A5051395377- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- SARS-CoV-2 and COVID-19 Research
- Reproductive tract infections research
- Gut microbiota and health
- Antibiotic Resistance in Bacteria
- Bacteriophages and microbial interactions
- Mycobacterium research and diagnosis
- RNA and protein synthesis mechanisms
- SARS-CoV-2 detection and testing
- Legionella and Acanthamoeba research
- Antimicrobial Resistance in Staphylococcus
- COVID-19 Clinical Research Studies
- Microbial infections and disease research
- Parasitic Infections and Diagnostics
- Microbial Community Ecology and Physiology
- Plant and fungal interactions
- Cell Image Analysis Techniques
- Cystic Fibrosis Research Advances
- COVID-19 epidemiological studies
- Probiotics and Fermented Foods
- Diet and metabolism studies
- Bacterial Genetics and Biotechnology
- Animal Virus Infections Studies
- Machine Learning in Bioinformatics
University of Lausanne
2015-2024
University Hospital of Lausanne
2016-2023
Czech Academy of Sciences, Institute of Microbiology
2021-2023
Simon Fraser University
2017-2022
SIB Swiss Institute of Bioinformatics
2013-2017
Queensland University of Technology
2014
Institute of Microbiology
2013
IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions probable horizontal origin) in bacterial archaeal genomes. GIs disproportionately encode factors that enhance adaptability competitiveness microbe within niche, including virulence other medically or environmentally important adaptations. We report here release 4, with novel features to accommodate needs larger-scale...
The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on comparison closely related genomes. By utilizing comparative approaches gene level it is possible gain insights into core genes which represent set shared features organisms under study. Vice versa singleton can be identified elucidate specific properties an individual genome. Since initial publication, EDGAR platform...
Abstract Background The Amoebozoa constitute one of the primary divisions eukaryotes, encompassing taxa both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis a whole genome assembly Acanthamoeba castellanii ( Ac ) first representative from solitary free-living amoebozoan. Results encodes 15,455 compact intron-rich genes, significant number which are predicted to have arisen through inter-kingdom lateral gene transfer...
Summary Large viruses infecting algae or amoebae belong to the NucleoCytoplasmic DNA Viruses (NCLDV) and present genotypic phenotypic characteristics that have raised major interest among microbiologists. Here, we describe a new large virus discovered in Acanthamoeba castellanii co‐culture of an environmental sample. The virus, referred as Lausannevirus, has very limited host range, spp. but being unable infect other mammalian cell lines tested. Within A. , this icosahedral about 200 nm...
Administration of probiotics to premature newborns has been shown prevent necrotizing enterocolitis and reduce all-cause mortality.In our hospital, we documented 2 cases Bifidobacterium longum subspecies infantis bacteremia in receiving probiotics.By comparative genomics, confirmed that the strains isolated from each patient originated probiotics.
Abstract Motivation Genomic islands (GIs) are clusters of genes probable horizontal origin that play a major role in bacterial and archaeal genome evolution microbial adaptability. They high medical industrial interest, due to their enrichment virulence factors, some antimicrobial resistance adaptive metabolic pathways. The development more sensitive but precise prediction tools, using either sequence composition-based methods or comparative genomics, is needed as large-scale analyses...
The human pathogen Listeria monocytogenes is a large concern in the food industry where its continuous detection products has caused string of recalls North America and Europe. Most recognized for ability to grow foods during refrigerated storage, L. can also tolerate several other food-related stresses with some strains possessing higher levels tolerances than others. objective this study was use combination phenotypic analyses whole genome sequencing elucidate potential relationships...
In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering with no or reduced chlorine could potentially decrease the selection for antimicrobial resistant microorganisms, favor regrowth and result in changes populations. To evaluate feasibility of reduction local DWDS while ensuring safety, quality was measured over two months different networks, each them harboring sub-areas normal chlorine. Water remained good...
Growing evidence suggests that a novel member of the Chlamydiales order, Waddlia chondrophila, is potential agent miscarriage in humans and abortion ruminants. Due to lack genetic tools manipulate chlamydia, genomic analysis proving be most incisive tool stimulating investigations into biology these obligate intracellular bacteria. 454/Roche Solexa/Illumina technologies were thus used sequence assemble de novo full genome first representative Waddliaceae family, W. chondrophila. The bacteria...
Bacterial classification is a long-standing problem for taxonomists and species definition itself constantly debated among specialists. The of strict intracellular bacteria such as members the order Chlamydiales mainly relies on DNA- or protein-based phylogenetic reconstructions because these organisms exhibit few phenotypic differences are difficult to culture. availability full genome sequences allows comparison performance conserved protein reconstruct phylogeny. This approach permits...
Pseudomonas aeruginosa is an important opportunistic pathogen, especially in the context of infections cystic fibrosis (CF). In order to facilitate coordinated study this international reference panel P. isolates was assembled. Here we report genome sequencing and analysis 33 these 7 genomes further characterise panel. Core single nucleotide variant phylogeny demonstrated that strains are widely distributed amongst population. Common loss-of-function mutations reported as adaptive during CF...
Outbreaks of virulent and/or drug-resistant bacteria have a significant impact on human health and major economic consequences. Genomic islands (GIs; defined as clusters genes probable horizontal origin) are high interest because they disproportionately encode virulence factors, some antimicrobial-resistance (AMR) genes, other adaptations medical or environmental interest. While microbial genome sequencing has become rapid inexpensive, current computational methods for GI analysis not...
Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes Switzerland in 2020-the sixth largest effort globally. Using a representative subset these data, we estimated viral to their persistence over the course 2020. contrasted estimates with simple null models representing absence certain public health measures. show that...
The Swiss Pathogen Surveillance Platform (SPSP) is a shared secure surveillance platform between human and veterinary medicine, to also include environmental foodborne isolates. It enables rapid detailed transmission monitoring outbreak of pathogens using whole genome sequencing data associated metadata. features controlled access, complex dynamic queries, dedicated dashboards automated sharing with international repositories, providing actionable results for public health the vision improve...
With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete data may be sufficiently informative to derive pursued information. For emerging pathogens, i.e. newly identified lack release during closure stage is clearly medically counterproductive.We thus investigated feasibility dirty...
Summary P seudomonas knackmussii B 13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery prologue for subsequent characterization of numerous bacterial metabolic pathways, genetic and biochemical studies, which spurred ideas pollutant bioremediation. In this study, we determined complete genome sequence using next generation sequencing technologies optical mapping. Genome annotation indicated has a variety pathways degrading...
Abstract Whole genome sequencing (WGS) is a powerful tool for public health infectious disease investigations owing to its higher resolution, greater efficiency, and cost-effectiveness over traditional genotyping methods. Implementation of WGS in routine microbiology laboratories impeded by lack user-friendly automated semi-automated pipelines, restrictive jurisdictional data sharing policies, the proliferation non-interoperable analytical reporting systems. To address these issues, we...
Although many laboratories worldwide have developed their sequencing capacities in response to the need for SARS-CoV-2 genome-based surveillance of variants, only a few reported some quality criteria ensure sequence before lineage assignment and submission public databases. Hence, we aimed here provide simple control prevent erroneous interpretation low-quality or contaminated data. We retrospectively investigated 647 genomes obtained over 10 tiled amplicons runs. extracted 26 potentially...
The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) Brazil has led to definition variants concern (VoCs) recommendations for lineage specific surveillance. In Switzerland, during last weeks December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological microbiological definitions. January 2021, validated implemented an N501Y-specific PCR...
Genotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in monitoring viral evolution and transmission during the pandemic. The quality sequence data obtained from these genotyping efforts depends on several factors, including quantity/integrity input material, technology, laboratory-specific implementation. current lack guidelines for SARS-CoV-2 leads to inclusion error-containing genome sequences genomic epidemiology studies. We aimed establish...