Setting: Secondary tuberculosis may follow reinfection or endogenous reactivation. The design of effective preventive and treatment protocols requires knowledge about the relative importance of these mechanisms in specific communities. Molecular typing of Mycobacterium tuberculosis has permitted linkage of cases and demonstration of patterns of inter- or intrapatient strain diversity correlating with reinfection and reactivation.

Objective: The use of DNA fingerprinting to examine intrapatient strain diversity in autopsied, HIV-negative individuals resident in a high incidence community.

Design: Autopsy (12 cases) and pneumonectomy (one case) permitted multilesional sampling for bacterial culture and comparative genotyping. Mycobacterium tuberculosis strains were typed using probes directed against IS6110 , the direct repeat sequence (DR) and MTB484(1).

Results: In two patients, the demonstration of pulmonary infection by two distinct strains suggested dual infection of these individuals. In one other case, the strain isolated from a Ghon-focus was identical to that obtained from all secondary cavitating lesions, which suggested reactivation of the primary infection. In the remaining cases, all isolates were identical, but primary lesions could not be identified with certainty or were culture negative. One of these cases showed evidence of strain evolution.

Conclusions: Multilesional strain genotyping suggested both reinfection and reactivation in a series of HIV-negative autopsied patients with secondary tuberculosis. In most (11/13) cases, the same strain (or clonal variant) was present in all lesions, pulmonary and extrapulmonary.