title: Mycobacteriophage-drived diversification of Mycobacterium abscessus.
abstract: BACKGROUND
  Mycobacterium abscessus is an emerging opportunistic pathogen which diversity was acknowledged by the recent description of two subspecies accommodating M. abscessus, Mycobacterium bolletii and Mycobacterium massiliense isolates.
  
  
  RESULTS
  Here, genome analysis found 1-8 prophage regions in 47/48 M. abscessus genomes ranging from small prophage-like elements to complete prophages. A total of 20,304 viral and phage proteins clustered into 853 orthologous groups. Phylogenomic and phylogenetic analyses based on prophage region homology found three main clusters corresponding to M. abscessus, M. bolletii and M. massiliense. Analysing 135 annotated Tape Measure Proteins found thirteen clusters and four singletons, suggesting that at least 17 mycobacteriophages had infected M. abscessus during its evolution. The evolutionary history of phages differed from that of their mycobacterial hosts. In particular, 33 phage-related proteins have been horizontally transferred within M. abscessus genomes. They comprise of an integrase, specific mycobacteriophage proteins, hypothetical proteins and DNA replication and metabolism proteins. Gene exchanges, loss and gains which occurred in M. abscessus genomes have been driven by several mycobacteriophages.
  
  
  CONCLUSIONS
  This analysis of phage-mycobacterium co-evolution suggests that mycobacteriophages are playing a key-role in the on-going diversification of M. abscessus.
  
  
  METHODS
  This article was reviewed by Eric Bapteste, Patrick Forterre and Eugene Koonin.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Sassi
authors.forename: Philippe
authors.initials: P
authors.lastname: Gouret
authors.forename: Olivier
authors.initials: O
authors.lastname: Chabrol
authors.forename: Pierre
authors.initials: P
authors.lastname: Pontarotti
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR CNRS 6236 IRD198, IFR48, Institut Méditerranée Infection, Aix Marseille Université, Marseille, France. michel.drancourt@univ-amu.fr.
authors.forename: Michel
authors.initials: M
authors.lastname: Drancourt
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D002874:Chromosome Mapping; D016000:Cluster Analysis; D022761:Gene Transfer, Horizontal / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics; D058977:Molecular Sequence Annotation; D009160:Mycobacteriophages / Q000502:physiology*; D009161:Mycobacterium / Q000235:genetics* / Q000821:virology*; D010802:Phylogeny; D039002:Prophages / Q000235:genetics
chemical_list: D001426:Bacterial Proteins