Long-read DNA sequencing technologies have been rapidly evolving in recent years, and their ability to assess large and complex regions of the genome makes them ideal for clinical applications in molecular diagnosis and therapy selection, thereby providing a valuable tool for precision medicine. In the third-generation sequencing duopoly, Oxford Nanopore Technologies and Pacific Biosciences work towards increasing the accuracy, throughput, and portability of long-read sequencing methods while trying to keep costs low. These trades have made long-read sequencing an attractive tool for use in research and clinical settings. This article provides an overview of current clinical applications and limitations of long-read sequencing and explores its potential for point-of-care testing and health care in remote settings.
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http://dx.doi.org/10.1186/s40246-023-00522-3 | DOI Listing |
Microb Genom
January 2025
Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.
Genes encoding OXA-48-like carbapenem-hydrolyzing enzymes are often located on plasmids and are abundant among carbapenemase-producing (CPE) worldwide. After a large plasmid-mediated outbreak in 2011, routine screening of patients at risk of CPE carriage on admission and every 7 days during hospitalization was implemented in a large hospital in the Netherlands. The objective of this study was to investigate the dynamics of the hospitals' 2011 outbreak-associated plasmid among CPE collected from 2011 to 2021.
View Article and Find Full Text PDFMicrobiol Spectr
January 2025
Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
The emergence of carbapenem-resistant (CRKP) poses a significant public health threat, particularly in low- and middle-income countries (LMICs) with limited surveillance and treatment options. This study examines the genetic diversity, resistance patterns, and transmission dynamics of 66 CRKP isolates recovered over 5 years (2015-2019) after the first case of CRKP was identified at a tertiary care hospital in Lima, Peru. Our findings reveal a shift from to as the dominant carbapenemase gene after 2017.
View Article and Find Full Text PDFmSystems
January 2025
Institute for Infection Prevention and Control, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
The surveillance of mobile genetic elements facilitating the spread of antimicrobial resistance genes has been challenging. Here, we tracked both clonal and plasmid transmission in colistin- and carbapenem-resistant using short- and long-read sequencing technologies. We observed three clonal transmissions, all containing Incompatibility group (Inc) L plasmids and New Delhi metallo-beta-lactamase , although not co-located on the same plasmid.
View Article and Find Full Text PDFGigaByte
December 2024
Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 904-0495, Onna-son, Okinawa, Japan.
The number of high-quality genomes is rapidly increasing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus .
View Article and Find Full Text PDFPlant Dis
January 2025
Microbiology, Campus Universitário s/n, Viçosa, Minas Gerais, Brazil, 36570-000;
The Ralstonia solanacearum Species Complex (RSSC) is the most significant plant pathogen group with a wide host range. It is genetically related but displays distinct biological features, such as restrictive geography occurrence. The RSSC comprises three species: Ralstonia pseudosolanacearum (phylotype I and III), Ralstonia solanacearum (phylotype IIA and IIB), and Ralstonia syzygii (phylotype IV) (Fegan and Prior 2005).
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