Microevolution of Mycobacterium tuberculosis hetero-resistance subpopulations in a patient receiving 27 years of tuberculosis treatment in Germany
Pre-existing and newly emerging resistant pathogen subpopulations (hetero-resistance) are potential risk factors for treatment failure of multi/extensively drug resistant (MDR/XDR) tuberculosis (TB). Intra-patient evolutionary dynamics of Mycobacterium tuberculosis complex (Mtbc) strains and their implications on treatment outcomes are still not completely understood. Methods To elucidate how Mtbc strains escape therapy, we analysed 13 serial isolates by whole genome sequencing from a German patient. Sequencing data was compared to phenotypic drug susceptibility profiles, and the patient’s collective 27-year treatment history, to further elucidate factors fostering intra-patient resistance evolution. Results The patient endured five distinct TB episodes, ending in resistances to 16 drugs and a nearly untreatable XDR-TB infection. The first isolate obtained, during the patient’s 5th TB episode, presented fixed resistance mutations to seven anti-TB drugs including isoniazid, rifampicin, streptomycin, pyrazinamide, prothionamide, para-aminosalicyclic acid and cycloserin/terizidone. Over the next 13 years a dynamic evolution with co-existing, heterogeneous subpopulations was observed in six out of 13 sequential bacterial isolates. The emergence of drug-resistant subpopulations coincided with frequent changes in treatment regimens, which often included two or less active compounds. This evolutionary arms race between competing sub-populations, ultimately resulted in the fixation of a single XDR variant. Conclusion Our data demonstrates the complex intra-patient microevolution of Mtbc subpopulations during failing MDR/XDR-TB treatment. Designing effective treatment regimens based on rapid detection of (hetero-) resistance is key to avoid resistance development and treatment failure.