title: A novel multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) method for Propionibacterium acnes.
abstract: Propionibacterium acnes plays a central role in the pathogenesis of acne and is responsible for severe opportunistic infections. Numerous typing schemes have been developed that allow the identification of phylotypes, but they are often insufficient to differentiate subtypes. To better understand the genetic diversity of this species and to perform epidemiological analyses, high throughput discriminant genotyping techniques are needed. Here we describe the development of a multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) method. Thirteen VNTRs were identified in the genome of P. acnes and were used to genotype a collection of clinical isolates. In addition, publically available sequencing data for 102 genomes were analyzed in silico, providing an MLVA genotype. The clustering of MLVA data was in perfect congruence with whole genome based clustering. Analysis of the clustered regularly interspaced short palindromic repeat (CRISPR) element uncovered new spacers, a supplementary source of genotypic information. The present MLVA13 scheme and associated internet database represents a first line genotyping assay to investigate large number of isolates. Particular strains may then be submitted to full genome sequencing in order to better analyze their pathogenic potential.
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91405 Orsay cedex, France.
authors.forename: Yolande
authors.initials: Y
authors.lastname: Hauck
authors.affiliation: Laboratoire de biologie clinique, HIA Percy, Clamart, France.
authors.forename: Charles
authors.initials: C
authors.lastname: Soler
authors.affiliation: Service de biologie médicale, HIA Desgenettes, 69275 Lyon cedex 03, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Gérôme
authors.affiliation: Laboratoire de biologie clinique, HIA Percy, Clamart, France.
authors.forename: Rithy
authors.initials: R
authors.lastname: Vong
authors.affiliation: Laboratoire de biologie clinique, HIA Percy, Clamart, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Macnab
authors.affiliation: Laboratoire de biologie clinique, HIA Percy, Clamart, France.
authors.forename: Géraldine
authors.initials: G
authors.lastname: Appere
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91405 Orsay cedex, France; ENSTA ParisTech, Université Paris-Saclay, 91762 Palaiseau cedex, France.
authors.forename: Gilles
authors.initials: G
authors.lastname: Vergnaud
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91405 Orsay cedex, France. Electronic address: christine.pourcel@u-psud.fr.
authors.forename: Christine
authors.initials: C
authors.lastname: Pourcel
mesh_terms: D016000:Cluster Analysis; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D005798:Genes, Bacterial; D016908:Gram-Positive Bacterial Infections / Q000382:microbiology; D006801:Humans; D018598:Minisatellite Repeats; D058889:Molecular Typing; D058885:Multilocus Sequence Typing; D011425:Propionibacterium acnes / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA
keywords: CRISPR; Genotyping; In silico MLVA; Post-surgery infection; VNTR