{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T01:59:03Z","timestamp":1793066343828,"version":"4.5.0"},"reference-count":113,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,6,17]],"date-time":"2020-06-17T00:00:00Z","timestamp":1592352000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006162","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Ci\u00eancia e Tecnologia do Estado de Pernambuco","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006162","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2020.01176","type":"journal-article","created":{"date-parts":[[2020,6,17]],"date-time":"2020-06-17T04:36:21Z","timestamp":1592368581000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":44,"title":["Comparative Genomics of Acinetobacter baumannii Clinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes"],"prefix":"10.3389","volume":"11","author":[{"given":"Nilma C.","family":"Leal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T\u00falio L.","family":"Campos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio M.","family":"Rezende","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C\u00e1ssia","family":"Docena","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carina L.","family":"Mendes-Marques","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felipe L.","family":"de S\u00e1 Cavalcanti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel L.","family":"Wallau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Igor V.","family":"Rocha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmelita L. B.","family":"Cavalcanti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dyana L.","family":"Veras","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lilian R.","family":"Alves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana","family":"Andrade-Figueiredo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria P. Silva","family":"de Barros","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alzira M. Paiva","family":"de Almeida","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcia M. Camargo","family":"de Morais","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tereza C.","family":"Leal-Balbino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danilo E.","family":"Xavier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osvaldo P.","family":"de-Melo-Neto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2020,6,17]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"3837","DOI":"10.1128\/AAC.00570-08","article-title":"Genetic basis of multidrug resistance in Acinetobacter baumannii clinical isolates at a tertiary medical center in Pennsylvania.","volume":"52","author":"Adams-Haduch","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks406","article-title":"PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity-and composition-based strategies.","volume":"40","author":"Akhter","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-015-0515-2","article-title":"aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data.","volume":"16","author":"Allen","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1089\/mdr.2017.0300","article-title":"Molecular characterization of carbapenem-resistant Acinetobacter baumannii in the intensive care unit of Uruguay\u2019s University hospital identifies the first rmtC gene in the species.","volume":"24","author":"Bado","year":"2018","journal-title":"Microb. Drug Resist."},{"key":"B6","doi-asserted-by":"publisher","first-page":"4382","DOI":"10.1128\/JCM.43.9.4382-4390.2005","article-title":"Development of a Multilocus Sequence Typing scheme for characterization of clinical isolates of Acinetobacter baumannii.","volume":"43","author":"Bartual","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1093\/nar\/30.1.276","article-title":"The Pfam protein families database.","volume":"30","author":"Bateman","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02526-18","article-title":"Large-scale identification of AbaR-type Genomic Islands in Acinetobacter baumannii reveals diverse insertion sites and clonal lineage-specific antimicrobial resistance gene profiles.","volume":"63","author":"Bi","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"B9","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1128\/AAC.02662-15","article-title":"Evolution of AbGRI2-0, the progenitor of the AbGRI2 resistance island in global clone 2 of Acinetobacter baumannii.","volume":"60","author":"Blackwell","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"B10","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data.","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B11","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1128\/AAC.01384-12","article-title":"Wide dissemination of GES-type carbapenemases in Acinetobacter baumannii isolates in Kuwait.","volume":"57","author":"Bonnin","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0059388","article-title":"Acinetobacter baumannii utilizes a Type VI Secretion System for bacterial competition.","volume":"8","author":"Carruthers","year":"2013","journal-title":"PLoS One"},{"key":"B13","doi-asserted-by":"publisher","first-page":"2053","DOI":"10.1093\/jac\/dkr267","article-title":"Structure\u2013function relationships of CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii.","volume":"66","author":"Catel-Ferreira","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"B14","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1016\/j.diagmicrobio.2014.03.006","article-title":"Characterization of carbapenem-resistant Acinetobacter baumannii in Brazil (2008-2011): countrywide spread of OXA-23-producing clones (CC15 and CC79).","volume":"79","author":"Chagas","year":"2014","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"B15","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1590\/0074-02760150158","article-title":"Draft genome sequence of a multidrug-resistant Acinetobacter baumannii ST15 (CC15) isolated from Brazil.","volume":"110","author":"Chagas","year":"2015","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0701-6","article-title":"A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii.","volume":"16","author":"Chan","year":"2015","journal-title":"Genome Biol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: a reference database for bacterial virulence factors.","volume":"33","author":"Chen","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"B18","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/j.meegid.2013.06.024","article-title":"Clonal complexes 104, 109 and 113 playing a major role in the dissemination of OXA-carbapenemase-producing Acinetobacter baumannii in Southeast Brazil.","volume":"19","author":"Cl\u00edmaco","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"B19","year":"2015","journal-title":"Performance Standards for Antimicrobial Disk Susceptibility Tests; Approved Standard\u2014Twelfth Edition."},{"key":"B20","year":"2018","journal-title":"Performance Standards for Antimicrobial Susceptibility Testing. 28th ed. CLSI supplement M100."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0209367","article-title":"A high mortality rate associated with multidrug-resistant Acinetobacter baumannii ST79 and ST25 carrying OXA-23 in a Brazilian intensive care unit.","volume":"13","author":"Da Silva","year":"2018","journal-title":"PLoS One"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements.","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-2136-6","article-title":"Biofilm-associated proteins: news from Acinetobacter.","volume":"16","author":"De Gregorio","year":"2015","journal-title":"BMC Genomics"},{"key":"B24","doi-asserted-by":"publisher","first-page":"e1309","DOI":"10.1128\/AAC.01309-16","article-title":"High frequency of OXA-253-producing Acinetobacter baumannii in different hospitals in Recife, Brazil.","volume":"61","author":"de S\u00e1 Cavalcanti","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-11-224","article-title":"Genome organization of epidemic Acinetobacter baumannii strains.","volume":"11","author":"Di Nocera","year":"2011","journal-title":"BMC Microbiol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1111\/j.1469-0691.2010.03254.x","article-title":"Molecular epidemiological investigation of multidrug-resistant Acinetobacter baumannii strains in four Mediterranean countries with a multilocus sequence typing scheme.","volume":"17","author":"Di Popolo","year":"2011","journal-title":"Clin. Microbiol. Infect."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0010034","article-title":"The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool.","volume":"5","author":"Diancourt","year":"2010","journal-title":"PLoS One"},{"key":"B28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41426-018-0030-4","article-title":"Acinetobacter: an emerging pathogen with a versatile secretome.","volume":"7","author":"Elhosseiny","year":"2018","journal-title":"Emerg. Microbes Infect."},{"key":"B29","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1345\/aph.1P084","article-title":"Genetic mechanisms of antimicrobial resistance of Acinetobacter baumannii.","volume":"45","author":"Esterly","year":"2011","journal-title":"Ann. Pharmacother."},{"key":"B30","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1093\/jac\/dkg097","article-title":"Relationship between beta-lactamase production, outer membrane protein and penicillin-binding protein profiles on the activity of carbapenems against clinical isolates of Acinetobacter baumannii.","volume":"51","author":"Fern\u00e1ndez-Cuenca","year":"2003","journal-title":"J. Antimicrob. Chemother."},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00930","article-title":"Comparative analysis of the two Acinetobacter baumannii multilocus sequence typing (MLST) schemes.","volume":"10","author":"Gaiarsa","year":"2019","journal-title":"Front. Microbiol."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004691","article-title":"Antibiotic modulation of capsular exopolysaccharide and virulence in Acinetobacter baumannii.","volume":"11","author":"Geisinger","year":"2015","journal-title":"PLoS Pathog."},{"key":"B33","doi-asserted-by":"publisher","first-page":"2976","DOI":"10.1128\/AAC.02640-13","article-title":"OXA-253, a variant of the carbapenem-hydrolyzing class D beta-lactamase OXA-143 in Acinetobacter baumannii.","volume":"58","author":"Girlich","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/msphere.00801-19","article-title":"Origin of OXA-23 variant OXA-239 from a recently emerged lineage of Acinetobacter baumannii international clone V.","volume":"5","author":"Gra\u00f1a-Miraglia","year":"2020","journal-title":"mSphere"},{"key":"B35","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.drup.2018.10.003","article-title":"The AbaR antibiotic resistance islands found in Acinetobacter baumannii global clone 1 \u2013 Structure, origin and evolution.","volume":"41","author":"Hamidian","year":"2018","journal-title":"Drug Resist. Updat."},{"key":"B36","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/jac\/dkt454","article-title":"A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid.","volume":"69","author":"Hamidian","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"B37","doi-asserted-by":"publisher","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. Genomics"},{"key":"B38","doi-asserted-by":"publisher","first-page":"2833","DOI":"10.1093\/jac\/dks318","article-title":"Variants of the gentamicin and tobramycin resistance plasmid pRAY are widely distributed in Acinetobacter.","volume":"67","author":"Hamidian","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"B39","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1038\/nrmicro.2017.148","article-title":"Uncovering the mechanisms of Acinetobacter baumannii virulence.","volume":"16","author":"Harding","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000052","article-title":"Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.","volume":"2","author":"Holt","year":"2016","journal-title":"Microb. Genomics"},{"key":"B41","doi-asserted-by":"publisher","first-page":"3844","DOI":"10.1128\/AAC.01512-06","article-title":"An OXA-66\/OXA-51-like carbapenemase and possibly an efflux pump are associated with resistance to imipenem in Acinetobacter baumannii.","volume":"51","author":"Hu","year":"2007","journal-title":"Antimicrob. Agents Chemother."},{"key":"B42","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.1002\/iub.531","article-title":"The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity.","volume":"63","author":"Imperi","year":"2011","journal-title":"IUBMB Life"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-014-0090-6","article-title":"SRST2: rapid genomic surveillance for public health and hospital microbiology labs.","volume":"6","author":"Inouye","year":"2014","journal-title":"Genome Med."},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002758","article-title":"Identification of a general O-linked protein glycosylation system in Acinetobacter baumannii and its role in virulence and biofilm formation.","volume":"8","author":"Iwashkiw","year":"2012","journal-title":"PLoS Pathog."},{"key":"B45","doi-asserted-by":"publisher","first-page":"2924","DOI":"10.1107\/S1399004714019543","article-title":"Structure of ADC-68, a novel carbapenem-hydrolyzing class C extended-spectrum \u03b2-lactamase isolated from Acinetobacter baumannii.","volume":"70","author":"Jeon","year":"2014","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0176695","article-title":"Database for the ampC alleles in Acinetobacter baumannii.","volume":"12","author":"Karah","year":"2017","journal-title":"PLoS One"},{"key":"B47","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":"B48","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0062160","article-title":"Variation in the complex carbohydrate biosynthesis loci of Acinetobacter baumannii genomes.","volume":"8","author":"Kenyon","year":"2013","journal-title":"PLoS One"},{"key":"B49","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.carres.2017.10.005","article-title":"Acinetobacter baumannii K13 and K73 capsular polysaccharides differ only in K-unit side branches of novel non-2-ulosonic acids: di- N -acetylated forms of either acinetaminic acid or 8-epiacinetaminic acid.","volume":"452","author":"Kenyon","year":"2017","journal-title":"Carbohydr. Res."},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0107833","article-title":"Variation in the OC locus of Acinetobacter baumannii genomes predicts extensive structural diversity in the lipooligosaccharide.","volume":"9","author":"Kenyon","year":"2014","journal-title":"PLoS One"},{"key":"B51","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1016\/j.ijbiomac.2019.09.163","article-title":"K17 capsular polysaccharide produced by Acinetobacter baumannii isolate G7 contains an amide of 2-acetamido-2-deoxy-d-galacturonic acid with d-alanine.","volume":"144","author":"Kenyon","year":"2019","journal-title":"Int. J. Biol. Macromol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"3201","DOI":"10.1128\/AAC.00221-11","article-title":"Diversity and evolution of AbaR genomic resistance islands in Acinetobacter baumannii strains of European clone I.","volume":"55","author":"Krizova","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"B53","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1111\/j.1469-0691.2011.03703.x","article-title":"EUCAST expert rules in antimicrobial susceptibility testing.","volume":"19","author":"Leclercq","year":"2013","journal-title":"Clin. Microbiol. Infect."},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2017.00055","article-title":"Biology of Acinetobacter baumannii: pathogenesis, antibiotic resistance mechanisms, and prospective treatment options.","volume":"7","author":"Lee","year":"2017","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B55","doi-asserted-by":"publisher","first-page":"W242","DOI":"10.1093\/nar\/gkw290","article-title":"Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.","volume":"44","author":"Letunic","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0208468","article-title":"Acquisition and transfer of antibiotic resistance genes in association with conjugative plasmid or class 1 integrons of Acinetobacter baumannii.","volume":"13","author":"Leungtongkam","year":"2018","journal-title":"PLoS One"},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1038\/s41426-018-0127-9","article-title":"Emergence and spread of carbapenem-resistant Acinetobacter baumannii international clones II and III in Lima, Peru article.","volume":"7","author":"Levy-Blitchtein","year":"2018","journal-title":"Emerg. Microbes Infect."},{"key":"B58","doi-asserted-by":"publisher","first-page":"1168","DOI":"10.1128\/AAC.04609-14","article-title":"Evolution of carbapenem-resistant Acinetobacter baumannii revealed through whole-genome sequencing and comparative genomic analysis.","volume":"59","author":"Li","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"B59","doi-asserted-by":"publisher","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: identification of ortholog groups for eukaryotic genomes.","volume":"13","author":"Li","year":"2003","journal-title":"Genome Res."},{"key":"B60","doi-asserted-by":"publisher","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: a comparative pathogenomic platform with an interactive web interface.","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-15-1163","article-title":"Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants.","volume":"15","author":"Liu","year":"2014","journal-title":"BMC Genomics"},{"key":"B62","doi-asserted-by":"publisher","first-page":"210.e1","DOI":"10.1016\/j.cmi.2016.11.020","article-title":"MALDI-TOF\/MS identification of species from the Acinetobacter baumannii (Ab) group revisited: inclusion of the novel A. seifertii and A. dijkshoorniae species.","volume":"23","author":"Mar\u00ed-Almirall","year":"2017","journal-title":"Clin. Microbiol. Infect."},{"key":"B63","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1111\/j.1574-6976.2012.00344.x","article-title":"Acinetobacter baumannii: human infections, factors contributing to pathogenesis and animal models.","volume":"37","author":"McConnell","year":"2013","journal-title":"FEMS Microbiol. Rev."},{"key":"B64","doi-asserted-by":"crossref","first-page":"9.12.1","DOI":"10.1002\/0471250953.bi0912s31","article-title":"Using the generic synteny browser (GBrowse_syn).","volume":"31","author":"McKay","year":"2010","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01601","article-title":"The mechanisms of disease caused by Acinetobacter baumannii.","volume":"10","author":"Morris","year":"2019","journal-title":"Front. Microbiol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"5155","DOI":"10.1128\/AAC.01486-13","article-title":"Globally expanding carbapenemase finally appears in Spain: nosocomial outbreak of Acinetobacter baumannii producing plasmid-encoded OXA-23 in Barcelona, Spain.","volume":"57","author":"Mosqueda","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"B67","doi-asserted-by":"publisher","first-page":"917","DOI":"10.1080\/14756366.2017.1344235","article-title":"Beta-lactamase database (BLDB) \u2013 structure and function.","volume":"32","author":"Naas","year":"2017","journal-title":"J. Enzyme Inhib. Med. Chem."},{"key":"B68","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1093\/jac\/dks459","article-title":"A novel family of genomic resistance islands, AbGRI2, contributing to aminoglycoside resistance in Acinetobacter baumannii isolates belonging to global clone 2.","volume":"68","author":"Nigro","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"B69","doi-asserted-by":"publisher","first-page":"61","DOI":"10.5603\/FHC.a2016.0009","article-title":"Acinetobacter baumannii: biology and drug resistance - role of carbapenemases.","volume":"54","author":"Nowak","year":"2016","journal-title":"Folia Histochem. Cytobiol."},{"key":"B70","doi-asserted-by":"publisher","DOI":"10.1038\/srep08643","article-title":"Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors.","volume":"5","author":"Ou","year":"2015","journal-title":"Sci. Rep."},{"key":"B71","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1017\/ice.2016.287","article-title":"Emergence of OXA-72-producing Acinetobacter baumannii belonging to high-risk clones (CC15 and CC79) in different Brazilian states.","volume":"38","author":"Pagano","year":"2017","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"B72","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2013.00048","article-title":"\u201cStormy waters ahead\u201d: global emergence of carbapenemases.","volume":"4","author":"Patel","year":"2013","journal-title":"Front. Microbiol."},{"key":"B73","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0036493","article-title":"The Acinetobacter baumannii entA gene located outside the Acinetobactin cluster is critical for siderophore production, iron acquisition and virulence.","volume":"7","author":"Penwell","year":"2012","journal-title":"PLoS One"},{"key":"B74","doi-asserted-by":"publisher","first-page":"951","DOI":"10.1016\/j.cmi.2019.03.014","article-title":"Carbapenem-resistant Acinetobacter baumannii: in pursuit of an effective treatment.","volume":"25","author":"Piperaki","year":"2019","journal-title":"Clin. Microbiol. Infect."},{"key":"B75","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1586\/eri.13.14","article-title":"Carbapenem-resistant Acinetobacter baumannii: epidemiology, surveillance and management.","volume":"11","author":"Pogue","year":"2013","journal-title":"Expert Rev. Anti. Infect. Ther."},{"key":"B76","doi-asserted-by":"publisher","first-page":"W45","DOI":"10.1093\/nar\/gkh362","article-title":"CVTree: a phylogenetic tree reconstruction tool based on whole genomes.","volume":"32","author":"Qi","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"B77","doi-asserted-by":"publisher","DOI":"10.1155\/2018\/9519718","article-title":"The growing genetic and functional diversity of extended spectrum Beta-Lactamases.","volume":"2018","author":"Rahman","year":"2018","journal-title":"Biomed Res Int."},{"key":"B78","doi-asserted-by":"publisher","first-page":"5179","DOI":"10.1128\/AAC.49.12.5179-5181.2005","article-title":"Novel rearrangement of a Class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii.","volume":"49","author":"Ramirez","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"B79","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1385\/1-59259-192-2:243","article-title":"Phylogenetic analysis using PHYLIP.","volume":"132","author":"Retief","year":"2000","journal-title":"Methods Mol. Biol."},{"key":"B80","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1016\/j.bjid.2018.08.004","article-title":"Multidrug-resistant Acinetobacter baumannii clones persist on hospital inanimate surfaces.","volume":"22","author":"Rocha","year":"2018","journal-title":"Brazilian J. Infect. Dis."},{"key":"B81","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1111\/j.1574-6968.2007.00828.x","article-title":"Prevalence of ISAba1 in epidemiologically unrelated Acinetobacter baumannii clinical isolates.","volume":"274","author":"Ruiz","year":"2007","journal-title":"FEMS Microbiol. Lett."},{"key":"B82","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1093\/bioinformatics\/16.10.944","article-title":"Artemis: sequence visualization and annotation.","volume":"16","author":"Rutherford","year":"2000","journal-title":"Bioinformatics"},{"key":"B83","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/srep15188","article-title":"Phylogenetic and genomic diversity in isolates from the globally distributed Acinetobacter baumannii ST25 lineage.","volume":"5","author":"Sahl","year":"2015","journal-title":"Sci. Rep."},{"key":"B84","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B85","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1111\/jam.13037","article-title":"Studies on Acinetobacter baumannii involving multiple mechanisms of carbapenem resistance.","volume":"120","author":"Sen","year":"2016","journal-title":"J. Appl. Microbiol."},{"key":"B86","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/j.carres.2015.02.006","article-title":"Structure of a new pseudaminic acid-containing capsular polysaccharide of Acinetobacter baumannii LUH5550 having the KL42 capsule biosynthesis locus.","volume":"407","author":"Senchenkova","year":"2015","journal-title":"Carbohydr. Res."},{"key":"B87","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1093\/glycob\/cwv168","article-title":"Acinetobacter baumannii K27 and K44 capsular polysaccharides have the same K unit but different structures due to the presence of distinct wzy genes in otherwise closely related K gene clusters.","volume":"26","author":"Shashkov","year":"2016","journal-title":"Glycobiology"},{"key":"B88","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.carres.2017.05.017","article-title":"Structures of the K35 and K15 capsular polysaccharides of Acinetobacter baumannii LUH5535 and LUH5554 containing amino and diamino uronic acids.","volume":"448","author":"Shashkov","year":"2017","journal-title":"Carbohydr. Res."},{"key":"B89","doi-asserted-by":"publisher","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: the reference centre for bacterial insertion sequences.","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"B90","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1101\/gad.1510307","article-title":"New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.","volume":"21","author":"Smith","year":"2007","journal-title":"Genes Dev."},{"key":"B91","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.lfs.2016.02.015","article-title":"KatG and KatE confer Acinetobacter resistance to hydrogen peroxide but sensitize bacteria to killing by phagocytic respiratory burst.","volume":"148","author":"Sun","year":"2016","journal-title":"Life Sci."},{"key":"B92","doi-asserted-by":"publisher","first-page":"2.3.1","DOI":"10.1002\/0471250953.bi0203s00","article-title":"Multiple sequence alignment using ClustalW and ClustalX.","volume":"2","author":"Thompson","year":"2003","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"B93","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.diagmicrobio.2016.06.005","article-title":"Presence of high-risk clones of OXA-23-producing Acinetobacter baumannii (ST79) and SPM-1-producing Pseudomonas aeruginosa (ST277) in environmental water samples in Brazil.","volume":"86","author":"Turano","year":"2016","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"B94","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1093\/jac\/39.6.757","article-title":"Quinolone-resistance mutations in the topoisomerase IV parC gene of Acinetobacter baumannii.","volume":"39","author":"Vila","year":"1997","journal-title":"J. Antimicrob. Chemother."},{"key":"B95","doi-asserted-by":"publisher","first-page":"2477","DOI":"10.1128\/AAC.38.10.2477","article-title":"Association between double mutation in gyrA gene of ciprofloxacin-resistant clinical isolates of Escherichia coli and MICs.","volume":"38","author":"Vila","year":"1994","journal-title":"Antimicrob. Agents Chemother."},{"key":"B96","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1093\/jac\/dks448","article-title":"Epidemiology of the Acinetobacter-derived cephalosporinase, carbapenem-hydrolysing oxacillinase and metallo-\u03b2-lactamase genes, and of common insertion sequences, in epidemic clones of Acinetobacter baumannii from Spain.","volume":"68","author":"Villal\u00f3n","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"B97","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01606-18","article-title":"CpaA is a glycan-specific Adamalysin-like protease secreted by Acinetobacter baumannii that inactivates coagulation factor XII.","volume":"9","author":"Waack","year":"2018","journal-title":"mBio"},{"key":"B98","doi-asserted-by":"publisher","first-page":"E334","DOI":"10.1128\/AAC.00334-19","article-title":"Intercellular transfer of chromosomal antimicrobial resistance genes between Acinetobacter baumannii strains mediated by prophages.","volume":"63","author":"Wachino","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"B99","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.plipres.2009.06.002","article-title":"Lipopolysaccharide: biosynthetic pathway and structure modification.","volume":"49","author":"Wang","year":"2010","journal-title":"Prog. Lipid Res."},{"key":"B100","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1128\/JB.00906-15","article-title":"Pathogenic Acinetobacter: from the cell surface to infinity and beyond.","volume":"198","author":"Weber","year":"2016","journal-title":"J. Bacteriol."},{"key":"B101","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1016\/j.tim.2017.01.005","article-title":"The secrets of Acinetobacter secretion.","volume":"25","author":"Weber","year":"2017","journal-title":"Trends Microbiol."},{"key":"B102","doi-asserted-by":"publisher","first-page":"e212","DOI":"10.1128\/AAC.00212-18","article-title":"Complete genome sequencing of Acinetobacter baumannii strain K50 discloses the large conjugative plasmid pK50a encoding carbapenemase OXA-23 and extended-spectrum \u03b2-Lactamase GES-11.","volume":"62","author":"Wibberg","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"B103","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00197-18","article-title":"Kaptive web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes.","volume":"56","author":"Wick","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"B104","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1128\/CMR.00058-16","article-title":"Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges.","volume":"30","author":"Wong","year":"2017","journal-title":"Clin. Microbiol. Rev."},{"key":"B105","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/mBio.00963-13","article-title":"New insights into dissemination and variation of the health care- associated pathogen Acinetobacter baumannii from genomic analysis.","volume":"5","author":"Wright","year":"2014","journal-title":"mBio"},{"key":"B106","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000339","article-title":"Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive.","volume":"6","author":"Wyres","year":"2020","journal-title":"Microb. genomics"},{"key":"B107","doi-asserted-by":"publisher","first-page":"W174","DOI":"10.1093\/nar\/gkp278","article-title":"CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes.","volume":"37","author":"Xu","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"B108","doi-asserted-by":"publisher","first-page":"D624","DOI":"10.1093\/nar\/gku985","article-title":"PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands.","volume":"43","author":"Yoon","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B109","doi-asserted-by":"publisher","first-page":"2704","DOI":"10.1128\/AAC.02618-13","article-title":"Characterization of blaOXA-143 variants in Acinetobacter baumannii and Acinetobacter pittii.","volume":"58","author":"Zander","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B110","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes.","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"B111","doi-asserted-by":"publisher","first-page":"11.5.1","DOI":"10.1002\/0471250953.bi1105s31","article-title":"Using the Velvet de novo assembler for short-read sequencing technologies.","volume":"31","author":"Zerbino","year":"2010","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"B112","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0066584","article-title":"Complete genome analysis of three Acinetobacter baumannii clinical isolates in China for insight into the diversification of drug resistance elements.","volume":"8","author":"Zhu","year":"2013","journal-title":"PLoS One"},{"key":"B113","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1016\/j.gpb.2015.08.004","article-title":"CVTree3 Web Server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy.","volume":"13","author":"Zuo","year":"2015","journal-title":"Genomics Proteomics Bioinformatics"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2020.01176\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,17]],"date-time":"2020-06-17T04:36:29Z","timestamp":1592368589000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2020.01176\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,17]]},"references-count":113,"alternative-id":["10.3389\/fmicb.2020.01176"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2020.01176","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,17]]},"article-number":"1176"}}