title: New polymorphisms within the variable number tandem repeat (VNTR) 7 locus of Mycobacterium avium subsp. paratuberculosis.
abstract: Variable number tandem repeat (VNTR) is a frequently employed typing method of Mycobacterium avium paratuberculosis (MAP) isolates. Based on whole genome sequencing in a previous study, allelic diversity at some VNTR loci seems to over- or under-estimate the actual phylogenetic variance among isolates. Interestingly, two closely related isolates on one farm showed polymorphism at the VNTR 7 locus, raising concerns about the misleading role that it might play in genotyping. We aimed to investigate the underlying basis of VNTR 7-polymorphism by analyzing sequence data for published genomes and field isolates of MAP and other M. avium complex (MAC) members. In contrast to MAP strains from cattle, strains from sheep displayed an "imperfect" repeat within VNTR 7, which was identical to respective allele types in other MAC genomes. Subspecies- and strain-specific single nucleotide polymorphisms (SNPs) and two novel (16 and 56 bp) repeats were detected. Given the combination of the three existing repeats, there are at least five different patterns for VNTR 7. The present findings highlight a higher polymorphism and probable instability of VNTR 7 locus that needs to be considered and challenged in future studies. Until then, sequencing of this locus in future studies is important to correctly assign the underlying allele types.(1).
authors.affiliation: Justus Liebig Universität, Institut für Hygiene und Infektionskrankheiten der Tiere, Frankfurter Straße 85-89 35392, Gießen, Germany; Landesbetrieb Hessisches Landeslabor, Schubertstraße 60 D-35392 Gießen, Germany; Cairo University, Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Giza Square 12211, Egypt. Electronic address: dr.ahmedfawzy_vet@yahoo.com.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Fawzy
authors.affiliation: Landesbetrieb Hessisches Landeslabor, Schubertstraße 60 D-35392 Gießen, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Zschöck
authors.affiliation: Justus Liebig Universität, Institut für Hygiene und Infektionskrankheiten der Tiere, Frankfurter Straße 85-89 35392, Gießen, Germany.
authors.forename: Christa
authors.initials: C
authors.lastname: Ewers
authors.affiliation: Justus Liebig Universität, Institut für Hygiene und Infektionskrankheiten der Tiere, Frankfurter Straße 85-89 35392, Gießen, Germany; Landesbetrieb Hessisches Landeslabor, Schubertstraße 60 D-35392 Gießen, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Eisenberg
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D002417:Cattle; D003198:Computer Simulation; D004587:Electrophoresis, Agar Gel; D056426:Genetic Loci; D016680:Genome, Bacterial; D018598:Minisatellite Repeats / Q000235:genetics*; D016927:Mycobacterium avium subsp. paratuberculosis / Q000235:genetics*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
keywords: Imperfect SNPs; Mycobacterium; Paratuberculosis; VNTR