title: Amplicon identification using SparsE representation of multiplex PYROsequencing signal (AdvISER-M-PYRO): application to bacterial resistance genotyping.
abstract: BACKGROUND
  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 ('SElecting the Nucleotide dispensATion Order') algorithm.
  
  
  RESULTS
  In this proof-of-concept study, quintuplex pyrosequencing was applied on eight bacterial DNA and targeted genetic alterations underlying resistance to β-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 'unsafe' label.
authors.affiliation: Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and Epidemiology and Biostatistics Department (EPID), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Ambroise
authors.affiliation: Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and Epidemiology and Biostatistics Department (EPID), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium.
authors.forename: Yann
authors.initials: Y
authors.lastname: Deccache
authors.affiliation: Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and Epidemiology and Biostatistics Department (EPID), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and Epidemiology and Biostatistics Department (EPID), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium.
authors.forename: Leonid
authors.initials: L
authors.lastname: Irenge
authors.affiliation: Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and Epidemiology and Biostatistics Department (EPID), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium.
authors.forename: Encho
authors.initials: E
authors.lastname: Savov
authors.affiliation: Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and Epidemiology and Biostatistics Department (EPID), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium.
authors.forename: Annie
authors.initials: A
authors.lastname: Robert
authors.affiliation: Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and Epidemiology and Biostatistics Department (EPID), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Defence Laboratories Department, Belgian Armed Forces, 1800 Vilvoorde, Belgium, Department of Epidemiology and Hygiene, Military Medical Academy of Sofia, 1000 Sofia, Bulgaria and Epidemiology and Biostatistics Department (EPID), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium.
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Gala
mesh_terms: D000465:Algorithms; D017931:DNA Primers; D004269:DNA, Bacterial / Q000737:chemistry*; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D060005:Genotyping Techniques / Q000379:methods*; D009711:Nucleotides / Q000032:analysis; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D009711:Nucleotides