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Journal of Clinical Microbiology, June 2004, p. 2573-2580, Vol. 42, No. 6
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.6.2573-2580.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Genomic Characterization of an Endemic Mycobacterium tuberculosis Strain: Evolutionary and Epidemiologic Implications

Dao Nguyen,1 Paul Brassard,1,2 Dick Menzies,3 Louise Thibert,4 Rob Warren,5 Serge Mostowy,2 and Marcel Behr1,2*

Department of Medicine,1 Research Institute, McGill University Health Centre,2 Respiratory Epidemiology Unit, Montreal Chest Institute,3 Laboratoire de Santé Publique du Québec, Montreal, Quebec, Canada,4 Stellenbosch University, Cape Town, South Africa5

Received 15 December 2003/ Returned for modification 27 January 2004/ Accepted 8 March 2004

In a study of 302 Mycobacterium tuberculosis clinical isolates from the low-incidence Canadian-born population of Quebec, we characterized a large endemic strain family by using genomic deletions. The DS6Quebec deleted region (11.4 kb) defined a strain family of 143 isolates encompassing two subgroups: one characterized by pyrazinamide (PZA) susceptibility and the other marked by a PZA-monoresistant phenotype. A second deletion (8 bp) in the pncA gene was shared by all 76 isolates with the PZA resistance phenotype, whereas a third DRv0961 deletion (970 bp) defined a further subset of 15 isolates. From their deletion profiles, we derived a most parsimonious evolutionary scenario and compared multiple standard genotyping modalities (using IS6110 restriction fragment length polymorphism [RFLP], spoligotyping, and mycobacterial interspersed repetitive units [MIRU]) across the deletion-based subgroups. The use of a single genotyping modality yielded an unexpectedly high proportion of clustered isolates for a high IS6110 copy strain (27% by IS6110 RFLP, 61% by MIRU, and 77% by spoligotyping). By combining all three modalities, only 14% were genotypically clustered overall, a result more congruent with the epidemiologic profile of reactivation tuberculosis, as suggested by the older age (mean age, 60 years), rural setting, and low proportion of epidemiologic links. These results provide insight into the evolution of genotypes in endemic strains and the potential for false clustering in molecular epidemiologic studies.

* Corresponding author. Mailing address: Division of Infectious Diseases and Medical Microbiology, A5-156, Montreal General Hospital, 1650 Cedar Ave., Montreal, Quebec H3G 1A4, Canada. Phone: (514) 934-1934, x42815. Fax: (514) 934-8423. E-mail: marcel.behr{at}mcgill.ca.

Journal of Clinical Microbiology, June 2004, p. 2573-2580, Vol. 42, No. 6
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.6.2573-2580.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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