title: A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection.
abstract: Polymicrobial infections represent a great challenge for the clarification of disease etiology and the development of comprehensive diagnostic or therapeutic tools, particularly for fastidious and difficult-to-cultivate bacteria. Using bovine digital dermatitis (DD) as a disease model, we introduce a novel strategy to study the pathogenesis of complex infections.
  
  
  
  The strategy combines meta-transcriptomics with high-density peptide-microarray technology to screen for in vivo-expressed microbial genes and the host antibody response at the site of infection. Bacterial expression patterns supported the assumption that treponemes were the major DD pathogens but also indicated the active involvement of other phyla (primarily Bacteroidetes). Bacterial genes involved in chemotaxis, flagellar synthesis and protection against oxidative and acidic stress were among the major factors defining the disease.
  
  
  
  The extraordinary diversity observed in bacterial expression, antigens and host antibody responses between individual cows pointed toward microbial variability as a hallmark of DD. Persistence of infection and DD reinfection in the same individual is common; thus, high microbial diversity may undermine the host's capacity to mount an efficient immune response and maintain immunological memory towards DD. The common antigenic markers identified here using a high-density peptide microarray address this issue and may be useful for future preventive measures against DD.
authors.affiliation: Center for Biological Sequence analysis, Technical University of Denmark, Kemitorvet, 2800 Kgs., Lyngby, Denmark. paolo.marcatili@gmail.com.
authors.forename: Paolo
authors.identifier: 0000-0003-2615-5695
authors.initials: P
authors.lastname: Marcatili
authors.affiliation: National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
authors.forename: Martin W
authors.initials: MW
authors.lastname: Nielsen
authors.affiliation: Center for Biological Sequence analysis, Technical University of Denmark, Kemitorvet, 2800 Kgs., Lyngby, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Pontén
authors.affiliation: National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
authors.forename: Tim K
authors.initials: TK
authors.lastname: Jensen
authors.affiliation: Schafer-N ApS, Lersø Parkallé 42, 2100, Copenhagen, Denmark.
authors.forename: Claus
authors.initials: C
authors.lastname: Schafer-Nielsen
authors.affiliation: Molecular Diagnostic and Clinical Research Unit, Hospital of Southern Jutland, 6400, Sønderborg, Denmark.
authors.forename: Mette
authors.initials: M
authors.lastname: Boye
authors.affiliation: Center for Biological Sequence analysis, Technical University of Denmark, Kemitorvet, 2800 Kgs., Lyngby, Denmark.|Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.
authors.forename: Morten
authors.initials: M
authors.lastname: Nielsen
authors.affiliation: National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
authors.forename: Kirstine
authors.initials: K
authors.lastname: Klitgaard
mesh_terms: D000818:Animals; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D002417:Cattle; D002418:Cattle Diseases / Q000235:genetics* / Q000382:microbiology / Q000473:pathology; D060085:Coinfection / Q000235:genetics* / Q000382:microbiology / Q000473:pathology; D058066:Digital Dermatitis / Q000235:genetics* / Q000382:microbiology / Q000473:pathology; D004195:Disease Models, Animal; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics*; D007136:Immunoglobulins / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D040081:Protein Array Analysis; D012313:RNA / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D037521:Virulence Factors / Q000235:genetics
chemical_list: D007136:Immunoglobulins; D012336:RNA, Ribosomal, 16S; D037521:Virulence Factors; D012313:RNA
keywords: Digital dermatitis; High-density peptide arrays; Integrated pipeline; RNAseq