title: Repeat-based Sequence Typing of Carnobacterium maltaromaticum.
abstract: Carnobacterium maltaromaticum is a Lactic Acid Bacterium (LAB) of technological interest for the food industry, especially the dairy as bioprotection and ripening flora. The industrial use of this LAB requires accurate and resolutive typing tools. A new typing method for C. maltaromaticum inspired from MLVA analysis and called Repeat-based Sequence Typing (RST) is described. Rather than electrophoresis analysis, our RST method is based on sequence analysis of multiple loci containing Variable-Number Tandem-Repeats (VNTRs). The method described here for C. maltaromaticum relies on the analysis of three VNTR loci, and was applied to a collection of 24 strains. For each strain, a PCR product corresponding to the amplification of each VNTR loci was sequenced. Sequence analysis allowed delineating 11, 11, and 12 alleles for loci VNTR-A, VNTR-B, and VNTR-C, respectively. Considering the allele combination exhibited by each strain allowed defining 15 genotypes, ending in a discriminatory index of 0.94. Comparison with MLST revealed that both methods were complementary for strain typing in C. maltaromaticum.
authors.affiliation: Université de Lorraine, Laboratoire d'Ingénierie des Biomolécules (LIBio), ENSAIA, 2 avenue de la Forêt de Haye, TSA, 40602 54518 Vandœuvre-lès-Nancy, France; National University of Sciences and Technology, Atta ur Rahman School of Applied Biosciences, Department of Industrial Biotechnology, 44000, H-12, Islamabad, Pakistan.
authors.forename: Abdur
authors.initials: A
authors.lastname: Rahman
authors.affiliation: Université de Lorraine, Laboratoire d'Ingénierie des Biomolécules (LIBio), ENSAIA, 2 avenue de la Forêt de Haye, TSA, 40602 54518 Vandœuvre-lès-Nancy, France.
authors.forename: Sara M
authors.initials: SM
authors.lastname: El Kheir
authors.affiliation: Université de Lorraine, Laboratoire d'Ingénierie des Biomolécules (LIBio), ENSAIA, 2 avenue de la Forêt de Haye, TSA, 40602 54518 Vandœuvre-lès-Nancy, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Back
authors.affiliation: Université de Lorraine, Laboratoire d'Ingénierie des Biomolécules (LIBio), ENSAIA, 2 avenue de la Forêt de Haye, TSA, 40602 54518 Vandœuvre-lès-Nancy, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Mangavel
authors.affiliation: Université de Lorraine, Laboratoire d'Ingénierie des Biomolécules (LIBio), ENSAIA, 2 avenue de la Forêt de Haye, TSA, 40602 54518 Vandœuvre-lès-Nancy, France.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Revol-Junelles
authors.affiliation: Université de Lorraine, Laboratoire d'Ingénierie des Biomolécules (LIBio), ENSAIA, 2 avenue de la Forêt de Haye, TSA, 40602 54518 Vandœuvre-lès-Nancy, France. Electronic address: frederic.borges@univ-lorraine.fr.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Borges
mesh_terms: D000483:Alleles; D056573:Carnobacterium / Q000145:classification* / Q000235:genetics*; D005516:Food Microbiology; D014644:Genetic Variation; D005838:Genotype; D018598:Minisatellite Repeats / Q000235:genetics; D058885:Multilocus Sequence Typing; D016133:Polymerase Chain Reaction; D013045:Species Specificity