{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T04:09:11Z","timestamp":1759205351872},"reference-count":44,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2013,8,1]],"date-time":"2013-08-01T00:00:00Z","timestamp":1375315200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2013,8]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            <jats:named-content content-type=\"genus-species\">Burkholderia cenocepacia<\/jats:named-content>\n            is the most prevalent and feared member of the\n            <jats:named-content content-type=\"genus-species\">Burkholderia cepacia<\/jats:named-content>\n            complex in lung infections of cystic fibrosis (CF). Genotyping and monitoring of long-term colonization are critical at clinical units; however, the differentiation of specific lineages performed by multilocus sequence typing (MLST) is still limited to a small number of isolates due to the high cost and time-consuming procedure. The aim of this study was to optimize a protocol (the\n            <jats:italic>SNaPBcen<\/jats:italic>\n            assay) for extensive bacterial population studies. The strategy used for the\n            <jats:italic>SNaPBcen<\/jats:italic>\n            assay is based on targeting single nucleotide polymorphisms (SNPs) located in MLST genes instead of sequencing full MLST sequences. Nonpolymorphic and redundant MLST positions were eliminated, and a set of 24 polymorphisms included in the\n            <jats:italic>SNaPBcen<\/jats:italic>\n            assay ensures a high-resolution genomic characterization. These polymorphisms were identified based on the comparative analysis of 137\n            <jats:named-content content-type=\"genus-species\">B. cenocepacia<\/jats:named-content>\n            MLST profiles available online (\n            <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/pubmlst.org\/bcc\/\">http:\/\/pubmlst.org\/bcc\/<\/jats:ext-link>\n            ). The group of 81 clinical isolates of\n            <jats:named-content content-type=\"genus-species\">B. cenocepacia<\/jats:named-content>\n            examined in this study using the\n            <jats:italic>SNaPBcen<\/jats:italic>\n            assay revealed 51 distinct profiles, and a final discriminatory power of 0.9997 compared with MLST was determined. The\n            <jats:italic>SNaPBcen<\/jats:italic>\n            assay was able to reveal isolates with microvariations and the presence of multiple clonal variants in patients chronically colonized with\n            <jats:named-content content-type=\"genus-species\">B. cenocepacia<\/jats:named-content>\n            . Main phylogenetic subgroups IIIA, IIIB, and IIIC of\n            <jats:named-content content-type=\"genus-species\">B. cenocepacia<\/jats:named-content>\n            could be separated by the Gl94R polymorphism included in the panel. The\n            <jats:italic>SNaPBcen<\/jats:italic>\n            assay proved to be a rapid and robust alternative to the standard MLST for\n            <jats:named-content content-type=\"genus-species\">B. cenocepacia<\/jats:named-content>\n            , allowing the simultaneous analysis of multiple polymorphisms following amplification and mini-sequencing reactions.\n          <\/jats:p>","DOI":"10.1128\/jcm.01019-13","type":"journal-article","created":{"date-parts":[[2013,6,13]],"date-time":"2013-06-13T03:53:26Z","timestamp":1371095606000},"page":"2646-2653","update-policy":"http:\/\/dx.doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":9,"title":["<i>SNaPBcen<\/i>\n            : a Novel and Practical Tool for Genotyping Burkholderia cenocepacia"],"prefix":"10.1128","volume":"51","author":[{"given":"Nadia","family":"Eusebio","sequence":"first","affiliation":[{"name":"IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal"},{"name":"Faculty of Sciences, University of Porto, Porto, Portugal"}]},{"given":"Carla P.","family":"Coutinho","sequence":"additional","affiliation":[{"name":"IBB\u2014Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior T\u00e9cnico, Technical University of Lisbon, Lisbon, Portugal"}]},{"given":"Isabel","family":"S\u00e1-Correia","sequence":"additional","affiliation":[{"name":"IBB\u2014Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior T\u00e9cnico, Technical University of Lisbon, Lisbon, Portugal"}]},{"given":"Ricardo","family":"Araujo","sequence":"additional","affiliation":[{"name":"IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal"},{"name":"Faculty of Sciences, University of Porto, Porto, Portugal"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.001123-0"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.65634-0"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1462-2920.2003.00471.x"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2010.03237.x"},{"key":"e_1_3_3_6_2","first-page":"81","volume-title":"Burkholderia: molecular microbiology and genomics","author":"Burns JL","year":"2007","unstructured":"BurnsJL. 2007. Antibiotic resistance of Burkholderia spp., p 81\u201391. In CoenyeT VandammeP (ed), Burkholderia: molecular microbiology and genomics. Horizon Scientific Press, Norfolk, United Kingdom."},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.60.3.539-574.1996"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00068-09"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.32.4.924-930.1994"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1086\/340279"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.43.9.4665-4673.2005"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01796-09"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-5-86"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.59.030804.121325"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-012-1701-z"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2012.08.011"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2010.01.008"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.8.4784-4792.2005"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1002\/elps.201100508"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0066083"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.01366-10"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2011.00012"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.41.9.4113-4120.2003"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00234-07"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-008-0552-0"},{"key":"e_1_3_3_26_2","first-page":"365","volume-title":"Methods in molecular biology","author":"Rozen S","year":"2000","unstructured":"RozenS SkaletskyHJ. 2000. Primer3 on the WWW for general users and for biologist programmers, p 365\u2013386. In KrawetzS MisenerS (ed), Methods in molecular biology. Humana Press, Totowa, NJ."},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.2144\/04372ST03"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1002\/elps.200406177"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-6377(02)00185-2"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1177\/117693430500100003"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00770-09"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2011.03.006"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.997"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-12-373"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2010.00237.x"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.2006\/004077-0"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2010.08.008"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.42.7.3052-3058.2004"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-51-7-533"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0602138103"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1461"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1086\/599360"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.4.1316-1325.2003"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1018249108"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0039630"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01019-13","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01019-13","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T11:46:27Z","timestamp":1646480787000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.01019-13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,8]]},"references-count":44,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2013,8]]}},"alternative-id":["10.1128\/JCM.01019-13"],"URL":"https:\/\/doi.org\/10.1128\/jcm.01019-13","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,8]]},"assertion":[{"value":"2013-04-16","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2013-06-02","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2013-07-16","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}