Need for caution when interpreting Xpert (R) MTB/RIF results for rifampin resistance among children

BACKGROUND: Recommended by the World Health Organization as an initial diagnostic test for TB in children, Xpert (R) MTB/RIF is widely implemented in many countries, including Kenya. METHODS: Three hundred HIV-positive and negative children (<5 years) were enrolled in Kisumu County, Kenya, from October 2013 to August 2015. Multiple specimen types were collected from each child and tested using Xpert, liquid culture, and phenotypic drug susceptibility testing (DST). Samples positive for rifampin (RIF) resistance on Xpert were tested using line-probe assay and sequencing. RESULTS: Of 32 children with bacteriologically confirmed TB, 27 had positive Xpert results. Of these, 3/27 (11%, 95% CI 4-28) had RIF resistance detected on Xpert, but not by phenotypic DST, line-probe assay, or sequencing. For these three children, five Xpert tests showed RIF resistance; all five tests had semi-quantitative 'very low' results and delay or absence of probe D signal, whereas no Xpert results with higher semi quantitative results showed RIF resistance. All three children responded well to standard TB treatment. CONCLUSIONS: False RIF resistance maybe detected in pediatric specimens. Further study is needed to determine if false RIF resistance is associated with low bacterial load.