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ABSTRACT: ESBL producers from fish and soil samples in Tanzania

PROVIDER: PRJEB12361 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1211710_1.fastq.gz	Fastqsanger.gz
	ERR1211710_2.fastq.gz	Fastqsanger.gz
	ERR1211720_1.fastq.gz	Fastqsanger.gz
	ERR1211720_2.fastq.gz	Fastqsanger.gz
	ERR1211730_1.fastq.gz	Fastqsanger.gz

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ESBL-producing isolates from neonates in Tanzania

Project description:ESBL-producing isolates from neonates in Tanzania

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Comprehensive Assessment of Initial Adaptation of ESBL Positive ST131 E. coli to Carbapenem Exposure

Project description:Background: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in its progression to becoming carbapenem resistant. Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/H30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. Results: All thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P<1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific adaptations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, insertion sequence 26 (IS26) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. Conclusions: ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2 subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.

2024-08-04 | GSE273456 | GEO

Project description:Sequencing of ESBL-producing E. coli from humans in Tanzania

| PRJEB12376 | ENA

Transcriptional alterations of virulence-associated genes in extended spectrum beta-lactamase (ESBL)-producing uropathogenic Escherichia coli during morphologic transitions induced by ineffective antibiotics

Project description:The present study examines changes in global gene expression patterns and in virulence factor-associated genes in an extended spectrum beta-lactamase (ESBL)-producing UPEC (ESBL019) during the morphologic transitions induced by an ineffective antibiotic and in the presence of human primary bladder epithelial cells. The morphological shifts induced by ineffective antibiotics are associated with significant transcriptional virulence alterations in ESBL-producing UPEC, which may affect survival and persistence in the urinary tract.

2017-06-06 | GSE99661 | GEO

Project description:ESBL-encoding E. coli from companion animals and livestock in Tanzania

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Project description:FISH-RACS-Seq for soil and marine samples

| PRJNA890413 | ENA

Nkya et al 2014 - Insecticide resistance mechanisms associated with different environments in the malaria vector Anopheles gambiae. A case study in Tanzania

Project description:Nine Anopheles gambiae populations were sampled in three areas of Tanzania showing contrasting agriculture activity, urbanization and usage of insecticides for vector control. Insecticide resistance levels were measured in larvae and adults through bioassays with deltamethrin, DDT and bendiocarb. A microarray approach was used for identifying transcription level variations associated to different environments and insecticide resistance. the Ifakara strain originating from central Tanzania and susceptible to all insecticides was used as a reference strain.

2013-10-31 | E-MEXP-3987 | biostudies-arrayexpress

Identification, synthesis, and in vitro activity of antimicrobial peptide from African catfish against the Extended-Spectrum Beta-Lactamase (ESBL) producing Escherichia coli.

Project description:The global surge in multi-drug resistant bacteria, including extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has led to a growing need for new antibacterial compounds. Despite being promising, the potential of fish-derived antimicrobial peptides (AMPs) in combating ESBL-E. coli is largely unexplored. In this study, native peptides were extracted from the skin mucus of farmed African Catfish, Clarias gariepinus, using a combination of 10 % acetic acid solvent hydrolysis, 5 kDa ultrafiltration, and C18 hydrophobic interactions. Peptides were then sequenced using Orbitrap Fusion Lumos Tribrid Mass Spectrometry. The identified peptides were screened for potential antibacterial activity using Random Forest and AdaBoost machine learning algorithms. The most promising peptide was then chemically synthesized and evaluated in vitro for safety on Rabbit red blood cells and activity against ESBL-E. coli (ATCC 35218) utilizing the spot-on-lawn and broth dilution methods. Eight short peptides were identified with 13 - 22 amino acid residues and molecular weight range of 968.42 to 2434.11 Da. Peptide, FACAP-II was non-hemolytic to rabbit erythrocytes (p>0.05), with Zone of Inhibition (ZOI) of 22.7 mm and Minimum Inhibitory concentration (MIC) of 91.3 μg/mL. The peptide is thus a candidate antibacterial compound with enormous potential applications in the pharmaceutical industry. However, further studies are still required to establish the upscale production strategy and optimize its activity and safety in vivo.

2024-06-25 | PXD049239 | Pride

Assessment of short-read shotgun sequencing and microbiome analysis of faecal samples to discriminate between equol producers and non-producers

Project description:Equol producers and non-producers

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The plasma membrane NADPH oxidase OsRbohA plays a crucial role in developmental regulation and drought-stress response in rice

Project description:Plasma membrane NADPH oxidases (NOXs) are major producers of reactive oxygen species (ROS) in plant cells under normal growth and stress conditions. Rice NOXs have multiple homologs but their functional mechanisms are largely unknown. We used microarrays to detail the global gene expression profiles in rice wild-type (WT, Dongjin) and a mutant osnox2 which loss the functions of OsNOX2 protein under drought and identified distinct classes of genes between the two type rice plants under both normal growth and drought stressed conditions. The youngest fully expanded leaves from 2.5-month-old WT and osnox2 plants (three replicates each), grown under normal growth (soil moisture, 47.3%) and drought conditions (soil moisture, 8.5%), were used for RNA extraction and hybridization on Affymetrix microarrays. Control: normal growth condition; Drought: drought stress condition.

2015-12-31 | E-GEOD-54466 | biostudies-arrayexpress

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