title: Investigation of intra-herd spread of Mycobacterium caprae in cattle by generation and use of a whole-genome sequence.
abstract: Single nucleotide polymorphisms (SNPs) calculated from whole genome sequencing (WGS) are ideally suited to study evolutionary relationships of pathogens and their epidemiology. Mycobacterium caprae infections have been documented frequently in cattle and red deer along the Bavarian and Austrian Alps during the last decade. However, little is still known about the transmission within cattle holdings and possible alterations of the genomes of M. caprae during such events. The aim of this study was to study the molecular epidemiology of bovine tuberculosis (bTB) in selected herds based on isolate-specific genome-wide SNPs and to perform a phylogenetic network analysis. In total, 61 M. caprae isolates were collected originating from eight cattle farms over a period of twelve years between 2004 and 2015. Analysis of their sequence data revealed that the M. caprae isolates of an affected farm differ at all in a few SNPs. In contrast, many more SNPs were found when comparing the M. caprae genomes originating from different herds. The results demonstrated that the spread of bTB in the affected farms occurred by direct transmission between the members of each herd rather than between herds and a M. caprae introduction in farms after contact events e. g. on summer pastures can readily be traced by WGS analysis. Furthermore, we assembled a nearly complete whole genome sequence of M. caprae derived from several cattle isolates originating from bTB cases in the Bavarian Alpine region.
authors.affiliation: Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764, Oberschleissheim, Germany.
authors.forename: S
authors.initials: S
authors.lastname: Broeckl
authors.affiliation: Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University (LMU) Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany.
authors.forename: S
authors.initials: S
authors.lastname: Krebs
authors.affiliation: Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University (LMU) Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany.
authors.forename: A
authors.initials: A
authors.lastname: Varadharajan
authors.affiliation: Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University (LMU) Munich, Veterinaerstr. 13, 80539, Munich, Germany.
authors.forename: R K
authors.initials: RK
authors.lastname: Straubinger
authors.affiliation: Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University (LMU) Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany.
authors.forename: H
authors.initials: H
authors.lastname: Blum
authors.affiliation: Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764, Oberschleissheim, Germany. buemat5@web.de.
authors.forename: M
authors.initials: M
authors.lastname: Buettner
mesh_terms: D000818:Animals; D002417:Cattle; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D005858:Germany / Q000453:epidemiology; D060885:Multiplex Polymerase Chain Reaction / Q000662:veterinary; D009161:Mycobacterium / Q000235:genetics* / Q000472:pathogenicity; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D014380:Tuberculosis, Bovine / Q000453:epidemiology / Q000382:microbiology / Q000635:transmission*
chemical_list: D004269:DNA, Bacterial
keywords: Bovine tuberculosis (bTB); Cattle; Molecular epidemiology; Mycobacterium caprae; Single nucleotide polymorphism (SNP); Whole genome sequencing (WGS)