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Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium
Publication Type: Peer reviewed scientific article Authors: Berbers, Bas; Vanneste, Kevin; Roosens, Nancy H. C. J.; Marchal, Kathleen; Pieter-Jan Ceyssens *; De Keersmaecker, Sigrid C. J. Source: Microbial Genomics, Volume 9, Issue 1 (2023) Health Topics: ...
Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities
Although few classifiers designed for long reads exist, they generally exhibit better performance. Our comprehensive benchmarking provides concrete recommendations, supported by publicly available code for ...
Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes
Publication Type: Peer reviewed scientific article Authors: Mathieu Gand; Navickaite, Indre; Bartsch, Lee-Julia; Grützke, Josephine; Overballe-Petersen, Søren; Rasmussen, Astrid; Otani, Saria; Michelacci, Valeria; Matamoros, Bosco Rodríguez; González-Zorn ...
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens.
long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which ...
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens.
long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which ...
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens.
long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which ...
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens.
with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may ...
Development of strain-level shotgun metagenomics approaches to detect and characterize microbiological contaminants in the context of food safety
compared to the conventional methods. The meat previously spiked with STEC was also used to investigate the difference between Illumina short reads or Oxford Nanopore Technologies (ONT) long reads ...
Using a combination of short and long read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum-beta-lactamases (ESBL) in clinical Shigella and Salmonella isolates in Belgium
Publication Type: Peer reviewed scientific article Authors: Bas Berbers; Kevin Vanneste; Nancy Roosens; Marchal,K.; Pieter-Jan Ceyssens; Sigrid C.J. De Keersmaecker Source: Microbial Genomics, Volume 9:000925, Number 23 (2023) Keywords: Antimicrobial resi ...
Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteriaAbstractBackgroundResultsConclusion
Keywords: DNA extraction HMW DNA Long-read Metagenomics Method evaluation nanopore Abstract: Background: Oxford Nanopore Technologies (ONT) offers an accessible platform for long-read sequencing, which ...