Biology subjects

Dötsch, A.

Publications and source records attributed to Dötsch, A..

4 recordsLinked to original sources

bioRxiv2025

Epistasis between drug resistance-conferring mutations in Mycobacterium tuberculosis

Studies in model organisms show that mutations conferring resistance to different antibiotics can interact epistatically, but the biological and epidemiological consequences of such interactions are unknown. Here we show that in Mycobacterium tuberculosis (Mtb), positive sign epistasis between RpoB and GyrA mutations causing resistance to rifampicin and fluoroquinolone, respectively, can lead to double-resistant strains with high in vitro fitness. Two of these RpoB-GyrA mutation combinations account for 53% in a global collection of highly drug-resistant Mtb clinical isolates, compared to <0.7% for RpoB-GyrA combinations with low in vitro fitness. Moreover, the two high-fitness RpoB-GyrA combinations are associated with a more benign and idiosyncratic proteome perturbation compared to low-fitness combinations. Our findings highlight the relevance of epistasis for the emergence and spread of antimicrobial resistance.

microbiology↗

bioRxiv2025

Within-host evolution of drug tolerance in Mycobacterium tuberculosis.

SynopsisO_ST_ABSBackgroundC_ST_ABSMycobacterium tuberculosis (Mtb) causes tuberculosis (TB) in humans. Poor treatment responses are a threat to global TB control, as such, understanding contributing factors to poor responses is important. We hypothesized that antibiotic tolerance could contribute to delayed culture conversion (recalcitrant TB), and resistance amplification in patients during TB treatment. ObjectivesTo investigate the role of drug tolerance in delayed culture conversion and resistance amplification in TB patients. MethodsWe collected serial Mtb isolates from i) patients with drug-susceptible TB who remained culture positive for up to 6 years (i.e. recalcitrant TB), and ii) patients with multidrug-resistant TB (MDR-TB) where resistance amplified during treatment. We measured tolerance to rifampicin (RIF) in drug-susceptible TB strains and tolerance to moxifloxacin (MFX) in MDR-TB strains using a real-time time-kill assay. ResultsRIF tolerance evolved within-host, increasing up to and ~1.5-fold, however, there was no apparent contribution of RIF tolerance to delayed culture conversion. Tolerance to Mfx in MDR-TB patients appeared negatively associated with resistance amplification and consistently decreased over time in patients. ConclusionOur findings confirm that antibiotic tolerance evolves in Mtb within patients over time during treatment. However, there was no evidence that this tolerance influences treatment responses, calling for further investigation of contributors to adverse treatment responses and their mitigation.

microbiology↗

bioRxiv2025

Variability in intrinsic drug tolerance in Mycobacterium tuberculosis corresponds with phylogenetic lineage

Drug tolerance allows bacteria to survive extended exposure to bactericidal drugs and is thought to play a role in drug resistance evolution. In Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), multidrug resistant TB (MDR-TB) outbreaks are frequently caused by strains belonging to two phylogenetic lineages of the human-adapted strains of the Mtb Complex, namely lineages (L) 2 and L4. We hypothesized that members of L2 and L4 are more intrinsically drug tolerant, and as such, more readily evolve drug resistance. To explore this, we devised a high throughput in vitro assay to measure drug tolerance in Mtb. We selected a cohort of strains representative of the globally most frequent lineages L1 - L4. We measured tolerance to rifampicin and bedaquiline and found L3 and L4 strains to have higher tolerance compared to L1 and L2 strains. In addition, phylogenetically closely related strains exhibited similar levels of tolerance, suggesting that tolerance is heritable. Finally, we explored genes previously reported to be associated with tolerance in Mtb and found significant enrichment in mutations in genes involved in cell wall and cell processes, intermediary metabolism and respiration, as well as lipid metabolism in high-tolerance strains.

microbiology↗

bioRxiv2024

Large contribution of repeats to genetic variation in a transmission cluster of Mycobacterium tuberculosis

Repeats are the most diverse and dynamic, but also the least well understood component of microbial genomes. For all we know, repeat-associated mutations such as duplications, deletions, inversions, and gene conversion might be as common as point mutations, but because of short-read myopia and methodological bias they have received much less attention. Long-read sequencing opens the perspective of resolving repeats and systematically investigating the mutations they induce. For this study, we assembled the genomes of 16 closely related strains of the bacterial pathogen Mycobacterium tuberculosis from PacBio HiFi reads, with the aim of characterizing the full spectrum of DNA polymorphisms. We find that complete and accurate genomes can be assembled from HiFi reads, with read size being the main limitation in the presence of duplications. By combining a reference-free pangenome graph with extensive repeat annotation, we identified 110 variants, 58 of which can be assigned to repeat-associated mutational mechanisms such as strand slippage and homologous recombination. While recombination events are less frequent than point mutations, they can affect large regions and introduce multiple variants at once, as shown by three gene conversion events and a duplication of 7.3 kb that involve ppe18 and ppe57, two genes possibly involved in immune subversion. Our study shows that the contribution of repeat-associated mechanisms of mutation can be similar to that of point mutations at the microevolutionary scale of an outbreak. A large reservoir of unstudied genetic variation in this "monomorphic" bacterial pathogen awaits investigation.

genomics↗