Bedaquiline micro-heteroresistance after tuberculosis treatment cessation

Bedaquiline improves survival among individuals with multidrug-resistant tuberculosis (MDR-TB). We report a 65-year old HIV-negative South African male diagnosed in 2013 with MDR-TB (resistant to rifampicin and isoniazid; phenotypically susceptible to a fluoroquinolone and amikacin). Baseline X-ray showed bilateral TB disease with left apex cavitation. He initiated standardised treatment including moxifloxacin, pyrazinamide, kanamycin, ethionamide, isoniazid and terizidone. After initial sputum culture conversion (month 3) and clinical improvement, the patient reconverted to culture positive and developed bilateral cavitation. Following detection of phenotypic ofloxacin resistance (month 6), treatment was revised (month 8) to include high-dose isoniazid, ethambutol, pyrazinamide, terizidone, linezolid, para-aminosalicylic acid and kanamycin. Bedaquiline was added 22 days later and administered for 6 months. The patient remained culture positive (treatment failure) and treatment was stopped 15 months after revision of the regimen. The patient died 7 months later.Overall, eight M. tuberculosis isolates underwent whole genome sequencing (WGS), targeted deep sequencing of Rv0678 and phenotypic bedaquiline resistance testing. WGS of isolate A collected 4.7 months after standard MDR-TB treatment initiation revealed a Beijing strain with mutations conferring resistance to rifampicin, isoniazid, ethambutol, ethionamide, fluoroquinolones, pyrazinamide and streptomycin. WGS of isolate C, collected 2 months after treatment revision, suggested that bedaquiline (to which the isolate was phenotypically susceptible) was added to a regimen with 5 potentially effective drugs. Targeted deep sequencing of isolate C showed a base pair insertion in Rv06784 at a variant frequency of 0.05% (position 192), which was not present in isolate B taken before bedaquiline treatment. Isolate D, collected after bedaquiline cessation, showed the presence of this insertion in >90% of the bacterial population. The frequency of the Rv0678 192 insertion decreased in subsequent isolates, but two different insertions in Rv0678 emerged (GA and G at position 138, isolates F and G, respectively). The G insertion at position 138 became fixed after all treatment was stopped (isolates G and H). Isolates D, E, F, G, and H were phenotypically resistant to bedaquiline. This case demonstrates the emergence of bedaquiline resistance despite the presence of five potentially effective drugs and good adherence (based on clinical notes). The emergence of Rv0678 variants, after completion of 6 months of bedaquiline treatment, demonstrates the risk of resistance amplification after cessation of a drug with a long half-life (5.5 months for bedaquiline).