GeneXpert MTB/RIF, a tool widely used for diagnosing tuberculosis, has limitations for detecting rifampin resistance in certain variants. We report transmission of a pre-extensively drug-resistant variant in Botswana that went undetected by GeneXpert. The public health impact of misdiagnosis emphasizes the need for comprehensive molecular testing to identify resistance and guide treatment.
Keywords: Botswana; antimicrobial resistance; bacteria; molecular diagnostics; molecular epidemiology; multidrug-resistant tuberculosis; pre–XDR TB; respiratory infections; rifampin resistance; tuberculosis and other mycobacteria; whole-genome sequencing.