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J Med Microbiol 56 (2007), 1152-1160; DOI: 10.1099/jmm.0.47075-0
© 2007 Society for General Microbiology
ISSN 1473-5644

Amplified fragment length polymorphism analysis of Mycobacterium avium complex isolates recovered from southern California

Stacy L. Pfaller1, Timothy W. Aronson2, Alan E. Holtzman2 and Terry C. Covert3

1 National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, OH, USA

2 Education and Research Institute, Olive View – University of California Los Angeles (UCLA), Medical Center, Sylmar, Los Angeles, CA, USA

3 SHAW Environmental and Infrastructure, Inc., Cincinnati, OH, USA

Correspondence
Stacy L. Pfaller
pfaller.stacy{at}epa.gov

Received 14 November 2006
Accepted 18 April 2007

Fine-scale genotyping methods are necessary in order to identify possible sources of human exposure to opportunistic pathogens belonging to the Mycobacterium avium complex (MAC). In this study, amplified fragment length polymorphism (AFLP) analysis was evaluated for fingerprinting 159 patient and environmental MAC isolates from southern California. AFLP analysis accurately identified strains belonging to M. avium and Mycobacterium intracellulare and differentiated between strains within each species. The method was also able to differentiate strains that were presumed to be genetically identical in two previous studies using large RFLP analysis with PFGE, or PCR-amplification of DNA segments located between insertion sequences IS1245 and IS1311. For M. avium, drinking-water isolates clustered more closely with each other than with patient or food isolates. Patient isolates were more genetically diverse. None of the environmental isolates shared identical AFLP patterns with patient isolates for either species. There were, however, environmental isolates that shared identical patterns, and patient isolates that shared identical patterns. A subset of the isolates, which are referred to as MX isolates due to their ambiguous identification with the Gen-Probe system, produced AFLP patterns similar to those obtained from M. intracellulare isolates. Sequence analysis of 16S rDNA obtained from the MX isolates suggests that they are strains of M. intracellulare that were not correctly identified by the M. intracellulare AccuProbe from Gen-Probe.

Abbreviations: AFLP, amplified fragment length polymorphism; IWGMT, International Working Group on Mycobacterial Taxonomy; LRF, large RFLP; MAC, Mycobacterium avium complex; RFU, relative fluorescent unit.

The GenBank/EMBL/DDBJ accession nos for the 16S rDNA sequences of the MX isolates are AY648863–AY648870 and AY652954–AY652961.

Tables of strains and peak data are available as supplementary material with the online version of this paper.






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