Use of multiple markers in population-based molecular epidemiologic studies of tuberculosis

SETTING: Many epidemiologic studies of tuberculosis are being conducted wor ldwide. Fingerprinting with a secondary marker in strains with fewer than s ix IS6110-hybridizing bands enhances the tracking of strains, but its impac t on population-level inferences has not been well studied. OBJECTIVE: To investigate the effects of secondary genotyping for low-copy Mycobacterium tuberculosis isolates with polymorphic guanine-cytosine-rich repetitive sequence (PGRS) on epidemiologic inferences in population-based research settings. DESIGN: For San Francisco tuberculosis cases (1991-1996), clusters were def ined by IS6110 alone and by PGRSlIS6110 to 1) estimate recent transmission, 2) evaluate the theoretical influence of bacterial population parameters o n these estimates, and 3) assess risk factors for recent transmission. RESULTS: Secondary typing on low-copy strains (20.3% of all isolates) decre ased the estimate of recent transmission from 29.1% to 25.3% (P = 0.03). Th e most influential parameters in determining whether supplemental genotypin g results in different estimates were the proportion of low-copy strains an d the amount of clustering. Risk factors for recent transmission were ident ical for both definitions of clustering. CONCLUSION: The statistical and inferred effects of sec ondary genotyping o f M. tuberculosis seem to depend on the proportion of low-copy strains in t he population, When this proportion is low or when few secondary patterns m atch, supplemental genotyping may yield minimal insight into population-lev el investigations.