Publications tagged "Water testing"
Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing
Background Wastewater surveillance has been proposed as an epidemiological tool to define the prevalence and evolution of the SARS-CoV-2 epidemics. However, most implemented SARS-CoV-2 wastewater su...
Phenotypic characterization and whole-genome analysis of a novel bacteriophage HCF1 infecting citrobacter amalonaticus and C. freundii
Citrobacter species often occur in sewage, food, soil, wastewater, and in the intestinal tract of animals and humans. Citrobacter spp. cause urinary tract infections (UTIs) and infantile meningitis ...
Haploflow: Strain-resolved de novo assembly of viral genomes
In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembl...
Genomic network analysis of an environmental and livestock IncF plasmid population
IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacteriacea...
Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
Escherichia coli and other Enterobacteriaceae are highly diverse species with ‘open’ pangenomes, where genes move intra- and inter-species via horizontal gene transfer. These species can cause clini...
Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in a Dutch drinking water treatment plant
Elevated concentrations of ammonium and methane in groundwater can cause severe problems during drinking water production. To avoid their accumulation, raw water in the Netherlands, and many other c...
Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter
A total of four strains of the ‘environmental superbug’ Pedobacter isolated from sludge produced at Norwegian drinking water treatment plants, were characterized by whole genome sequencing and antib...
Metagenomic characterization of a harmful algal bloom using nanopore sequencing
Water bodies around the world are increasingly threatened by harmful algal blooms (HABs) under current trends of rising water temperature and nutrient load. Metagenomic characterization of HABs can...
The wastewater microbiome: A novel insight for COVID-19 surveillance
Wastewater-Based Epidemiology is a tool to face and mitigate COVID-19 outbreaks by evaluating conditions in a specific community. This study aimed to analyze the microbiome profiles using nanopore ...
Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function
Background Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic ...
A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality
Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around th...
Metagenomic profiling of microbial pathogens in the Little Bighorn River, Montana
Metagenomic sequencing and analysis were performed to identify potential microbial pathogens in the Little Bighorn River. Rapid, real-time sequencing was achieved using the portable MinION platform,...
Liquid co-substrates repower sewage microbiomes
A range of parameters are known to shape the methanogenic communities of biogas-producing digesters and to strongly influence the amount of biogas produced. In this work, liquid and solid fractions ...
Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing
Dissemination of carbapenem resistance among pathogenic Gram-negative bacteria is a looming medical emergency. Efficient spread of resistance within and between bacterial species is facilitated by m...
Yaniv Erlich: A vision for Ubiquitous Sequencing
Yaniv Erlich outlines his vision for a future where “the next goal of the revolution can be ushered in by the advent of sequencing sensors – miniaturized sequencing devices that are manufactured for...