{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T22:44:50Z","timestamp":1768776290364,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation : Pyrosequencing is a cost-effective DNA sequencing technology that has many applications, including rapid genotyping of a broad spectrum of bacteria. When molecular typing requires to genotype multiple DNA stretches, several pyrosequencing primers could be used simultaneously but this would create overlapping primer-specific signals, which are visually uninterpretable. Accordingly, the objective was to develop a new method for signal processing (AdvISER-M-PYRO) to automatically analyze and interpret multiplex pyrosequencing signals. In parallel, the nucleotide dispensation order was improved by developing the SENATOR (\u2018SElecting the Nucleotide dispensATion Order\u2019) algorithm.<\/jats:p>\n               <jats:p>Results : In this proof-of-concept study, quintuplex pyrosequencing was applied on eight bacterial DNA and targeted genetic alterations underlying resistance to \u03b2 -lactam antibiotics. Using SENATOR-driven dispensation order, all genetic variants (31 of 31; 100%) were correctly identified with AdvISER-M-PYRO. Among nine expected negative results, there was only one false positive that was tagged with an \u2018unsafe\u2019 label.<\/jats:p>\n               <jats:p>Availability and implementation : SENATOR and AdvISER-M-PYRO are implemented in the AdvISER-M-PYRO R package ( http:\/\/sites.uclouvain.be\/md-ctma\/index.php\/softwares ) and can be used to improve the dispensation order and to analyze multiplex pyrosequencing signals generated in a broad range of typing applications.<\/jats:p>\n               <jats:p>Contact : jerome.ambroise@uclouvain.be<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu516","type":"journal-article","created":{"date-parts":[[2014,8,31]],"date-time":"2014-08-31T00:26:27Z","timestamp":1409444787000},"page":"3590-3597","source":"Crossref","is-referenced-by-count":7,"title":["Amplicon identification using SparsE representation of multiplex PYROsequencing signal (AdvISER-M-PYRO): application to bacterial resistance genotyping"],"prefix":"10.1093","volume":"30","author":[{"given":"J\u00e9r\u00f4me","family":"Ambroise","sequence":"first","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, 2 Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, 3 Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and 4 Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Yann","family":"Deccache","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, 2 Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, 3 Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and 4 Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Leonid","family":"Irenge","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, 2 Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, 3 Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and 4 Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"},{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, 2 Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, 3 Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and 4 Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Encho","family":"Savov","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, 2 Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, 3 Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and 4 Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Annie","family":"Robert","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, 2 Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, 3 Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and 4 Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Jean-Luc","family":"Gala","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, 2 Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, 3 Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and 4 Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"},{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, 2 Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, 3 Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and 4 Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2014,8,30]]},"reference":[{"key":"2023012712050357700_btu516-B1","doi-asserted-by":"crossref","first-page":"1963","DOI":"10.1093\/bioinformatics\/btt339","article-title":"Adviser-pyro: amplicon identification using sparse representation of pyrosequencing signal","volume":"29","author":"Ambroise","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712050357700_btu516-B2","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.cca.2006.02.046","article-title":"Multiplex pcr-pyrosequencing assay for genotyping CYP3A5 polymorphisms","volume":"372","author":"Aquilante","year":"2006","journal-title":"Clinica Chimica Acta"},{"key":"2023012712050357700_btu516-B3","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1002\/pros.22757","article-title":"Does genotyping of risk-associated single nucleotide polymorphisms improve patient selection for prostate biopsy when combined with a prostate cancer risk calculator?","volume":"74","author":"Butoescu","year":"2014","journal-title":"Prostate"},{"key":"2023012712050357700_btu516-B4","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1093\/jac\/dkq146","article-title":"Rapid detection of tem, shv and ctx-m extended-spectrum beta-lactamases in enterobacteriaceae using ligation-mediated amplification with microarray analysis","volume":"65","author":"Cohen Stuart","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"2023012712050357700_btu516-B5","doi-asserted-by":"crossref","first-page":"e38140","DOI":"10.1371\/journal.pone.0038140","article-title":"mpsqed: a software for the design of multiplex pyrosequencing assays","volume":"7","author":"Dabrowski","year":"2012","journal-title":"PloS One"},{"key":"2023012712050357700_btu516-B6","doi-asserted-by":"crossref","first-page":"e60055","DOI":"10.1371\/journal.pone.0060055","article-title":"Multipsq: a software solution for the analysis of diagnostic n-plexed pyrosequencing reactions","volume":"8","author":"Dabrowski","year":"2013","journal-title":"PloS One"},{"key":"2023012712050357700_btu516-B7","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.mimet.2011.04.007","article-title":"Development of a pyrosequencing assay for rapid assessment of quinolone resistance in acinetobacter baumannii isolates","volume":"86","author":"Deccache","year":"2011","journal-title":"J. Microbiol. Methods"},{"key":"2023012712050357700_btu516-B8","author":"Goeman","year":"2008"},{"key":"2023012712050357700_btu516-B9","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1016\/S0140-6736(98)22018-6","article-title":"Action against antibiotic resistance: no time to lose","volume":"351","author":"Hawkey","year":"1998","journal-title":"Lancet"},{"key":"2023012712050357700_btu516-B10","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/1471-2350-10-80","article-title":"Rapid detection of the cyp2a6* 12 hybrid allele by pyrosequencing\u00ae technology","volume":"10","author":"Koontz","year":"2009","journal-title":"BMC Med. Genet."},{"key":"2023012712050357700_btu516-B11","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.mrfmmm.2004.07.023","article-title":"Genetic variation analyses by pyrosequencing","volume":"573","author":"Langaee","year":"2005","journal-title":"Mutat. Res."},{"key":"2023012712050357700_btu516-B12","doi-asserted-by":"crossref","first-page":"e31","DOI":"10.1093\/nar\/30.7.e31","article-title":"Multiplex pyrosequencing","volume":"30","author":"Pourmand","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012712050357700_btu516-B13","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1101\/gr.150601","article-title":"Pyrosequencing sheds light on dna sequencing","volume":"11","author":"Ronaghi","year":"2001","journal-title":"Genome Res."},{"key":"2023012712050357700_btu516-B14","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/S1570-0232(02)00693-1","article-title":"Pyrosequencing for microbial typing","volume":"782","author":"Ronaghi","year":"2002","journal-title":"J. Chromatogr. B"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/24\/3590\/48931390\/bioinformatics_30_24_3590.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/24\/3590\/48931390\/bioinformatics_30_24_3590.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:03:10Z","timestamp":1674824590000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/24\/3590\/2422173"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,8,30]]},"references-count":14,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2014,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu516","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,12,15]]},"published":{"date-parts":[[2014,8,30]]}}}