Comparative evaluation of the identification of rapidly growing non-tuberculous mycobacteria by mass spectrometry (MALDI-TOF MS), GenoType Mycobacterium CM/AS assay and partial sequencing of the rpoβ gene with phylogenetic analysis as a reference method
| Autor: | Antonio Aguilera, José María González-Alba, Juan Carlos Galán, María Luisa Pérez-del-Molino, Gema Barbeito-Castiñeiras, José Javier Costa-Alcalde |
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| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Microbiology (medical) DNA Bacterial Genotype 030106 microbiology Biology Mass spectrometry DNA sequencing Comparative evaluation 03 medical and health sciences 0302 clinical medicine Bacterial Proteins Humans 030212 general & internal medicine Gene Phylogeny Genetics Bacteriological Techniques Phylogenetic tree Base Sequence Nontuberculous Mycobacteria DNA-Directed RNA Polymerases biology.organism_classification Matrix-assisted laser desorption/ionization Spectrometry Mass Matrix-Assisted Laser Desorption-Ionization Mycobacterium |
| Zdroj: | Enfermedades infecciosas y microbiologia clinica (English ed.). 37:160-166 |
| ISSN: | 2529-993X |
| DOI: | 10.1016/j.eimce.2018.04.020 |
| Popis: | Introduction The American Thoracic Society and the Infectious Diseases Society of America recommend that clinically significant non-tuberculous mycobacteria (NTM) should be identified to the species level in order to determine their clinical significance. The aim of this study was to evaluate identification of rapidly growing NTM (RGM) isolated from clinical samples by using MALDI-TOF MS and a commercial molecular system. The results were compared with identification using a reference method. Methods We included 46 clinical isolates of RGM and identified them using the commercial molecular system GenoType® CM/AS (Hain, Lifescience, Germany), MALDI-TOF MS (Bruker) and, as reference method, partial rpoβ gene sequencing followed by BLAST and phylogenetic analysis with the 1093 sequences available in the GeneBank. Results The degree of agreement between GenoType® and MALDI-TOF MS and the reference method, partial rpoβ sequencing, was 27/43 (62.8%) and 38/43 cases (88.3%) respectively. For all the samples correctly classified by GenoType®, we obtained the same result with MALDI-TOF MS (27/27). However, MALDI-TOF MS also correctly identified 68.75% (11/16) of the samples that GenoType® had misclassified (p=0.005). Conclusions MALDI-TOF MS classified significantly better than GenoType®. When a MALDI-TOF MS score >1.85 was achieved, MALDI-TOF MS and partial rpoβ gene sequencing were equivalent. GenoType® was not able to distinguish between species belonging to the M. fortuitum complex. MALDI-TOF MS methodology is simple, rapid and associated with lower consumable costs than GenoType®. The partial rpoβ sequencing methods with BLAST and phylogenetic analysis were not able to identify some RGM unequivocally. Therefore, sequencing of additional regions would be indicated in these cases. |
| Databáze: | OpenAIRE |
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