A5101919626- Genomics and Phylogenetic Studies
- Tuberculosis Research and Epidemiology
- Viral gastroenteritis research and epidemiology
- Mycobacterium research and diagnosis
- SARS-CoV-2 and COVID-19 Research
- Bacterial Identification and Susceptibility Testing
- Animal Virus Infections Studies
- Viral Infections and Immunology Research
- Infective Endocarditis Diagnosis and Management
- Plant Virus Research Studies
- RNA and protein synthesis mechanisms
- Metabolism, Diabetes, and Cancer
- Respiratory viral infections research
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- Bacteriophages and microbial interactions
- Pancreatic function and diabetes
- Growth Hormone and Insulin-like Growth Factors
- Pneumonia and Respiratory Infections
- Antimicrobial Resistance in Staphylococcus
- Cancer Genomics and Diagnostics
University of Bern
2019-2025
Infectious Diseases Institute
2025
National Institutes of Health
1994
National Institute of Diabetes and Digestive and Kidney Diseases
1994
Shotgun metagenomics using next generation sequencing (NGS) is a promising technique to analyze both DNA and RNA microbial material from patient samples. Mostly used in research setting, it now increasingly being the clinical realm as well, notably support diagnosis of viral infections, thereby calling for quality control implementation ring trials (RT) benchmark pipelines ensure comparable results. The Swiss NGS virology community therefore decided conduct RT 2018, order current metagenomic...
The SARS-CoV-2 Delta variant, corresponding to the Pangolin lineage B.1.617.2, was first detected in India July 2020 and rapidly became dominant worldwide. ARTIC v3 protocol for whole-genome sequencing, which relies on a large number of PCR primers, among available early pandemic, but may be prone coverage dropouts that result incomplete genome sequences. A new set primers (v4) designed circumvent this issue June 2021. In study, we investigated whether sequencing community adopted sets...
ABSTRACT Rapid and comprehensive drug susceptibility testing (DST) is essential for diagnosing treating drug-resistant tuberculosis effectively, next-generation sequencing can be an effective genotypic DST method. We implemented evaluated the performance of a nanopore targeted assay, called Tuberculosis Drug Resistance Test (TBDR, Oxford Nanopore Diagnostics, Ltd., United Kingdom), which predicts resistance to 16 TB drugs, at South African reference laboratory district diagnostic in Zambia....
Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden disease with a broad spectrum symptoms. In routine diagnostic laboratories, enteroviruses identified PCR-based methods, often combined partial sequencing for genotyping. this proof-of-principle study, we assessed direct (DRS) using nanopore technology fast whole-genome directly from clinical samples. The approach was complemented the corresponding viral cDNA via Illumina MiSeq...
This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic Molecular Diagnostics (ESGMD) Swiss (SSM), aims to build a framework between laboratories in order improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out 15 clinical that had free choice...
Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) isolates can be used to get an accurate diagnosis, guide clinical decision making, control (TB) and for outbreak investigations. We evaluated the performance long-read (LR) and/or short-read (SR) anti-TB drug-resistance prediction using TBProfiler Mykrobe tools, fraction genome recovery, assembly accuracies robustness two typing approaches based on core-genome SNP (cgSNP) multi-locus sequence (cgMLST). Most discrepancies...
Amplicon sequencing of the 16S rRNA gene is commonly used for identification bacterial isolates in diagnostic laboratories and mostly relies on Sanger method. The latter, however, suffers from a number limitations, with most significant being inability to resolve mixed amplicons when closely related species are coamplified culture. This often leads either increased turnaround time or absence usable sequence data. Short-read next-generation (NGS) technologies could solve amplicon issue but...
Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given large palette reagents bioinformatics tools, Swiss bacteriology community decided conduct a ring trial (RT) foster harmonization NGS-based bacterial typing. The RT aimed at assessing methicillin-susceptible Staphylococcus aureus strain...
Abstract Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden disease with a broad spectrum symptoms. In routine diagnostic laboratories, those identified PCR based methods, often combined partial sequencing for genotyping. this proof-of-principle study, we assessed direct (DRS) using nanopore technology fast whole-genome directly from clinical samples. Results the approach were complemented obtained corresponding viral cDNA via Illumina...
Abstract Amplicon sequencing of 16S rRNA gene is commonly used for the identification bacterial isolates in diagnostic laboratories, and mostly relies on Sanger method. The latter, however, suffers from a number limitations with most significant being inability to resolve mixed amplicons when closely related species are co-amplified culture. This often leads either increased turnover time or absence usable sequence data. Short-read NGS technologies could address amplicon issue, but would...
Abstract We are reporting on the observation of a large, under-sequenced region S gene SARS-CoV2 Delta variant genomes, identified in sequences originating from various sequencing centres worldwide (e.g. USA, India, England, Switzerland, France, Germany). This poorly sequenced was early phases spread and phenomenon is still ongoing. As many commonly-used protocols rely amplicon-based procedures, we investigated likely origin issue. established its biological as resulting mutations viral...