Implementation of sequencing-based surveillance for drug-resistant tuberculosis in Nigeria

Sequencing for drug-resistant tuberculosis (DR-TB) surveillance was established in Nigeria for the first time, demonstrating a nationally coordinated referral network for multi-disease sequencing services. Mycobacterium tuberculosis isolates previously identified as resistant to rifampicin and/or isoniazid by genotypic or phenotypic drug susceptibility testing were selected proportionately across all six geopolitical zones in Nigeria. Programmatic use of sequence data for DR-TB surveillance was prioritized, demonstrating additional resistance detection and enhanced monitoring as new TB treatment regimens are scaled up. Sanger sequencing identified resistance to rifampicin and isoniazid missed by drug susceptibility tests routinely used in country, for 11% (5/47) and 2% (1/47) of isolates, respectively. This pilot study demonstrates feasibility and provides an example for programmatic implementation of integrated sequencing, supporting country efforts to strengthen genomic surveillance for DR-TB and improve prevention and control globally.