title: Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.
abstract: BACKGROUND
  Mycobacterium avium subspecies paratuberculosis (Map) is an infectious enteric pathogen that causes Johne's disease in livestock. Determining genetic diversity is prerequisite to understanding the epidemiology and biology of Map. We performed the first whole genome sequencing (WGS) of 141 global Map isolates that encompass the main molecular strain types currently reported. We investigated the phylogeny of the Map strains, the diversity of the genome and the limitations of commonly used genotyping methods.
  
  
  RESULTS
  Single nucleotide polymorphism (SNP) and phylogenetic analyses confirmed two major lineages concordant with the former Type S and Type C designations. The Type I and Type III strain groups are subtypes of Type S, and Type B strains are a subtype of Type C and not restricted to Bison species. We found that the genome-wide SNPs detected provided greater resolution between isolates than currently employed genotyping methods. Furthermore, the SNP used for IS1311 typing is not informative, as it is likely to have occurred after Type S and C strains diverged and does not assign all strains to the correct lineage. Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) differentiates Type S from Type C but provides limited resolution between isolates within these lineages and the polymorphisms detected do not necessarily accurately reflect the phylogenetic relationships between strains. WGS of passaged strains and coalescent analysis of the collection revealed a very high level of genetic stability, with the substitution rate estimated to be less than 0.5 SNPs per genome per year.
  
  
  CONCLUSIONS
  This study clarifies the phylogenetic relationships between the previously described Map strain groups, and highlights the limitations of current genotyping techniques. Map isolates exhibit restricted genetic diversity and a substitution rate consistent with a monomorphic pathogen. WGS provides the ultimate level of resolution for differentiation between strains. However, WGS alone will not be sufficient for tracing and tracking Map infections, yet importantly it can provide a phylogenetic context for affirming epidemiological connections.
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Cambridge, UK. j.bryant@ucl.ac.uk.|Division of Infection and Immunity, University College London, London, UK. j.bryant@ucl.ac.uk.
authors.forename: Josephine M
authors.initials: JM
authors.lastname: Bryant
authors.affiliation: Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. virginie.c.thibault@gmail.com.
authors.forename: Virginie C
authors.initials: VC
authors.lastname: Thibault
authors.affiliation: Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. David.G.E.Smith@moredun.ac.uk.|Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, G12 8QQ, UK. David.G.E.Smith@moredun.ac.uk.
authors.forename: David G E
authors.initials: DG
authors.lastname: Smith
authors.affiliation: Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. joyce.mcluckie@moredun.ac.uk.
authors.forename: Joyce
authors.initials: J
authors.lastname: McLuckie
authors.affiliation: Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. ianheron23@hotmail.com.
authors.forename: Ian
authors.initials: I
authors.lastname: Heron
authors.affiliation: Neiker-tecnalia, Dpto. de Producción y Sanidad Animal, Berreaga 1, 48160, Derio, Bizkaia, Spain. isevilla@neiker.net.
authors.forename: Iker A
authors.initials: IA
authors.lastname: Sevilla
authors.affiliation: INRA, UMR1282, Infectiologie Santé Publique (ISP-311), F-37380, Nouzilly, France. Franck.Biet@tours.inra.fr.
authors.forename: Franck
authors.initials: F
authors.lastname: Biet
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Cambridge, UK. sh16@sanger.ac.uk.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Cambridge, UK. djm47@cam.ac.uk.
authors.forename: Duncan J
authors.initials: DJ
authors.lastname: Maskell
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Cambridge, UK. sdb@sanger.ac.uk.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Cambridge, UK. Parkhill@sanger.ac.uk.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. karen.stevenson@moredun.ac.uk.
authors.forename: Karen
authors.initials: K
authors.lastname: Stevenson
mesh_terms: D005838:Genotype; D016927:Mycobacterium avium subsp. paratuberculosis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics
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