Abstract
Non-tuberculous mycobacteria (NTM) represent a significant disease burden in the cystic fibrosis (CF) population. Whilst the acquisition of NTM to the respiratory tract is predominantly attributed to environmental exposures, the contribution of the gut-lung axis to NTM pulmonary disease remains poorly understood. In this study, we retrospectively examined 1285 stool microbiomes from 121 children and 52 adults with CF, and 135 healthy control (HC) children, in order to assess the prevalence, abundance and clinical significance of NTM in the gut. We detected various species of low clinical concern in the stool of 2% of people with CF and 1% of HC sampled, with longitudinal sampling revealing their occurrence to be sporadic and transient. Of the participants studied, only 11 had a history of prior clinical NTM respiratory colonisation or infection, but there was limited evidence to support ongoing persistence in the intestinal tract. This study suggests that the gut is not a meaningful reservoir for pulmonary NTM infections and it is unlikely to serve as a transmission route within the CF population.