E-GEOD-43629 - New rapid scheme for distinguishing subspecies of the Mycobacterium abscessus group and identification of Mycobacterium massiliense with inducible clarithromycin resistance

Released on 17 July 2013, last updated on 2 June 2014
Mycobacterium abscessus, Mycobacterium abscessus subsp. bolletii
Samples (10)
Array (1)
Protocols (5)
Mycobacterium abscessus [M. abscessus (sensu lato) or M. abscessus group] comprises three closely related taxa with taxonomic status under revision: M. abscessus sensu stricto, M. bolletii and M. massiliense. We describe here a simple, robust and cost effective PCR-based method for distinguishing among M. abscessus, M. massiliense and bolletii. Based on the M. abscessus ATCC 19977T genome, discriminatory regions were identified between M. abscessus and M. massiliense from array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense and 2 M. bolletii previously identified by multi-target sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full length erm(41) instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for a straightforward identification of M. abscessus, M. massiliense and M. bolletii and assessment of inducible clarithromycin resistance. This method can be easily implemented into a routine workflow providing subspecies level identification within 24 hours of isolation of M. abscessus group. Two-color CGH with 4 independent Mycobacterium clinical isolates and the M massiliense type strain (CCUG 48898) labeled with Cy3 were cohybridized with the M abscessus type strain (ATCC 19977) labeled with Cy5 on a tiling array designed against the M abscessus type strain
Experiment type
comparative genomic hybridization by array 
Adrian M Zelazny, Elizabeth P Sampaio, Gulbu Uzel, Hervé Tettelin, Kenneth N Olivier, Patricia Conville, Paul J Gardina, Shamira J Shallom, Steven M Holland, Timothy G Myers, Yinong Sebastian
Investigation descriptionE-GEOD-43629.idf.txt
Sample and data relationshipE-GEOD-43629.sdrf.txt
Raw data (2)E-GEOD-43629.raw.1.zip, E-GEOD-43629.raw.2.zip
Processed data (1)E-GEOD-43629.processed.1.zip
Array designA-GEOD-16525.adf.txt