{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T20:07:13Z","timestamp":1791317233489,"version":"4.3.1"},"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2016,9,26]],"date-time":"2016-09-26T00:00:00Z","timestamp":1474848000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000180","name":"U.S. Department of Homeland Security","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000180","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0163458","type":"journal-article","created":{"date-parts":[[2016,9,26]],"date-time":"2016-09-26T13:38:58Z","timestamp":1474897138000},"page":"e0163458","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":20,"title":["Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing"],"prefix":"10.1371","volume":"11","author":[{"given":"Crystal J.","family":"Jaing","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin S.","family":"McLoughlin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James B.","family":"Thissen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Zemla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shea N.","family":"Gardner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa M.","family":"Vergez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feliza","family":"Bourguet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shalini","family":"Mabery","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viacheslav Y.","family":"Fofanov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather","family":"Koshinsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul J.","family":"Jackson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,9,26]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"2362","DOI":"10.1128\/AAC.47.7.2362-2365.2003","article-title":"In vitroselection and characterization of Bacillus anthracis mutants with high-level resistance to ciprofloxacin","volume":"47","author":"LB Price","year":"2000","journal-title":"Antimicrob Agents Chemother"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"3904","DOI":"10.1128\/jb.177.14.3904-3910.1995","article-title":"Two highly similar multi-drug transporters of Bacillus subtilis whose expression is differentially regulated","volume":"177","author":"M Ahmed","year":"1995","journal-title":"J Bacteriol"},{"issue":"7","key":"ref3","doi-asserted-by":"crossref","first-page":"2787","DOI":"10.1128\/AAC.01405-09","article-title":"Genomewide screening for novel genetic variations associated with ciprofloxacin resistance in Bacillus anthracis","volume":"54","author":"M Serizawa","year":"2010","journal-title":"Antimicrob Agents Chemother"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/S0890-8508(02)00111-1","article-title":"Development of a 5' nuclease assay to detect ciprofloxacin resistant isolates of the biowarfare agent Yersinia pestis","volume":"17","author":"LE Lindler","year":"2003","journal-title":"Mol Cell Probes"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"2971","DOI":"10.1128\/AAC.00015-06","article-title":"MarA-like regulator of multidrug resistance in Yersinia pestis","volume":"50","author":"RA Udani","year":"2006","journal-title":"Antimicrob Agents Chemother"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1949","DOI":"10.1128\/IAI.74.3.1949-1953.2006","article-title":"Routine Markerless Gene Replacement in Bacillus anthracis","volume":"74","author":"BK Janes","year":"2006","journal-title":"Infection and Immunity"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"6496","DOI":"10.1128\/AEM.01669-09","article-title":"Versatile dual-technology system for markerless allele replacement in Burkholderia pseudomallei","volume":"75","author":"C L\u00f3pez","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.mimet.2009.10.013","article-title":"Utilization of an unstable plasmid and the I-SceI endonuclease to generate routine markerless deletion mutants in Francisella tularensis","volume":"80","author":"J Horzempaa","year":"2010","journal-title":"J Microbiol Methods"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.ijantimicag.2008.03.017","article-title":"A bioinformatic approach to understanding antibiotic resistance in intracellular bacteria through whole genome analysis","volume":"32","author":"S Biswas","year":"2008","journal-title":"Inter J Antimicrob Agents"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1093\/jac\/46.2.287","article-title":"In vitro antibiotic susceptibility of Francisella tularensis isolated from humans and animals","volume":"46","author":"I Ik\u00e4heimo","year":"2000","journal-title":"J Antimicrob Chemother"},{"key":"ref11","first-page":"84","article-title":"Sensitivity to macrolide antibiotics and lincomycin in Francisella tularensis holarctica","volume":"24","author":"R Kudelina","year":"1980","journal-title":"J Hyg Epidemiol Microbiol Immunol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"W577","DOI":"10.1093\/nar\/gki591","article-title":"DNAMelt web server for nucleic acid melting prediction","volume":"33","author":"NR Markham","year":"2005","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"ref13","doi-asserted-by":"crossref","first-page":"e2163","DOI":"10.1371\/journal.pone.0002163","article-title":"A functional gene array for detection of bacterial virulence elements","volume":"3","author":"C Jaing","year":"2008","journal-title":"PLoS ONE"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1932","DOI":"10.1126\/science.1123726","article-title":"Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray","volume":"311","author":"D Gresham","year":"2006","journal-title":"Science"},{"issue":"25","key":"ref15","doi-asserted-by":"crossref","first-page":"2438","DOI":"10.1093\/bioinformatics\/btp429","article-title":"PIQA: pipeline for Illumina G1 genome analyzer data quality assessment","volume":"5","author":"A Mart\u00ednez-Alc\u00e1ntara","year":"2009","journal-title":"Bioinformatics"},{"key":"ref16","first-page":"365","article-title":"Bioinformatics Methods and Protocols: Methods in Molecular Biology","author":"S Rozen","year":"2000"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1093\/nar\/gki457","article-title":"AS2TS system for protein structure modeling and analysis","volume":"33","author":"A Zemla","year":"2005","journal-title":"Nucleic Acids Research"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"3370","DOI":"10.1093\/nar\/gkg571","article-title":"LGA\u2014A Method for Finding 3-D Similarities in Protein Structures","volume":"31","author":"A Zemla","year":"2003","journal-title":"Nucleic Acids Research"},{"key":"ref19","article-title":"StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase","author":"A Zemla","journal-title":"BMC bioinformatics"},{"issue":"5958","key":"ref20","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1126\/science.1179123","article-title":"A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to DNA Gyrase","volume":"326","author":"MJ Edwards","year":"2009","journal-title":"Science"},{"issue":"31","key":"ref21","doi-asserted-by":"crossref","first-page":"8999","DOI":"10.1021\/bi700751d","article-title":"Molecular Architecture of DesI: A Key Enzyme in the Biosynthesis of Desosamine","volume":"46","author":"ES Burgie","year":"2007","journal-title":"Biochemistry"},{"issue":"9","key":"ref22","doi-asserted-by":"crossref","first-page":"2833","DOI":"10.1021\/bi702430d","article-title":"GDP-Perosamine Synthase: Structural Analysis and Production of a Novel Trideoxysugar","volume":"47","author":"PD Cook","year":"2008","journal-title":"Biochemistry"},{"issue":"33","key":"ref23","doi-asserted-by":"crossref","first-page":"7227","DOI":"10.1021\/bi100805b","article-title":"Structural Analysis of WbpE from Pseudomonas aeruginosa PAO1: A Nucleotide Sugar Aminotransferase Involved in O-Antigen Assembly","volume":"49","author":"A Larkin","year":"2010","journal-title":"Biochemistry"},{"key":"ref24","article-title":"Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-D-Manno-Octulosonic Acid","author":"TR Zachman-Brockmeyer","year":"2016","journal-title":"Biochemistry"},{"issue":"21","key":"ref25","doi-asserted-by":"crossref","first-page":"9911","DOI":"10.1093\/nar\/gkt749","article-title":"Structure of an \u2018open\u2019 clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport","volume":"41","author":"I Laponogov","year":"2013","journal-title":"Nucleic Acids Research"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1054\/drup.1998.0068","article-title":"Mechanisms of fluoroquinolone resistance","volume":"2","author":"D Hooper","year":"1999","journal-title":"Drug Resist Updat"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/BF00338386","article-title":"Quinolone-resistant mutations of the gyrA gene of Escherichia coli","volume":"211","author":"H Yoshida","year":"1988","journal-title":"Mol Gen Genet"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1128\/AAC.40.4.870","article-title":"Sequence of quinolone resistance-determining region of gyrA gene for clinical isolates and for an in vitro-selected quinolone-resistant strain of Coxiella burnetii","volume":"40","author":"D Musso","year":"1996","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"ref29","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1093\/jac\/dkt321","article-title":"Evolution toward high-level fluoroquinolone resistance in Francisella species","volume":"69","author":"V Sutera","year":"2014","journal-title":"Journal of Antimicrobial Chemotherapy"},{"issue":"5","key":"ref30","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1101\/gr.071266.107","article-title":"Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm","volume":"18","author":"B La Scola","year":"2008","journal-title":"Genome Research"},{"issue":"3","key":"ref31","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.mcp.2010.01.003","article-title":"Identification of ciprofloxacin resistance by SimpleProbe, High Resolution Melt and Pyrosequencing nucleic acid analysis in biothreat agents: Bacillus anthracis, Yersinia pestis and Francisella tularensis","volume":"24","author":"B Loveless","year":"2010","journal-title":"Mol Cell Probes"},{"issue":"12","key":"ref32","doi-asserted-by":"crossref","first-page":"6895","DOI":"10.1128\/IAI.01006-06","article-title":"Potential Source of Francisella tularensis Live Vaccine Strain Attenuation Determined by Genome Comparison","volume":"74","author":"L Rohmer","year":"2006","journal-title":"Infection and Immunity"},{"issue":"12","key":"ref33","doi-asserted-by":"crossref","first-page":"8345","DOI":"10.1128\/IAI.73.12.8345-8352.2005","article-title":"A Mutant of Francisella tularensis Strain SCHU S4 Lacking the Ability To Express a 58-Kilodalton Protein Is Attenuated for Virulence and Is an Effective Live Vaccine","volume":"73","author":"S Twine","year":"2005","journal-title":"Infection and Immunity"},{"issue":"1","key":"ref34","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.mimet.2009.10.013","article-title":"Utilization of an unstable plasmid and the I-SceI endonuclease to generate routine markerless deletion mutants in Francisella tularensis","volume":"80","author":"J Horzempa","year":"2010","journal-title":"Journal of microbiological methods"},{"issue":"11","key":"ref35","doi-asserted-by":"crossref","first-page":"3425","DOI":"10.1099\/mic.0.29121-0","article-title":"Genetic tools for highly pathogenic Francisella tularensis subsp. tularensis","volume":"152","author":"ED LoVullo","year":"2006","journal-title":"Microbiology"},{"issue":"10","key":"ref36","doi-asserted-by":"crossref","first-page":"2709","DOI":"10.1128\/AAC.44.10.2709-2714.2000","article-title":"Epidemiological Survey of Amoxicillin-Clavulanate Resistance and Corresponding Molecular Mechanisms in Escherichia coli Isolates in France: New Genetic Features of blaTEM Genes","volume":"44","author":"V Leflon-Guibout","year":"2000","journal-title":"Antimicrob Agents Chemother"},{"issue":"11","key":"ref37","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1128\/AAC.39.11.2478","article-title":"Incidence and mechanisms of resistance to the combination of amoxicillin and clavulanic acid in Escherichia coli","volume":"39","author":"P Stapleton","year":"1995","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"ref38","first-page":"51","article-title":"The mechanism of ampicillin resistance in enterobacteriaceae isolated in Vellore","volume":"43","author":"S Jesudason","year":"2000","journal-title":"Indian J Pathol Microbiol"},{"issue":"5","key":"ref39","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1093\/jac\/20.5.645","article-title":"Ampicillin resistance in Haemophilus influenzae: identification of resistance mechanisms","volume":"20","author":"AJ Reid","year":"1987","journal-title":"J Antimicro Chemother"},{"issue":"7","key":"ref40","doi-asserted-by":"crossref","first-page":"2954","DOI":"10.1128\/AAC.49.7.2954-2958.2005","article-title":"Mechanisms of Resistance to Imipenem and Ampicillin in Enterococcus faecalis","volume":"49","author":"S Ono","year":"2005","journal-title":"Antimicrob Agents Chemother"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1946","DOI":"10.1128\/AAC.01407-10","article-title":"Impact of ciprofloxacin exposure on Staphylococcus aureus genomic alternations linked with emergence of rifampin resistance","volume":"55","author":"J-P Didier","year":"2011","journal-title":"Antimicrob Agents Chemother"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0163458","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,13]],"date-time":"2019-09-13T21:01:25Z","timestamp":1568408485000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0163458"}},"subtitle":[],"editor":[{"given":"Junwen","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,9,26]]},"references-count":41,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2016,9,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0163458","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9,26]]}}}