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73 [60%] of 122; p0·0001). Administration of isoniazid preventive therapy reduced the prevalence of dPCR-detected complex DNA from 41 (95%) of 43 HIV-infected individuals at baseline to 23 (53%) of 43 after treatment (p0·0001), but it did not affect the prevalence of QuantiFERON positivity (17 [40%] of 43 at baseline 13 [30%] of 43 after treatment; p=0·13). We report a novel molecular microbiological biomarker of latent tuberculosis infection with properties that are distinct from those of a commercial interferon-γ release assay.