A5039763047- SARS-CoV-2 detection and testing
- SARS-CoV-2 and COVID-19 Research
- Child Nutrition and Water Access
- Advanced biosensing and bioanalysis techniques
- Fecal contamination and water quality
- COVID-19 epidemiological studies
- Wastewater Treatment and Reuse
- Pharmaceutical and Antibiotic Environmental Impacts
- Vibrio bacteria research studies
- Antibiotic Resistance in Bacteria
- Biosensors and Analytical Detection
- Innovative Microfluidic and Catalytic Techniques Innovation
- Respiratory viral infections research
- Ecosystem dynamics and resilience
- Bacterial biofilms and quorum sensing
- Water-Energy-Food Nexus Studies
- COVID-19 Clinical Research Studies
- Evolutionary Game Theory and Cooperation
- Bacteriophages and microbial interactions
- Microfluidic and Capillary Electrophoresis Applications
- Food Security and Health in Diverse Populations
- Microbial Community Ecology and Physiology
- Gut microbiota and health
Swiss Federal Institute of Aquatic Science and Technology
2018-2024
Background: The effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, estimate the effectiveness of interventions. It describes average number new infections caused by single infectious person through time. To date, Re estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These temporarily biased when testing or reporting strategies change. Objectives: We show that dynamics severe...
Abstract The continuing emergence of SARS-CoV-2 variants concern and interest emphasizes the need for early detection epidemiological surveillance novel variants. We used genomic sequencing 122 wastewater samples from three locations in Switzerland to monitor local spread B.1.1.7 (Alpha), B.1.351 (Beta) P.1 (Gamma) at a population level. devised bioinformatics method named COJAC (Co-Occurrence adJusted Analysis Calling) that uses read pairs carrying multiple variant-specific signature...
Abstract The emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance genomic variants. Wastewater samples provide an opportunity to assess circulating viral lineages in community. We performed sequencing 122 wastewater from three locations Switzerland analyze B.1.1.7, B.1.351, P.1 variants on a population level. called variant-specific signature mutations monitored variant prevalence...
Abstract Background The effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, estimate the effectiveness of interventions. It describes average number new infections caused by single infectious person through time. To date, Re estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These temporarily biased when testing or reporting strategies change. Objectives We show that dynamics...
Soil may represent a direct source or act as an intermediary for the transmission of antibiotic-resistant and pathogenic Escherichia coli strains, particularly in low-income rural settings. Thus, determining risk factors associated with detection, growth, long-term survival E. soil environments is important public health. Here, we demonstrate that household soils Bangladesh are reservoirs potentially strains can support growth survival, defined physicochemical characteristics drivers this...
Abstract Surface-attached microbial communities constitute a vast amount of life on our planet. They contribute to all major biogeochemical cycles, provide essential services society and environment, have important effects human health disease. typically consist different interacting genotypes that arrange themselves non-randomly across space (referred hereafter as spatial self-organization). While self-organization is for the functioning, ecology, evolution these communities, underlying...
BackgroundThroughout the COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterised by increased transmissibility, virulence or reduced neutralisation antibodies obtained from prior infection vaccination. Tracking introduction transmission relies on sequencing, typically whole genome sequencing clinical samples. Wastewater surveillance is increasingly used to track spread through approaches.AimHere, we adapt apply a...
Container-based sanitation (CBS) within a comprehensive service system value chain offers low-cost option with potential for revenue generation but may increase microbial health risks to workers. This study assessed occupational exposure rotavirus and Shigella spp. during CBS urine collection subsequent struvite fertilizer production in eThekwini, South Africa. Primary data included high resolution sequences of hand-object contacts from annotated video measurement fecal contamination...
ABSTRACT Wastewater-based surveillance systems can track trends in multiple pathogens simultaneously by leveraging efficient, streamlined laboratory processing. In Switzerland, wastewater is conducted for fourteen locations representing 2.3 million people, or 26% of the national population, with simultaneous four respiratory pathogens. Trends diseases are tracked using a novel, six-plex digital PCR assay targeting Influenza A, B, Respiratory Syncytial Virus, and SARS-CoV-2 N1 N2 genes, as...
Abstract Increasing incidence of antibiotic resistance in clinical and environmental settings calls for increased scalability their surveillance. Current screening technologies are limited by the number samples genes that can easily be screened. We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection workflow capable highly-parallel bacterial isolates multiple target gene regions simultaneously. Here, dMLA is used simultaneous 1187...
ABSTRACT Throughout the global COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterized by increased transmissibility, virulence, or reduced neutralization antibodies obtained from prior infection vaccination. Tracking introduction transmission relies on sequencing, typically whole-genome sequencing clinical samples. Wastewater surveillance is increasingly used to track spread through approaches. Here, we adapt apply a...
Abstract Quantitative PCR (qPCR) and digital (dPCR) are applied for quantifying molecular targets in disease diagnostics, pathogen detection ecological monitoring. Uptake of dPCR is increasing due to its higher quantification accuracy relative qPCR which stems from independence standard curves increased resistance inhibitors. Throughput can be through multiplexing, allows simultaneous multiple targets. However, multiplexing with faces unique challenges qPCR. Here we describe the three-phase...
Abstract The COVID-19 pandemic has accelerated the development and adoption of wastewater-based epidemiology. Wastewater samples can provide genomic information for detecting assessing spread SARS-CoV-2 variants in communities estimating important epidemiological parameters such as growth advantage variant. However, despite demonstrated successes, data derived from wastewater suffers potential biases. Of particular concern are differential shedding profiles that different exhibit, because...
Abstract The COVID-19 pandemic has accelerated the development and adoption of wastewater-based epidemiology. Wastewater samples can provide genomic information for detecting assessing spread SARS-CoV-2 variants in communities estimating important epidemiological parameters such as growth advantage variant. However, despite demonstrated successes, data derived from wastewater suffers potential biases. Of particular concern are differential shedding profiles that different exhibit, because...
SUMMARY Background Water, sanitation, and hygiene (WASH) services have the potential to interrupt transmission of antimicrobial-resistant bacteria reduce need for antibiotics, thereby reducing selection resistance. However, evidence WASH impacts on antimicrobial resistance (AMR) is lacking. Methods We evaluated extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli ESBL-KESC ( Klebsiella spp ., Enterobacter Serratia spp., Citrobacter spp.) carriage in feces 479 Bangladeshi...