Genotyping of Mycobacterium avium complex organisms using multispacer sequence typing.
Mycobacterium avium complex (MAC) currently comprises eight species of environmental and animal-associated, slowly-growing mycobacteria: Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium chimaera, Mycobacterium colombiense, Mycobacterium arosiense , Mycobacterium bouchedurhonense, Mycobacterium marseillense and Mycobacterium timonense. In humans, MAC organisms are responsible for opportunistic infections whose unique epidemiology remains poorly understood, in part due to the lack of a genotyping method applicable to all eight MAC species. In this study we developed multispacer sequence typing (MST), a sequencing-based method, for the genotyping of MAC organisms. An alignment of the genome sequence of M. avium subsp. hominissuis strain 104 and M. avium subsp. paratuberculosis strain K-10 revealed 621 intergenic spacers <1000 bp. From these, 16 spacers were selected that ranged from 300 to 800 bp and contained a number of variable bases, <50 within each of the 16 spacers. Four spacers were successfully PCR-amplified and sequenced in 11 reference strains. Combining the sequence of these four spacers in 106 MAC organisms, including 83 M. avium, 11 M. intracellulare , six M. chimaera, two M. colombiense and one each of M. arosiense, M. bouchedurhonense, M. marseillense and M. timonense, yielded a total of 45 spacer types, with an index of discrimination of 0.94. Each spacer type was specific for a species and certain spacer types were specific for subspecies of M. avium. MST is a new method for genotyping of organisms belonging to any one of the eight MAC species tested in this study.
Cayrou
Caroline
C
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 IRD 3R198, IFR 48 Faculté de Médecine, Université de la Méditerranée, Marseille, France.
Turenne
Christine
C
McGill University Health Centre, Montreal, Quebec, Canada.
Behr
Marcel A
MA
McGill University Health Centre, Montreal, Quebec, Canada.
Drancourt
Michel
M
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 IRD 3R198, IFR 48 Faculté de Médecine, Université de la Méditerranée, Marseille, France.
D015373:Bacterial Typing Techniques / Q000379:methods*; D017931:DNA Primers; D004269:DNA, Bacterial / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005838:Genotype; D008969:Molecular Sequence Data; D015269:Mycobacterium avium Complex / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA
D017931:DNA Primers; D004269:DNA, Bacterial; D021903:DNA, Ribosomal Spacer