Combined approach to the identification of clinically infrequent non-tuberculous mycobacteria in Argentina

J. Monteserin, R. Paul, B. Lopez, M. Cnockaert, E. Tortoli, C. Menéndez, M. J. García, J. C. Palomino, P. Vandamme, V. Ritacco, A. Martin

Research output: Contribution to journalArticle

Abstract

SETTING: Over 150 potentially pathogenic non-tuberculous mycobacteria (NTM) species have been described, posing an onerous challenge for clinical laboratory diagnosis. OBJECTIVE: 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. DESIGN: 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). RESULTS: 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. CONCLUSIONS: 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.

Original languageEnglish
JournalInternational Journal of Tuberculosis and Lung Disease
Volume20
Issue number9
DOIs
Publication statusPublished - Sep 1 2016

Fingerprint

Argentina
Mycobacterium
Mass Spectrometry
Lasers
Workflow
Clinical Laboratory Techniques
DNA Sequence Analysis
Sequence Analysis
Databases
Polymerase Chain Reaction
Genes
Proteins

Keywords

  • DNA probes
  • DNA sequence analysis
  • Matrix-assisted laser desorption-ionization mass spectrometry (MALDI-TOF MS)
  • Mycobacteriosis
  • Nucleic acid hybridisation

ASJC Scopus subject areas

  • Medicine(all)
  • Pulmonary and Respiratory Medicine
  • Infectious Diseases

Cite this

Combined approach to the identification of clinically infrequent non-tuberculous mycobacteria in Argentina. / Monteserin, J.; Paul, R.; Lopez, B.; Cnockaert, M.; Tortoli, E.; Menéndez, C.; García, M. J.; Palomino, J. C.; Vandamme, P.; Ritacco, V.; Martin, A.

In: International Journal of Tuberculosis and Lung Disease, Vol. 20, No. 9, 01.09.2016.

Research output: Contribution to journalArticle

Monteserin, J, Paul, R, Lopez, B, Cnockaert, M, Tortoli, E, Menéndez, C, García, MJ, Palomino, JC, Vandamme, P, Ritacco, V & Martin, A 2016, 'Combined approach to the identification of clinically infrequent non-tuberculous mycobacteria in Argentina', International Journal of Tuberculosis and Lung Disease, vol. 20, no. 9. https://doi.org/10.5588/ijtld.16.0122
Monteserin, J. ; Paul, R. ; Lopez, B. ; Cnockaert, M. ; Tortoli, E. ; Menéndez, C. ; García, M. J. ; Palomino, J. C. ; Vandamme, P. ; Ritacco, V. ; Martin, A. / Combined approach to the identification of clinically infrequent non-tuberculous mycobacteria in Argentina. In: International Journal of Tuberculosis and Lung Disease. 2016 ; Vol. 20, No. 9.
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abstract = "SETTING: Over 150 potentially pathogenic non-tuberculous mycobacteria (NTM) species have been described, posing an onerous challenge for clinical laboratory diagnosis. OBJECTIVE: 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. DESIGN: 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). RESULTS: 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. CONCLUSIONS: 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.",
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AU - Menéndez, C.

AU - García, M. J.

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N2 - SETTING: Over 150 potentially pathogenic non-tuberculous mycobacteria (NTM) species have been described, posing an onerous challenge for clinical laboratory diagnosis. OBJECTIVE: 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. DESIGN: 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). RESULTS: 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. CONCLUSIONS: 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.

AB - SETTING: Over 150 potentially pathogenic non-tuberculous mycobacteria (NTM) species have been described, posing an onerous challenge for clinical laboratory diagnosis. OBJECTIVE: 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. DESIGN: 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). RESULTS: 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. CONCLUSIONS: 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.

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