Nelson","year":"1999","journal-title":"Nature"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.","volume":"305","author":"A Krogh","year":"2001","journal-title":"J Mol Biol"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1126\/science.7542800","article-title":"Whole-genome random sequencing and assembly of <italic>Haemophilus influenzae<\/italic> Rd.","volume":"269","author":"RD Fleischmann","year":"1995","journal-title":"Science"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ref112","doi-asserted-by":"crossref","first-page":"D274","DOI":"10.1093\/nar\/gkl925","article-title":"TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels.","volume":"35","author":"Q Ren","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref113","doi-asserted-by":"crossref","first-page":"6841","DOI":"10.1128\/JB.00111-06","article-title":"Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria <italic>Hyphomonas neptunium<\/italic> and <italic>Caulobacter crescentus<\/italic>.","volume":"188","author":"JH Badger","year":"2006","journal-title":"J Bacteriol"},{"key":"ref114","article-title":"WU-BLAST.","author":"W Gish","year":"2004"},{"key":"ref115","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput.","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref116","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1093\/bioinformatics\/18.11.1546","article-title":"QuickTree: building huge Neighbour-Joining trees of protein sequences.","volume":"18","author":"K Howe","year":"2002","journal-title":"Bioinformatics"},{"key":"ref117","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1128\/AAC.44.1.156-163.2000","article-title":"Development of a long-term ascending urinary tract infection mouse model for antibiotic treatment studies.","volume":"44","author":"H Hvidberg","year":"2000","journal-title":"Antimicrob Agents Chemother"},{"key":"ref118","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1006\/mpat.2000.0363","article-title":"Pneumococcal pneumonia and bacteremia model in mice for the analysis of protective antibodies.","volume":"29","author":"E Saeland","year":"2000","journal-title":"Microb Pathog"},{"key":"ref119","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1128\/AAC.45.4.1078-1085.2001","article-title":"Penicillin pharmacodynamics in four experimental pneumococcal infection models.","volume":"45","author":"H Erlendsdottir","year":"2001","journal-title":"Antimicrob Agents Chemother"}],"container-title":["PLoS 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