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Background  Leprosy continues to be a health problem in endemic areas. More than 200,000 new cases of leprosy per year suggest that transmission of the disease is still ongoing, presumably as airborne infection through nasal droplets. Late diagnosis supports continued transmission and increases the individual risk for functional disabilities. Laboratory tools are considered beneficial to facilitate early detection and clinical assessment of cases. The aim of this study was to validate molecular tools allowing detection, quantification and assessment of viability of  M. leprae  from nasal swab samples which are easy to obtain without the need of any invasive procedures.    Methods  Validation of two real-time PCRs detecting  M. leprae  DNA (RLEP qPCR) and RNA (16S rRNA RT qPCR) was conducted on “must not detect”/“must detect” samples and 160 pre-treatment nasal swab samples from 20 clinically diagnosed multibacillary (MB) leprosy patients from Togo.    Results  Both assays were 100%  M. leprae  specific and showed analytical sensitivities of three templates each. Out of 20 clinically diagnosed MB leprosy patients, 15 (75.0%) had a positive RLEP qPCR result from nasal swab samples. The 16S rRNA RT qPCR detected viable bacilli in nasal swab samples of ten out of these 15 RLEP positive patients (66.7%).    Conclusion  The combined RLEP/16S rRNA (RT) qPCR assay provides a sensitive and specific tool to determine the bacterial load and viability of  M. leprae  from nasal swab samples and is applicable for early diagnosis, monitoring treatment response and investigating the role of nasal carriage of  M. leprae  in human-to-human transmission through aerosol infection.    Electronic supplementary material  The online version of this article (10.1186/s12879-019-4349-9) contains supplementary material, which is available to authorized users.

Development of a combined RLEP/16S rRNA (RT) qPCR assay for the detection of viable M. leprae from nasal swab samples