Background Tuberculosis (TB) is a major public health issue in resource-limited settings, including Gabon, which it is one of the top 30 countries worldwide with a high burden of the disease. Managing multidrug-resistant TB (MDR-TB) in these settings is challenging due to limited access to rapid diagnostics and drug susceptibility testing. Early detection of drug-resistant TB is crucial to controlling transmission of resistant strains and initiating appropriate treatment. The study aimed to determine the proportion and resistance patterns of pre-extensively drug-resistant (Pre-XDR) and extensively drug-resistant (XDR) TB among MDR-TB patients in Gabon and to identify the distribution of their lineages.

Methods In this cross-sectional study, we collected 92 TB isolates from rifampicin-resistant (RR) patients based on Genexpert. We performed BD MGIT liquid culture and whole-genome sequencing using the MinION according to standard procedures.

Results Our findings showed that the HIV-TB co-infection rate was 14.1%, and the mean age of the participants was 31.94 years. We observed that 65.2% of patients had MDR-TB, 19.6% had Pre-XDR, 14.1% had RR-TB, and 1.1% had XDR-TB. We identified three main lineages, with Lineage 4 being the most common (81.52%), followed by Lineage 5 (14.13%) and Lineage 2 (3.26%). The dominant genotypes were Cameroon, LAM, Harleem, West Africa 1b, and Beijing, accounting for 47.82%, 19.56%, 17.39%, 6.5%, and 4.3% of cases, respectively.

Conclusion Our study reveals a high proportion of Pre-XDR patients, underscoring the need to enhance laboratory capacities to monitor Pre-XDR and XDR-TB patients. This is the first detection of Lineage 2, the most virulent TB strain in Gabon, Further studies are needed to investigate the transmission dynamics of the Lineage 2 TB strain in Gabon. TB programs should prioritize the effective and rational use of second-line drugs for newly diagnosed MDR-TB patients to prevent the emergence of Pre-XDR/XDR-TB strains.