Abstract:BackgroundWhole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. T… Show more
“…The majority of the detected sequence heterogeneity therefore resulted from an abundance of rare alleles in the population—approximately 80% of the total heterogeneity was accounted for by v-SNPs with a frequency of less than 20%. This degree of variation is higher than reported previously [54–56] and shows that MTBC might explore its mutational space to a greater extent than previously thought. Importantly, the intra-patient SFS was very similar to the inter-host SFS reported by Pepperell and colleagues [57], suggesting that forces shaping the diversity at the host population level are already prominent within patients, before the bottleneck of transmission.Fig.…”
Section: Resultscontrasting
confidence: 62%
“…In a recent report of a detailed sampling of MTBC populations across several foci of infection within deceased TB patients, Lieberman et al [56] showed a large genetic diversity within each patient that may not be completely represented in tracheal aspirates—a proxy the authors used for sputum samples. Furthermore, several studies found a comparable degree of genetic diversity of MTBC within and between hosts [42, 54, 59]; these observations complement radiological findings of granuloma dynamics [14]. In the majority of these studies, authors comment on the transience of the detected polymorphisms and highlight the importance of sampling the host population as fully as possible.…”
BackgroundCombination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics.ResultsBy combining very deep whole genome sequencing (~1000-fold genome-wide coverage) with sequential sputum sampling, we were able to detect transient genetic diversity driven by the apparently continuous turnover of minor alleles, which could serve as the source of drug-resistant bacteria. However, we report that treatment efficacy has a clear impact on the population dynamics: sufficient drug pressure bears a clear signature of purifying selection leading to apparent genetic stability. In contrast, M. tuberculosis populations subject to less drug pressure show markedly different dynamics, including cases of acquisition of additional drug resistance.ConclusionsOur findings show that for a pathogen like M. tuberculosis, which is well adapted to the human host, purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals. Nonetheless, we also report a continuous turnover of minor variants, which could give rise to the emergence of drug resistance in cases of drug pressure weakening. Monitoring bacterial population dynamics could therefore provide an informative metric for assessing the efficacy of novel drug combinations.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1196-0) contains supplementary material, which is available to authorized users.
“…The majority of the detected sequence heterogeneity therefore resulted from an abundance of rare alleles in the population—approximately 80% of the total heterogeneity was accounted for by v-SNPs with a frequency of less than 20%. This degree of variation is higher than reported previously [54–56] and shows that MTBC might explore its mutational space to a greater extent than previously thought. Importantly, the intra-patient SFS was very similar to the inter-host SFS reported by Pepperell and colleagues [57], suggesting that forces shaping the diversity at the host population level are already prominent within patients, before the bottleneck of transmission.Fig.…”
Section: Resultscontrasting
confidence: 62%
“…In a recent report of a detailed sampling of MTBC populations across several foci of infection within deceased TB patients, Lieberman et al [56] showed a large genetic diversity within each patient that may not be completely represented in tracheal aspirates—a proxy the authors used for sputum samples. Furthermore, several studies found a comparable degree of genetic diversity of MTBC within and between hosts [42, 54, 59]; these observations complement radiological findings of granuloma dynamics [14]. In the majority of these studies, authors comment on the transience of the detected polymorphisms and highlight the importance of sampling the host population as fully as possible.…”
BackgroundCombination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics.ResultsBy combining very deep whole genome sequencing (~1000-fold genome-wide coverage) with sequential sputum sampling, we were able to detect transient genetic diversity driven by the apparently continuous turnover of minor alleles, which could serve as the source of drug-resistant bacteria. However, we report that treatment efficacy has a clear impact on the population dynamics: sufficient drug pressure bears a clear signature of purifying selection leading to apparent genetic stability. In contrast, M. tuberculosis populations subject to less drug pressure show markedly different dynamics, including cases of acquisition of additional drug resistance.ConclusionsOur findings show that for a pathogen like M. tuberculosis, which is well adapted to the human host, purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals. Nonetheless, we also report a continuous turnover of minor variants, which could give rise to the emergence of drug resistance in cases of drug pressure weakening. Monitoring bacterial population dynamics could therefore provide an informative metric for assessing the efficacy of novel drug combinations.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1196-0) contains supplementary material, which is available to authorized users.
“…We suspect that it is possible that PI treatment provided a strong selection for the emergence of glpK mutants in these mice. Variants with glpK frameshift mutations are detectable in sputum samples from many human TB patients and, furthermore, these glpK mutants were unstable (47,48).…”
The length and complexity of tuberculosis (TB) therapy, as well as the propensity of Mycobacterium tuberculosis to develop drug resistance, are major barriers to global TB control efforts. M. tuberculosis is known to have the ability to enter into a drug-tolerant state, which may explain many of these impediments to TB treatment. We have identified a novel mechanism of genetically encoded but rapidly reversible drug-tolerance in M. tuberculosis caused by transient frameshift mutations in a homopolymeric tract (HT) of seven cytosines (7C) in the glpK gene.Inactivating frameshift mutations associated with the 7C HT in glpK produce small colonies that exhibit heritable multi-drug increases in minimal inhibitory concentrations and decreases in drug-dependent killing; however, reversion back to a fully drug-susceptible large-colony phenotype occurs rapidly through the introduction of additional insertions or deletions in the same glpK HT region. These reversible frameshift mutations in the 7C HT of M. tuberculosis glpK occur in clinical isolates, accumulate in M. tuberculosis infected mice with further accumulation during drug treatment, and exhibit a reversible transcriptional profile including induction of dosR and sigH and repression of kstR regulons, similar to that observed in other in vitro models of M. tuberculosis tolerance. These results suggest that GlpK phase variation may contribute to drug-tolerance, treatment failure and relapse in human TB. Drugs effective against phase-variant M. tuberculosis may hasten TB treatment and improve cure rates.
“…The existence of genetically variable drug‐resistant bacterial populations within a single patient is now acknowledged and could affect drug resistance evolution (Black et al., 2015; Eldholm et al., 2014; Müller, Borrell, et al., 2013; Shamputa et al., 2004). Meacci et al.…”
Section: Intra‐host Genetic Variability Of Drug‐resistant Populationsmentioning
confidence: 99%
“…The intra-host evolution of bacterial resistance patterns is one of the key aspects of drug resistance emergence and spread (Eldholm et al, 2014;Meacci et al, 2005;Merker et al, 2013). The existence of genetically variable drug-resistant bacterial populations within a single patient is now acknowledged and could affect drug resistance evolution (Black et al, 2015;Eldholm et al, 2014;Müller, Borrell, et al, 2013;Shamputa et al, 2004). Meacci et al investigated M. tu-berculosis population evolution in a noncompliant patient during more than 12 years of active disease.…”
Section: Intr A-hos T G Ene Ti C Variab Ilit Y Of Drug -Re S Is Tanmentioning
At present, the successful transmission of drug‐resistant Mycobacterium tuberculosis, including multidrug‐resistant (MDR) and extensively drug‐resistant (XDR) strains, in human populations, threatens tuberculosis control worldwide. Differently from many other bacteria, M. tuberculosis drug resistance is acquired mainly through mutations in specific drug resistance‐associated genes. The panel of mutations is highly diverse, but depends on the affected gene and M. tuberculosis genetic background. The variety of genetic profiles observed in drug‐resistant clinical isolates underlines different evolutionary trajectories towards multiple drug resistance, although some mutation patterns are prominent. This review discusses the intrinsic processes that may influence drug resistance evolution in M. tuberculosis, such as mutation rate, drug resistance‐associated mutations, fitness cost, compensatory mutations and epistasis. This knowledge should help to better predict the risk of emergence of highly resistant M. tuberculosis strains and to develop new tools and strategies to limit the development and spread of MDR and XDR strains.
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