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Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from infected tissues.
Microbiol Spectr
January 2025
Ifremer, ASIM, La Tremblade, France.
Since the 1990s, the Pacific oyster has faced significant mortality, which has been associated with the detection of the Ostreid Herpesvirus type 1 (OsHV-1). Due to the complex genomic architecture and the presence of multiple genomic isomers, short-read sequencing using Illumina method struggles to accurately assemble tandem and repeat regions and to identify and characterize large structural variations in the OsHV-1 genome. Third-generation sequencing technologies, as long-read real-time nanopore sequencing from Oxford Nanopore Technologies (ONT), offer new possibilities for OsHV-1 whole-genome analysis.
View Article and Find Full Text PDFTetracycline and chloramphenicol exposure induce decreased susceptibility to tigecycline and genetic alterations in AcrAB-TolC efflux pump regulators in Escherichia coli and Klebsiella pneumoniae.
PLoS One
January 2025
Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
Tigecycline (Tgc), a third-generation tetracycline is found as the last line of defense against multi-drug resistant bacteria. Recent increased rate of resistance to tgc, a human-restricted agent among animal bacteria poses a significant global health challenge. Overuse of first generation tetracyclines (Tet) and phenicols in animals have been suggested to be associated with Tgc resistance development.
View Article and Find Full Text PDFYHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database.
BMC Biol
January 2025
Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China.
Background: The advancements in second-/third-generation sequencing technologies, alongside computational innovations, have significantly enhanced our understanding of the genomic structure of Y-chromosomes and their unique phylogenetic characteristics. These researches, despite the challenges posed by the lack of population-scale genomic databases, have the potential to revolutionize our approach to high-resolution, population-specific Y-chromosome panels and databases for anthropological and forensic applications.
Objectives: This study aimed to develop the highest-resolution Y-targeted sequencing panel, utilizing time-stamped, core phylogenetic informative mutations identified from high-coverage sequences in the YanHuang cohort.
SUMMER: an integrated nanopore sequencing pipeline for variants detection and clinical annotation on the human genome.
Funct Integr Genomics
January 2025
Children's Medical Center, Peking University First Hospital, No.5 Le Yuan Road, Daxing District, 100034, Beijing, China.
Long-read sequencing has emerged as a transformative technology in recent years, offering significant potential for the molecular diagnosis of unresolved genetic disorders. Despite its promise, the comprehensive detection and clinical annotation of genomic variants remain intricate and technically demanding. We present SUMMER, an integrated and structured workflow specifically designed to process raw Nanopore sequencing reads.
View Article and Find Full Text PDFMultidrug-resistant Gram-negative bacterial infections.
Lancet
January 2025
Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, VIC, Australia; Centre to Impact AMR, Monash University, Melbourne, VIC, Australia; Infection Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia. Electronic address:
Multidrug-resistant Gram-negative bacterial infections cause significant morbidity and mortality globally. These pathogens easily acquire antimicrobial resistance (AMR), further highlighting their clinical significance. Third-generation cephalosporin-resistant and carbapenem-resistant Enterobacterales (eg, Escherichia coli and Klebsiella spp), multidrug-resistant Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii are the most problematic and have been identified as priority pathogens.
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