title: The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements.
abstract: Mycobacterium haemophilum is an emerging pathogen associated with a variety of clinical syndromes, most commonly skin infections in immunocompromised individuals. M. haemophilum exhibits a unique requirement for iron supplementation to support its growth in culture, but the basis for this property and how it may shape pathogenesis is unclear. Using a combination of Illumina, PacBio, and Sanger sequencing, the complete genome sequence of M. haemophilum was determined. Guided by this sequence, experiments were performed to define the basis for the unique growth requirements of M. haemophilum. We found that M. haemophilum, unlike many other mycobacteria, is unable to synthesize iron-binding siderophores known as mycobactins or to utilize ferri-mycobactins to support growth. These differences correlate with the absence of genes associated with mycobactin synthesis, secretion, and uptake. In agreement with the ability of heme to promote growth, we identified genes encoding heme uptake machinery. Consistent with its propensity to infect the skin, we show at the whole-genome level the genetic closeness of M. haemophilum with Mycobacterium leprae, an organism which cannot be cultivated in vitro, and we identify genes uniquely shared by these organisms. Finally, we identify means to express foreign genes in M. haemophilum. These data explain the unique culture requirements for this important pathogen, provide a foundation upon which the genome sequence can be exploited to improve diagnostics and therapeutics, and suggest use of M. haemophilum as a tool to elucidate functions of genes shared with M. leprae.
  
  
  OBJECTIVE
  Mycobacterium haemophilum is an emerging pathogen with an unknown natural reservoir that exhibits unique requirements for iron supplementation to grow in vitro. Understanding the basis for this iron requirement is important because it is fundamental to isolation of the organism from clinical samples and environmental sources. Defining the molecular basis for M. haemophilium's growth requirements will also shed new light on mycobacterial strategies to acquire iron and can be exploited to define how differences in such strategies influence pathogenesis. Here, through a combination of sequencing and experimental approaches, we explain the basis for the iron requirement. We further demonstrate the genetic closeness of M. haemophilum and Mycobacterium leprae, the causative agent of leprosy which cannot be cultured in vitro, and we demonstrate methods to genetically manipulate M. haemophilum. These findings pave the way for the use of M. haemophilum as a model to elucidate functions of genes shared with M. leprae.
authors.affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA jacobsw@hhmi.org joann.tufariello@einstein.yu.edu.
authors.forename: JoAnn M
authors.initials: JM
authors.lastname: Tufariello
authors.affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Kerantzas
authors.affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: Catherine
authors.initials: C
authors.lastname: Vilchèze
authors.affiliation: Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: R Brent
authors.initials: RB
authors.lastname: Calder
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech University, Blacksburg, Virginia, USA.
authors.forename: Eric K
authors.initials: EK
authors.lastname: Nordberg
authors.affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: Jack A
authors.initials: JA
authors.lastname: Fischer
authors.affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: Travis E
authors.initials: TE
authors.lastname: Hartman
authors.affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: Eva
authors.initials: E
authors.lastname: Yang
authors.affiliation: Department of Biology (Microbial Metagenomics), West Virginia University, Morgantown, Virginia, USA.
authors.forename: Timothy
authors.initials: T
authors.lastname: Driscoll
authors.affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: Laura E
authors.initials: LE
authors.lastname: Cole
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, New York, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Sebra
authors.affiliation: Epigenomics Shared Facility, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: Shahina B
authors.initials: SB
authors.lastname: Maqbool
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech University, Blacksburg, Virginia, USA.
authors.forename: Alice R
authors.initials: AR
authors.lastname: Wattam
authors.affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York, USA jacobsw@hhmi.org joann.tufariello@einstein.yu.edu.
authors.forename: William R
authors.initials: WR
authors.lastname: Jacobs
mesh_terms: D001483:Base Sequence; D003470:Culture Media / Q000737:chemistry*; D016680:Genome, Bacterial; D006418:Heme / Q000235:genetics / Q000378:metabolism; D006454:Hemoglobins / Q000378:metabolism; D006801:Humans; D007501:Iron / Q000378:metabolism; D018393:Mycobacterium haemophilum / Q000235:genetics* / Q000254:growth & development*; D009166:Mycobacterium leprae / Q000235:genetics; D010080:Oxazoles / Q000378:metabolism; D010641:Phenotype; D017422:Sequence Analysis, DNA
chemical_list: D003470:Culture Media; D006454:Hemoglobins; D010080:Oxazoles; C018608:mycobactins; D006418:Heme; D007501:Iron