Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. | LitMetric
Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology's (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of and and two blood samples spiked with either or that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000-3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.
Background: The utilization of PD1 and CTLA4 inhibitors has revolutionized the treatment of malignant melanoma (MM). However, resistance to targeted and immune-checkpoint-based therapies still poses a significant problem.
Objective: Here, we mine large-scale MM proteogenomic data to identify druggable targets and forecast treatment efficacy and resistance.
Tuberous sclerosis complex (TSC) is a rare genetic disorder characterized by the formation of benign tumors in various organs, particularly in the central nervous system. We aimed to delineate the molecular profile of Turkish individuals diagnosed with TSC by analyzing the TSC1 and TSC2 genes using next-generation sequencing (NGS). Sophia Genetics' Sophia Inherited Disease Panel was used to perform NGS on 22 individuals diagnosed with TSC and to identify pathogenic variants in the TSC1 and TSC2 genes.
Background: Drought is one of main critical factors that limits sugarcane productivity and juice quality in tropical regions. The unprecedented changes in climate such as monsoon failure, increase in temperature and other factors warrant the need for development of stress tolerant cultivars to sustain sugar production. Plant Nuclear factor (NF-Y) is one of the major classes of transcription factors that have a major role in plant development and abiotic stress response.
Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China. Electronic address:
Streptozotocin (STZ) is widely used as a pancreatic beta-cell toxin to induce experimental diabetes in rodents. Strain-dependent variations in STZ-induced diabetes susceptibility have been reported in mice. Differences in STZ-induced diabetes susceptibility are putatively related to pancreatic beta-cell fragility via DNA damage response.
