Miguel A. Terrazos Miani
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View article: Evaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak‐associated bacterial isolates in the clinical setting
Evaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak‐associated bacterial isolates in the clinical setting Open
Accurate and efficient whole-genome sequencing (WGS) is crucial for clinical diagnostics and surveillance of bacterial infections. Here, we investigate the potential of a new Oxford Nanopore Technologies (ONT) workflow for WGS of clinicall…
View article: NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples
NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples Open
Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput se…
View article: NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A rapid, PCR-free method for whole genome sequencing of pathogens in clinical samples
NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A rapid, PCR-free method for whole genome sequencing of pathogens in clinical samples Open
Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput se…
View article: Genome Sequences of Rare Human Enterovirus Genotypes Recovered from Clinical Respiratory Samples in Bern, Switzerland
Genome Sequences of Rare Human Enterovirus Genotypes Recovered from Clinical Respiratory Samples in Bern, Switzerland Open
We report on genomic sequences of human enteroviruses (EVs) that were identified in respiratory samples in Bern, Switzerland, in 2018 and 2019. Besides providing sequences for coxsackievirus A2, echovirus 11, and echovirus 30, we determine…
View article: Investigating the Extent of Primer Dropout in SARS-CoV-2 Genome Sequences During the Early Circulation of Delta Variants
Investigating the Extent of Primer Dropout in SARS-CoV-2 Genome Sequences During the Early Circulation of Delta Variants Open
The SARS-CoV-2 Delta variant, corresponding to the Pangolin lineage B.1.617.2, was first detected in India in July 2020 and rapidly became dominant worldwide. The ARTIC v3 protocol for SARS-CoV-2 whole-genome sequencing, which relies on a …
View article: Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis
Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis Open
Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) isolates can be used to get an accurate diagnosis, to guide clinical decision making, to control tuberculosis (TB) and for outbreak investigations. We evaluated the performa…
View article: Investigating the biological and technical origins of unknown bases in the S region of the SARS-CoV-2 Delta variant genome sequences
Investigating the biological and technical origins of unknown bases in the S region of the SARS-CoV-2 Delta variant genome sequences Open
We are reporting on the observation of a large, under-sequenced region of the S gene of the SARS-CoV2 Delta variant genomes, identified in sequences originating from various sequencing centres worldwide (e.g. USA, India, England, Switzerla…
View article: Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis
Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis Open
Supplementary material for 'Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis'
View article: Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing
Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing Open
Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods…
View article: Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing
Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing Open
Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, those viruses are identified by PCR based methods…
View article: A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing
A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing Open
Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations,…
View article: A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing
A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing Open
Amplicon sequencing of 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories, and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations wit…
View article: Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells
Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells Open
Enteroviruses affect millions of people worldwide and are of significant clinical importance. The standard method for enterovirus identification and genotyping still relies on Sanger sequencing of short diagnostic amplicons. In this study,…
View article: Innate immunity restricts Citrobacter rodentium A/E pathogenesis initiation to an early window of opportunity
Innate immunity restricts Citrobacter rodentium A/E pathogenesis initiation to an early window of opportunity Open
Citrobacter rodentium infection is a mouse model for the important human diarrheal infection caused by enteropathogenic E. coli (EPEC). The pathogenesis of both species is very similar and depends on their unique ability to form intimately…
View article: Functional Intestinal Bile Acid 7α-Dehydroxylation by Clostridium scindens Associated with Protection from Clostridium difficile Infection in a Gnotobiotic Mouse Model
Functional Intestinal Bile Acid 7α-Dehydroxylation by Clostridium scindens Associated with Protection from Clostridium difficile Infection in a Gnotobiotic Mouse Model Open
Bile acids, important mediators of lipid absorption, also act as hormone-like regulators and as antimicrobial molecules. In all these functions their potency is modulated by a variety of chemical modifications catalyzed by bacteria of the …