title: Mycobacterium abscessus multispacer sequence typing.
abstract: BACKGROUND
  Mycobacterium abscessus group includes antibiotic-resistant, opportunistic mycobacteria that are responsible for sporadic cases and outbreaks of cutaneous, pulmonary and disseminated infections. However, because of their close genetic relationships, accurate discrimination between the various strains of these mycobacteria remains difficult. In this report, we describe the development of a multispacer sequence typing (MST) analysis for the simultaneous identification and typing of M. abscessus mycobacteria. We also compared MST with the reference multilocus sequence analysis (MLSA) typing method.
  
  
  RESULTS
  Based on the M. abscessus CIP104536T genome, eight intergenic spacers were selected, PCR amplified and sequenced in 21 M. abscessus isolates and analysed in 48 available M. abscessus genomes. MST and MLSA grouped 37 M. abscessus organisms into 12 and nine types, respectively; four formerly "M. bolletii" organisms and M. abscessus M139 into three and four types, respectively; and 27 formerly "M. massiliense" organisms grouped into nine and five types, respectively. The Hunter-Gaston index was off 0.912 for MST and of 0.903 for MLSA. The MST-derived tree was similar to that based on MLSA and rpoB gene sequencing and yielded three main clusters comprising each the type strain of the respective M. abscessus sub-species. Two isolates exhibited discordant MLSA- and rpoB gene sequence-derived position, one isolate exhibited discordant MST- and rpoB gene sequence-derived position and one isolate exhibited discordant MST- and MLSA-derived position. MST spacer n°2 sequencing alone allowed for the accurate identification of the different isolates at the sub-species level.
  
  
  CONCLUSIONS
  MST is a new sequencing-based approach for both identifying and genotyping M. abscessus mycobacteria that clearly differentiates formerly "M. massiliense" organisms from other M. abscessus subsp. bolletii organisms.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de médecine, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Sassi
authors.forename: Imen
authors.initials: I
authors.lastname: Ben Kahla
authors.forename: Michel
authors.initials: M
authors.lastname: Drancourt
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D021901:DNA, Intergenic / Q000737:chemistry / Q000235:genetics; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing / Q000379:methods*; D009161:Mycobacterium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D009164:Mycobacterium Infections / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic