MDR isolates
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA603241 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The identification of multidrug resistant (MDR), extensively and totally drug resistant Mycobacterium tuberculosis (Mtb), in vulnerable sites such as Mumbai, is a grave threat to the control of tuberculosis. The current study aimed at explaining the rapid expression of MDR in Directly Observed Treatment Short Course (DOTS) compliant patients, represents the first study comparing global transcriptional profiles of 3 pairs of clinical Mtb isolates, collected longitudinally at initiation and completion of DOTS. While the isolates were drug susceptible (DS) at onset and MDR at completion of DOTS, they exhibited identical DNA fingerprints at both points of collection. The whole genome transcriptional analysis was performed using total RNA from H37Rv and 3 locally predominant spoligotypes viz. MANU1, CAS and Beijing, hybridized on MTBv3 (BuG@S) microarray, and yielded 36, 98 and 45 differentially expressed genes respectively. Genes encoding transcription factors (sig, rpoB), cell wall biosynthesis (emb genes), protein synthesis (rpl) and additional central metabolic pathways (ppdK, pknH, pfkB) were found to be down regulated in the MDR isolates as compared to the DS isolate of the same genotype. Up regulation of drug efflux pumps, ABC transporters, trans-membrane proteins and stress response transcriptional factors (whiB) in the MDR isolates was observed. The data indicated that Mtb, without specific mutations in drug target genes may persist in the host due to additional mechanisms like drug efflux pumps and lowered rate of metabolism. Furthermore this population of Mtb, which also showed reduced DNA repair activity, would result in selection and stabilization of spontaneous mutations in drug target genes, causing selection of a MDR strain in the presence of drug pressures. Efflux pump such as drrA may play a significant role in increasing fitness of low level drug resistant cells and assist in survival of Mtb till acquisition of drug resistant mutations with least fitness cost. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-134]
2013-04-24 | E-BUGS-134 | biostudies-arrayexpress
Project description:To gain insight into the alterations of gene expression profile in the course of non-mutationally acquired resistance, we performed RNA-seq comparing MDR persister cells to MDR cancer cells.
2021-11-04 | GSE187441 | GEO
Project description:The emergence of multidrug resistant (MDR) Mycobacterium tuberculosis (Mtb) strains, resistant to the frontline anti-tubercular drugs rifampicin and isoniazid, forces treatment with less effective and toxic second-line drugs and stands to derail TB control efforts. However, the immune response to MDR Mtb infection remains poorly understood. Here, we determined the RNA transcriptional profile of in vitro generated macrophages to infection with either drug susceptible Mtb HN878 or MDR Mtb W_7642 infection.
2018-12-26 | GSE115495 | GEO
Project description:This study elucidates the whole proteome changes in the MDR isolates of K. penumoniae, A. baumannii, E. coli, and P. aeruginiosa in the presence of Ampicillin, Kanamycin, and Nalidixic acid. Label-free SWATH-MS is used for protein quantitation of antibiotics treated and untreated samples.
2023-07-26 | PXD039154 | Pride
Project description:Wastewater treatment plants use a variety of bioreactor types and configurations to remove organic matter and nutrients. Little is known regarding the effects of different configurations and within-plant immigration on microbial community dynamics. Previously, we found that the structure of ammonia-oxidizing bacterial (AOB) communities in a full-scale dispersed growth activated sludge bioreactor correlated strongly with levels of NO2- entering the reactor from an upstream trickling filter (Wells et al 2009). Here, to further examine this puzzling association, we profile within-plant microbial biogeography (spatial variation) and test the hypothesis that substantial microbial immigration occurs along a transect (raw influent, trickling filter biofilm, trickling filter effluent, and activated sludge) at the same full-scale wastewater treatment plant. AOB amoA gene abundance increased >30-fold between influent and trickling filter effluent concomitant with NO2- production, indicating unexpected growth and activity of AOB within the trickling filter. Nitrosomonas europaea was the dominant AOB phylotype in trickling filter biofilm and effluent, while a distinct ‘Nitrosomonas-like’ lineage dominated in activated sludge. Prior time series indicated that this ‘Nitrosomonas-like’ lineage was dominant when NO2- levels in the trickling filter effluent (i.e., activated sludge influent) were low, while N. europaea became dominant in the activated sludge when NO2- levels were high. This is consistent with the hypothesis that NO2- production may co-occur with biofilm sloughing, releasing N. europaea from the trickling filter into the activated sludge bioreactor. Phylogenetic microarray (PhyloChip) analyses revealed significant spatial variation in taxonomic diversity, including a large excess of methanogens in the trickling filter relative to activated sludge and attenuation of Enterobacteriaceae across the transect, and demonstrated transport of a highly diverse microbial community via the trickling filter effluent to the activated sludge bioreactor. Our results provide compelling evidence that substantial immigration between coupled process units occurs and may exert significant influence over microbial community dynamics within staged bioreactors.
2015-11-03 | GSE52079 | GEO
Project description:The emergence of multidrug-resistant (MDR) Klebsiella pneumoniae represents a major public health concern, primarily driven by its ability to evade a wide range of antibiotics. Despite extensive genomic studies, proteomic insights into antibiotic resistance mechanisms remain scarce. Here, we employed a data-independent acquisition (DIA)-based quantitative proteomics approach to investigate proteomic differences between 87 MDR and 20 antibiotic-sensitive K. pneumoniae clinical isolates. A total of 3,380 proteins were identified, with 896 showing significant differential expression. MDR isolates exhibited increased expression of efflux pumps, beta-lactamases, and transcriptional regulators, while proteins associated with glycerolipid metabolism and transport were enriched in sensitive strains. To validate our findings, an independent cohort of 10 MDR and 11 sensitive isolates was analyzed. Key biomarkers identified in the discovery cohort, including pyruvate decarboxylase and aldehyde dehydrogenase, were validated with high discriminatory power (AUC > 0.85) in the validation cohort. These findings provide novel insights into the molecular mechanisms of antibiotic resistance and identify promising biomarkers for diagnosing MDR K. pneumoniae, offering potential avenues for therapeutic intervention.
2024-10-14 | PXD056798 |
Project description:This experiment compares C.jejuni isolates from humans and chicken. The samples were collected during a Swedish outbreak. The chicken samples were collected from groceries from the same geographical reagions as the infected humans. The genotypes of the C.jejuni isolates were compared using three different methods.
2008-04-08 | E-TABM-460 | biostudies-arrayexpress
Project description:In this study, we exposed Caenorhabditis elegans wild types N2 to water collected from six sources in the Dutch village Sneek. The sources were: wastewater from a hospital, a community (80 households), a nursing home, influent into the local municipal wastewater treatment plant, effluent of the wastewater treatment plant, and surface water samples. The goal of the experiment was to determine if C. elegans can be used to identify pollutants in the water by transcriptional profiling. Age synchronized worms at developmental L4 larval stage were exposed to treatment for 24 hours. After flash freezing the samples, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.
2022-12-03 | E-MTAB-11260 | biostudies-arrayexpress