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Mycobacterium africanum Genotyping Using Novel Spacer Oligonucleotides in the Direct Repeat Locus

Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe,¹ Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France,² Clinical Mycobacteriology Laboratory, Wadsworth Center, New York State Department of Health,³ Department of Medicine, Albany Medical College, Albany, New York⁴

Received 4 December 2003/ Returned for modification 20 February 2004/ Accepted 23 June 2004

This study involves a first evaluation of 25 novel spacer oligonucleotides in addition to the 43 routine spacers for molecular characterization of a panel of 65 isolates of tubercle bacilli from different geographic origins that were initially classified as Mycobacterium africanum based on phenotypic characters. The 68-spacer format defined four additional patterns, and three groups were identified. The relatively homogeneous groups A1 and A2 included strains from West Africa, and A3-1 included strains from East Africa. The presence of deletion region RD9 confirmed the reclassification of the M. africanum subtype II spoligopattern within group A3-1 as Mycobacterium tuberculosis. These isolates may represent a diverging branch of M. tuberculosis in Africa. The use of new spacers also suggested an undergoing evolution of M. africanum subtype I in West Africa. Our results showed that the strain differentiation within the M. tuberculosis complex is improved by using novel spacers, and extensive studies using new-generation spoligotyping may be helpful to better understand the evolution of M. africanum.

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