title: Combined approach to the identification of clinically infrequent non-tuberculous mycobacteria in Argentina.
abstract: Over 150 potentially pathogenic non-tuberculous mycobacteria (NTM) species have been described, posing an onerous challenge for clinical laboratory diagnosis.
  
  
  
  To evaluate different approaches for the identification of 40 clinically relevant NTM isolates whose species were not reliably identified using our routine diagnostic workflow comprising phenotypic tests and hsp65 polymerase chain reaction restriction analysis.
  
  
  
  We used 1) sequencing analysis of four conserved gene targets: 16S rRNA, rpoB, hsp65 and sodA; 2) two commercial reverse hybridisation assays; and 3) protein analysis using matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS).
  
  
  
  Combined, but not individual, sequence analysis allowed reliable species identification for 30/40 (75%) isolates, including species previously unknown to be circulating in Argentina. Commercial kits outperformed our routine identification in only 5/35 isolates, and misclassified many more. MALDI-TOF MS accurately identified species in 22/36 (61%) isolates and did not misidentify any.
  
  
  
  Commercial kits did not resolve the problem of species of NTM isolates that elude identification. Combined DNA sequence analysis was the approach of choice. MALDI-TOF MS shows promise as a powerful, rapid and accessible tool for the rapid identification of clinically relevant NTM in the diagnostic laboratory, and its accuracy can be maximised by building up a customised NTM spectrum database.
authors: Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
authors: J
authors: J
authors: Monteserin
authors: Instituto Nacional de Enfermedades Infecciosas, Buenos Aires, Argentina.
authors: R
authors: R
authors: Paul
authors: Instituto Nacional de Enfermedades Infecciosas, Buenos Aires, Argentina.
authors: B
authors: B
authors: Lopez
authors: Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
authors: M
authors: M
authors: Cnockaert
authors: Emerging Bacterial Pathogens Unit, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy.
authors: E
authors: E
authors: Tortoli
authors: Departamento de Medicina Preventiva, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain.
authors: C
authors: C
authors: Menéndez
authors: Departamento de Medicina Preventiva, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain.
authors: M J
authors: MJ
authors: García
authors: Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
authors: J C
authors: JC
authors: Palomino
authors: Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
authors: P
authors: P
authors: Vandamme
authors: Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
authors: V
authors: V
authors: Ritacco
authors: Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
authors: A
authors: A
authors: Martin
mesh_terms: D001118:Argentina; D001426:Bacterial Proteins / Q000235:genetics; D001431:Bacteriological Techniques; D018834:Chaperonin 60 / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D005798:Genes, Bacterial; D006801:Humans; D009165:Mycobacterium Infections, Nontuberculous / Q000175:diagnosis*; D009170:Nontuberculous Mycobacteria / Q000235:genetics* / Q000302:isolation & purification*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013482:Superoxide Dismutase / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D018834:Chaperonin 60; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; C074119:heat-shock protein 65, Mycobacterium; C095500:SodA protein, Bacteria; D013482:Superoxide Dismutase