Ontology highlight
ABSTRACT:
PROVIDER: PRJNA828399 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:antibiotic resistance genes and aquaculture environment
| PRJEB40530 | ENA
Project description:Antibiotic resistance in aquaculture sediment
| PRJDB8503 | ENA
Project description:Infectious pancreatic necrosis (IPN) is a serious viral disease that causes significant economic losses in salmon aquaculture. To characterize the host-pathogen relationship in IPN, we analysed transcriptional profiles of salmon head kidney (SHK-1) cells infected with infectious pancreatic necrosis virus (IPNV) at three timepoints over six days (at 1, 3 & 6 days post infection. The transcriptome was investigated using the TRAITS / SGP 16950-feature Atlantic salmon cDNA microarray, which is enriched for genes with functions related to the immune response.
2011-01-01 | E-TABM-1000 | biostudies-arrayexpress
Project description:Antibiotic resistance (AMR) in aquatic bacteria affecting aquaculture has been a growing concern given the potential for mixing of bacterial populations in the aquatic environment and exposure to different pharmaceuticals from drugs used in aquaculture, as well as wastewater effluent and agricultural run-off. To better understand the mechanism for AMR in a common aquatic fish pathogen exposed to low dose antibiotics we monitored the genetic changes, as well as gene expression, in Aeromonas hydrophila as the bacteria was exposed to incremental doses of oxytetracycline (OTC), a commonly used drug in aquaculture. We were able to render all three isolates of our original A. hydrophila resistant to therapeutic levels of OTC (i.e. ≥100ppm). The relatively quick phenotypic adaptation (often less than 3 days) to different OTC concentrations was very similar across our replicates. Our whole genome sequencing data and transcriptome results suggested several genes underwent point mutations across all replicates. Further differential gene expression was observed and likely impacted several pathways which may explain the progressive resistance to OTC associated with incremental exposure to the drug. The specific mutations consistently identified in isolates exposed to OTC were on AHA_ 2785 (associated with an outer membrane protein), AHA_2910 (involved in the efflux pump mechanism), and AHA_0308 (associated with the small ribosomal subunit protein S10). The pathways involved in the differential gene expression included efflux- pump mechanisms, outer membrane proteins, and ribosomal protein OTC target. Our findings support the notion that AMR can occur via genetic regulation of several intrinsic mechanisms within a bacterial population. This finding could have implications in aquaculture where bacteria such as A. hydrophila can be exposed to varying levels of antibiotics during in-feed treatments.
2025-10-01 | GSE290492 | GEO
Project description:With the global increase in the use of carbapenems, several gram-negative bacteria have acquired carbapenem resistance, thereby limiting treatment options. Klebsiella pneumoniae is one of such notorious pathogen that is being widely studied to find novel resistance mechanisms and drug targets. These antibiotic-resistant clinical isolates generally harbor many genetic alterations, and identification of causal mutations will provide insights into the molecular mechanisms of antibiotic resistance. We propose a method to prioritize mutated genes responsible for antibiotic resistance, in which mutated genes that also show significant expression changes among their functionally coupled genes become more likely candidates. For network-based analyses, we developed a genome-scale co-functional network of K. pneumoniae genes, KlebNet (www.inetbio.org/klebnet). Using KlebNet, we could reconstruct functional modules for antibiotic-resistance, and virulence, and retrieved functional association between them. With complementation assays with top candidate genes, we could validate a gene for negative regulation of meropenem resistance and four genes for positive regulation of virulence in Galleria mellonella larvae. Therefore, our study demonstrated the feasibility of network-based identification of genes required for antimicrobial resistance and virulence of human pathogenic bacteria with genomic and transcriptomic profiles from antibiotic-resistant clinical isolates.
2018-06-10 | GSE115539 | GEO
Project description:Fate of high-risk antibiotic resistance genes in large-scale aquaculture sediments
| PRJEB61271 | ENA