{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T07:54:22Z","timestamp":1773302062296,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2020,11,5]],"date-time":"2020-11-05T00:00:00Z","timestamp":1604534400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Applied Molecular Biosciences Unit - UCIBIO"},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/04378\/2020"],"award-info":[{"award-number":["UIDB\/04378\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["SFRH\/BD\/88028\/2012"],"award-info":[{"award-number":["SFRH\/BD\/88028\/2012"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["SFRH\/BD\/132497\/2017"],"award-info":[{"award-number":["SFRH\/BD\/132497\/2017"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Transitional Norm","award":["DL57\/2016\/CP1346\/CT0034"],"award-info":[{"award-number":["DL57\/2016\/CP1346\/CT0034"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>In Portugal, carbapenem-resistant Acinetobacter baumannii (CRAB) has been associated with ST98, ST103 and ST208 (Oxford Scheme, Oxf) and a clone has usually been associated with a particular period of time. These clonal shifts were primarily explained by an increased antimicrobial resistance profile. Here we explore genomic and biochemical differences among these and more recent clones, which could further explain the diversity and evolution of this species.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>A total of 116 CRAB isolates (2010\u201315), together with representatives of a previously described CRAB collection (4 isolates, 2001\u201306) were characterized by attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR) and MLST. Representatives of different FTIR-ATR\/MLST clusters were selected for WGS (n\u200a=\u200a13), which allowed the in silico extraction of resistance and virulence genes, capsule locus and SNP analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>A. baumannii clonal shifts of OXA-58-producing ST103Oxf (2001\u201304), OXA-40-producing ST98Oxf (2002\u201306), OXA-23-producing ST208Oxf (2006\u201310) and OXA-23-producing ST218Oxf (2010\u201315) were accompanied by an increase in AMR genes and virulence factors. FTIR-ATR clustering was congruent with sugar composition predicted from the capsular locus: a fucosamine cluster comprising ST98Oxf, ST103Oxf and a single ST218Oxf isolate; a pseudaminic acid cluster of ST208Oxf and ST1557Oxf isolates; and legionaminic acid, resembling the sialic acid from mammalian cells, in a cluster comprising ST218Oxf isolates. The whole-genome phylogenetic tree was congruent with MLST, with isolates presenting 5\u201328\u200a938 SNPs. ST208Oxf and ST218Oxf presented \u223c1900 SNPs while ST103Oxf and ST1557Oxf showed a greater number of SNPs (\u223c28\u200a000).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Clonal shifts of CRAB were promoted, in our country, by consecutive virulence and AMR gene pool enlargement, together with features increasing pathogen\u2013host adaptation. Worldwide dominance of ST218Oxf is supported by the combination of high AMR and virulence levels.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jac\/dkaa453","type":"journal-article","created":{"date-parts":[[2020,10,15]],"date-time":"2020-10-15T19:16:49Z","timestamp":1602789409000},"page":"305-311","source":"Crossref","is-referenced-by-count":21,"title":["The success of particular <i>Acinetobacter baumannii<\/i> clones: accumulating resistance and virulence inside a sugary shield"],"prefix":"10.1093","volume":"76","author":[{"given":"Liliana","family":"Silva","sequence":"first","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"},{"name":"ESALD, Instituto Polit\u00e9cnico de Castelo Branco, Castelo Branco, Portugal"}]},{"given":"Filipa","family":"Grosso","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"}]},{"given":"Carla","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"}]},{"given":"Magdalena","family":"Ksiezarek","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"}]},{"given":"Helena","family":"Ramos","sequence":"additional","affiliation":[{"name":"Hospital Geral de Santo Ant\u00f3nio (HGSA), Porto, Portugal"}]},{"given":"Lu\u00edsa","family":"Peixe","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2020,11,5]]},"reference":[{"key":"2021110500090835600_dkaa453-B1","doi-asserted-by":"crossref","first-page":"55","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":"2021110500090835600_dkaa453-B2","year":"2017"},{"key":"2021110500090835600_dkaa453-B3","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1111\/j.1469-0691.2011.03469.x","article-title":"Understanding the dynamics of imipenem-resistant Acinetobacter baumannii lineages within Portugal","volume":"17","author":"Grosso","year":"2011","journal-title":"Clin Microbiol Infect"},{"key":"2021110500090835600_dkaa453-B4","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nrmicro.2017.148","article-title":"Uncovering the mechanisms of 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