title: Comparative genomics between human and animal associated subspecies of the Mycobacterium avium complex: a basis for pathogenicity.
abstract: BACKGROUND
  A human isolate of Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis 43525) was sequenced and compared genomically to other mycobacterial pathogens. M. paratuberculosis 43525 was recently isolated from a patient with ulcerative colitis and belongs to the M. avium complex, a group known to infect both humans and animals. While M. paratuberculosis is a known pathogen of livestock, there are only 20 human isolates from the last 20 years, therefore we took the opportunity to perform a whole genome comparison between human and animal mycobacterial pathogens. We also compared virulence determinants such as the mycobactin cluster, PE/PPE genes and mammalian cell entry (mce) operons between MAC subspecies that infect animals and those that infect humans. M. tuberculosis was also included in these analyses given its predominant role as a human pathogen.
  
  
  RESULTS
  This genome comparison showed the PE/PPE profile of M. paratuberculosis 43525 to be largely the same as other M. paratuberculosis isolates, except that it had one PPE and one PE_PGRS protein that are only present in human MAC strains and M. tuberculosis. PE/PPE proteins that were unique to M. paratuberculosis 43525, M. avium subsp. hominissuis and a caprine M. paratuberculosis isolate, were also identified. In addition, the mycobactin cluster differed between human and animal isolates and a unique mce operon flanked by two mycobactin genes, mbtA and mbtJ, was identified in all available M. paratuberculosis genomes.
  
  
  CONCLUSIONS
  Despite the whole genome comparison placing M. paratuberculosis 43525 as closely related to bovine M. paratuberculosis, key virulence factors were similar to human mycobacterial pathogens. This study highlights key factors of mycobacterial pathogenesis in humans and forms the basis for future functional studies.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. verlaine.timms@unswalumni.com.|Centre for Infectious Diseases and Microbiology, Institute of Clinical Microbiology and Medical Research, Westmead Hospital, Sydney, NSW, Australia. verlaine.timms@unswalumni.com.
authors.forename: Verlaine J
authors.initials: VJ
authors.lastname: Timms
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia. karl.hassan@mq.edu.au.
authors.forename: Karl A
authors.initials: KA
authors.lastname: Hassan
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. h.mitchell@unsw.edu.au.
authors.forename: Hazel M
authors.initials: HM
authors.lastname: Mitchell
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. b.neilan@unsw.edu.au.
authors.forename: Brett A
authors.initials: BA
authors.lastname: Neilan
mesh_terms: D000818:Animals; D001482:Base Composition; D002876:Chromosomes, Bacterial; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D023061:Gene Order; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D006801:Humans; D005810:Multigene Family; D015269:Mycobacterium avium Complex / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D015270:Mycobacterium avium-intracellulare Infection / Q000382:microbiology*; D016366:Open Reading Frames; D009876:Operon; D010080:Oxazoles; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D014774:Virulence / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics
chemical_list: D010080:Oxazoles; D037521:Virulence Factors; C018608:mycobactins