title: Region of difference 4 in alpine Mycobacterium caprae isolates indicates three variants.
abstract: The lack of complete genome sequence information for Mycobacterium caprae complicates a robust differentiation of M. caprae and Mycobacterium bovis. In this study, the presence or absence of M. caprae-specific single nucleotide polymorphisms in lepA and gyrB genes was assessed. The region of difference 4 (RD4) was analyzed for the identification and characterization of M. caprae. Molecular characteristics were evaluated in 12 recent M. caprae isolates from livestock and wildlife collected over a 3-year period in Bavaria, Germany. Conventional PCR strategies, sequence analysis of PCR fragments, and data from a next-generation sequencing approach together with variable-number tandem-repeat genotyping were utilized. Single nucleotide polymorphisms in the lepA and gyrB genes indicating the presence of M. caprae were detected in all the isolates. At least three different RD4 variants were found for Alpine M. caprae isolates. The results demonstrate that the RD4 region is rather heterogeneous in M. caprae genomes. As assumed by others, the presence of RD4 is critical for PCR-based differentiation of M. caprae from M. bovis, but in addition, the observed variability of RD4 allows the identification of M. caprae genotypes and may be indicative of a geographical-type appearance.
authors: Bavarian Health and Food Safety Authority, Oberschleissheim, Germany. janina.domogalla@lgl.bayern.de
authors: Janina
authors: J
authors: Domogalla
authors: Wolfgang M
authors: WM
authors: Prodinger
authors: Helmut
authors: H
authors: Blum
authors: Stefan
authors: S
authors: Krebs
authors: Susanne
authors: S
authors: Gellert
authors: Matthias
authors: M
authors: Müller
authors: Erdmute
authors: E
authors: Neuendorf
authors: Florian
authors: F
authors: Sedlmaier
authors: Mathias
authors: M
authors: Büttner
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D027081:DNA Gyrase / Q000235:genetics*; D004269:DNA, Bacterial / Q000032:analysis; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D018598:Minisatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D058889:Molecular Typing; D009161:Mycobacterium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D035602:Transcriptional Elongation Factors / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; D035602:Transcriptional Elongation Factors; D027081:DNA Gyrase