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PROVIDER: PRJNA1261920 | ENA |
REPOSITORIES: ENA
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Project description:Background: Mycobacterium avium complex (MAC) bacteria cause opportunistic infections in humans. Treatment yields cure rates of 60% and is comprised of a macrolide, a rifamycin and ethambutol; and in severe cases amikacin. Mechanisms of antibiotic tolerance remain mostly unknown. To elucidate these mechanisms, we studied the transcriptomic response to antibiotics and investigated the contribution of efflux and amikacin modification to susceptibility. Methods: M. avium was subjected to subinhibitory concentrations of clarithromycin, amikacin, ethambutol and rifampicin followed by RNA sequencing. Based thereupon, we characterized M. avium efflux pumps and performed time-kill kinetic analysis using each antibiotic in combination with the efflux pump inhibitors (EPIs) berberine, verapamil and CCCP to study the role of efflux on susceptibility. Finally, we studied the modification of amikacin by M. avium using metabolomic analysis. Results: Changes in respiratory state and changes in ribosome binding and protein folding likely contribute to clarithromycin and amikacin tolerance, respectively. No clear drug-specific mechanisms of tolerance are found for ethambutol and rifampicin. Of the EPIs, only berberine increased the susceptibility to rifampicin and clarithromycin. Finally, we show that M. avium, in contrast to M. abscessus, is not able to modify amikacin. Conclusion: M. avium likely relies on a combination of drug-specific and generic mechanisms of antibiotic tolerance including changes in respiratory and metabolic state in addition to drug efflux and target modification. Efflux inhibition can increase susceptibility but this effect is EPI and antibiotic specific. Finally, the lack of amikacin modifying activity in M. avium is important for its activity.
2024-01-01 | GSE213116 | GEO
Project description:Mycobacterium abscessus is an opportunistic pathogen notorious for its resistance to most classes of antibiotics and low cure rates. In addition to the highly impermeable mycomembrane, M. abscessus carries an array of shared and species-specific defence mechanisms. However, it remains unknown whether M. abscessus’ antibiotic stress response is fine-tuned or an all-or-nothing response. A deeper understanding of underlying resistance and tolerance mechanisms is pivotal in development of targeted therapeutic regimens. We elucidate the transcriptomic response of M. abscessus to antibiotics recommended in treatment guidelines. The M. abscessus ATCC 19977 strain was used. Bacteria were subjected to sub-inhibitory concentrations of drugs for 4- and 24-hours, followed by RNA sequencing. In addition, time-kill kinetic analysis was performed using bacteria after pre-exposure to clarithromycin, amikacin or tigecycline for 24-hours. Lastly, Pan-genome analysis of 35 strains from all three subspecies was performed. Mycobacterium abscessus shows both drug-specific and communal transcriptomic responses to antibiotic exposure. Key features of its tolerance to antibiotics are drug-specific converting enzymes, target protection and shifts in its respiratory chain and metabolic state. The observed transcriptomic responses are likely not strain-specific, as genes involved in tolerance are found in all included strains, with the exception of erm(41) in M. abscessus subspecies massiliense. Due to the communal response elicited by ribosomal-targeting antibiotics, exposure to any of these drugs rapidly induces tolerance mechanisms that decrease susceptibility to ribosome-targeting drugs from multiple classes. Screening high-risk patients (e.g. those with bronchiectasis) for M. abscessus infection prior to starting macrolide or aminoglycoside maintenance therapy is warranted.
2022-01-25 | GSE163621 | GEO
Project description:Mycobacterium abscessus [M. abscessus (sensu lato) or M. abscessus group] comprises three closely related taxa with taxonomic status under revision: M. abscessus sensu stricto, M. bolletii and M. massiliense. We describe here a simple, robust and cost effective PCR-based method for distinguishing among M. abscessus, M. massiliense and bolletii. Based on the M. abscessus ATCC 19977T genome, discriminatory regions were identified between M. abscessus and M. massiliense from array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense and 2 M. bolletii previously identified by multi-target sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full length erm(41) instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for a straightforward identification of M. abscessus, M. massiliense and M. bolletii and assessment of inducible clarithromycin resistance. This method can be easily implemented into a routine workflow providing subspecies level identification within 24 hours of isolation of M. abscessus group. Two-color CGH with 4 independent Mycobacterium clinical isolates and the M massiliense type strain (CCUG 48898) labeled with Cy3 were cohybridized with the M abscessus type strain (ATCC 19977) labeled with Cy5 on a tiling array designed against the M abscessus type strain
2013-07-17 | E-GEOD-43629 | biostudies-arrayexpress
Project description:Mycobacterium abscessus [M. abscessus (sensu lato) or M. abscessus group] comprises three closely related taxa with taxonomic status under revision: M. abscessus sensu stricto, M. bolletii and M. massiliense. We describe here a simple, robust and cost effective PCR-based method for distinguishing among M. abscessus, M. massiliense and bolletii. Based on the M. abscessus ATCC 19977T genome, discriminatory regions were identified between M. abscessus and M. massiliense from array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense and 2 M. bolletii previously identified by multi-target sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full length erm(41) instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for a straightforward identification of M. abscessus, M. massiliense and M. bolletii and assessment of inducible clarithromycin resistance. This method can be easily implemented into a routine workflow providing subspecies level identification within 24 hours of isolation of M. abscessus group.
2013-07-17 | GSE43629 | GEO
Project description:Mycobacterium abscessus is an emerging pathogen causing severe pulmonary infections, particularly in individuals with underlying conditions, such as cystic fibrosis or chronic obstructive pulmonary disease. Macrolides, including clarithromycin (CLR) and azithromycin (AZM), represent the current cornerstone of antibiotherapy against M. abscessus complex. However, prolonged exposure to macrolides can induce the apparition of Erm(41)-mediated resistance, limiting their spectrum of activity and often leading to therapeutic failure. Therefore, inhibiting Erm(41) could thwart this resistance mechanism to maintain macrolide susceptibility and avoid the therapeutic failure. In a previous study, the Erm(41) methyltransferase was identified as a target enzyme of Cyclipostins and Cyclophostin compounds (CyC). Herein, we took advantage of this feature to evaluate the in vitro activity of clarithromycin and azithromycin in combination with different CyC via the checkerboard assay on macrolide susceptible and induced macrolide-resistant M. abscessus generated by either clarithromycin or azithromycin exposure. Our results emphasize the use of the CyC to prevent/overcome Erm(41) induced resistance, restore macrolide susceptibility. This work should help to expand our therapeutic arsenal in the fight against a particularly antibiotic resistant mycobacterial species and could provide the opportunity to revisit the therapeutic regimen for combating M. abscessus pulmonary infections in CF patients, and particularly in erm(41)-positive strains.
2024-12-05 | PXD055560 | Pride
Project description:Human macrophages are a natural host of many mycobacterium species, including Mycobacterium abscessus (M. abscessus), an emerging pathogen affecting patients with lung diseases and immunocompromised individuals. There are few available treatments and the search for effective antibiotics against M. abscessus has been hindered by the lack of a tractable in vitro intracellular model of infection. Here, we established a reliable model for M. abscessus infection using human pluripotent stem cell-derived macrophages (hPSC-macrophages). hPSC differentiation permitted a reproducible generation of functional human macrophages that were highly susceptible to M. abscessus infection. Electron microscopy demonstrated that M. abscessus was present in the vacuoles of hPSC-macrophages. RNA-sequencing analysis revealed a time dependent host cell response to M. abscessus, with differing gene and protein expression patterns observed at 3-hours, 24-hours and 48-hours post-infection. Culture of engineered tdTOMATO-expressing hPSC-macrophages with GFP-expressing M. abscessus enabled rapid and image-based high-throughput analysis of intracellular infection and quantitative assessment of antibiotic resistance and efficacy. Our study describes the first hPSC-based model for M. abscessus infection, which represents a novel platform for studying M. abscessus-host interaction and an accessible tool for drug discovery.
2022-08-10 | GSE207456 | GEO
Project description:We have analysed transcriptional effects of BRAF(V600K) in the intestinal epithelium of transgenic mice that harbour an inducible BRAF(V600K) transgene. Mice used in this experiment were compound transgenic for a stem-cell specific Lgr5-EGFP Reporter and either an inducible TdTomato-2A-BRAF(V600K) transgene or an inducibe TdTomato-luciferase transgene.
2013-12-31 | GSE50678 | GEO
Project description:We discovered a cyanobacterial macrolide glycoside that contains an α,β-unsaturated carbonyl system a key motif required for the activation of the Keap1/Nrf2−ARE pathway that is involved in the activation of antioxidant and phase II detoxification enzymes. The compound was screened in ARE luciferase reporter gene assay which induced Nrf2 activity at 32 and 10µM. Given the established crosstalk between oxidative stress and inflammation, we aimed at investigating the antiinflammatory potential of our compound using RAW264.7 mouse macrophage. We carried RNAseq to capture the effects of the compound on transcript levels and identify additional pathways involved in inflammation that could be modulated. We further evaluated the cytotoxicity of the compound against HCT 116 and carried out RNAseq at the same cell line.
2024-11-06 | GSE262850 | GEO
Project description:The gene expression profiles of mycobacteriophage D29 and StarStuff were analyzed 15min, 30min, 60min and 150min post-infection (MOI=3), as well as a StarStuff lysogen. The gene expression profiles of 30min and 150min post-induction of an L5 thermo-inducible lysogen, as well as the L5 lysogen itself.
2017-11-13 | GSE99182 | GEO
Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the iTracer data of 12 cerebral organoids.
2021-11-03 | E-MTAB-10974 | biostudies-arrayexpress