To show that a strain of became resistant to carbapenems by interspecies transfer of a plasmid using long-read sequencing. Whole genome sequencing of the four isolates was done using Illumina Hiseq, while the plasmid was reconstructed using the MinION sequencer. The resistome was identified with ResFinder. Whole genome sequencing and long-read sequencing showed that all isolates carried a VIM-1 gene located on a 165 kb incA/C plasmid. ResFinder confirmed that the resistome of the plasmid, comprising 13 resistance genes, was identical within all isolates. Long-read sequencing using the MinION successfully reconstructed a plasmid that was identical in all isolates, providing evidence for horizontal gene transfer of this VIM-1 gene carrying plasmid within the patient.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.2217/fmb-2019-0091 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping.
NAR Genom Bioinform
March 2025
School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel.
Carcinogenesis often involves significant alterations in the cancer genome, marked by large structural variants (SVs) and copy number variations (CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping (OGM) and nanopore sequencing [Oxford Nanopore Technologies (ONT)] bridge this resolution gap and offer enhanced performance for cytogenetic applications.
View Article and Find Full Text PDFStructural polymorphism and diversity of human segmental duplications.
Nat Genet
January 2025
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Segmental duplications (SDs) contribute significantly to human disease, evolution and diversity but have been difficult to resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 human genome assemblies (from 85 samples representing 38 Africans and 47 non-Africans) in which the majority of autosomal SDs are fully resolved using long-read sequence assembly. Excluding the acrocentric short arms and sex chromosomes, we identify 173.
View Article and Find Full Text PDFProfiling the epigenome using long-read sequencing.
Nat Genet
January 2025
Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Spain.
The advent of single-molecule, long-read sequencing (LRS) technologies by Oxford Nanopore Technologies and Pacific Biosciences has revolutionized genomics, transcriptomics and, more recently, epigenomics research. These technologies offer distinct advantages, including the direct detection of methylated DNA and simultaneous assessment of DNA sequences spanning multiple kilobases along with their modifications at the single-molecule level. This has enabled the development of new assays for analyzing chromatin states and made it possible to integrate data for DNA methylation, chromatin accessibility, transcription factor binding and histone modifications, thereby facilitating comprehensive epigenomic profiling.
View Article and Find Full Text PDFPangenome graphs and their applications in biodiversity genomics.
Nat Genet
January 2025
The Vertebrate Genome Laboratory, New York, NY, USA.
Complete datasets of genetic variants are key to biodiversity genomic studies. Long-read sequencing technologies allow the routine assembly of highly contiguous, haplotype-resolved reference genomes. However, even when complete, reference genomes from a single individual may bias downstream analyses and fail to adequately represent genetic diversity within a population or species.
View Article and Find Full Text PDFSmall variant benchmark from a complete assembly of X and Y chromosomes.
Nat Commun
January 2025
Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, USA.
The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to evaluate variant detection on male sex chromosomes X and Y, we create a small variant benchmark set with 111,725 variants for the Genome in a Bottle HG002 reference material. We develop an active evaluation approach to demonstrate the benchmark set reliably identifies errors in challenging genomic regions and across short and long read callsets.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!