Zoologia (Curitiba), Journal Year: 2024, Volume and Issue: 41
Published: Jan. 1, 2024
Language: Английский
Antibiotics, Journal Year: 2023, Volume and Issue: 12(11), P. 1580 - 1580
Published: Oct. 30, 2023
Recent advancements in sequencing technology and data analytics have led to a transformative era pathogen detection typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming standard for analysis control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into epidemiology emergence antimicrobial-resistant strains. Antimicrobial resistance (AMR) is pressing global public health issue. While clinical laboratories traditionally relied on culture-based antimicrobial susceptibility testing, integration AMR holds immense promise. Genomic-based furnish swift, consistent, highly accurate predictions phenotypes specific strains or populations, all while contributing invaluable surveillance. Moreover, genome assumes pivotal role investigation hospital outbreaks. It aids identification infection sources, unveils genetic connections among isolates, informs strategies The One Health initiative, with its focus intricate interconnectedness humans, animals, environment, seeks develop comprehensive approaches disease surveillance, control, prevention. When integrated epidemiological systems, forecast expansion bacterial populations species transmissions. Consequently, this provides evolution relationships pathogens, hosts, environment.
Language: Английский
Citations
34
Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)
Published: June 28, 2024
Abstract Real-time genomics through nanopore sequencing holds the promise of fast antibiotic resistance prediction directly in clinical setting. However, concerns about accuracy genomics-based predictions persist, particularly when compared to traditional, clinically established diagnostic methods. Here, we leverage case a multi-drug resistant Klebsiella pneumoniae infection demonstrate how real-time can enhance profiling complex scenarios. Our results show that unlike diagnostics, data analysis accurately detect low-abundance plasmid-mediated resistance, which often remains undetected by conventional This capability has direct implications for practice, where such “hidden” profiles critically influence treatment decisions. Consequently, rapid, situ application significant improving decision-making and patient outcomes.
Language: Английский
Citations
18
npj Biodiversity, Journal Year: 2024, Volume and Issue: 3(1)
Published: Sept. 17, 2024
A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction have information available. In 2018, scientists across the world united under Earth BioGenome Project (EBP), aiming produce high-quality reference genomes containing ~1.5 million recognized species. As European node EBP, Reference Genome Atlas (ERGA) sought implement new decentralised, equitable and inclusive model for producing genomes. For this, ERGA launched Pilot establishing first distributed genome production infrastructure testing it on 98 from 33 countries. Here we outline explore its effectiveness scaling production, whilst considering equity inclusion. The outcomes lessons learned provide solid foundation while offering key learnings other transnational, national resource projects EBP.
Language: Английский
Citations
13
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: March 2, 2024
ABSTRACT Metagenomics has enabled the rapid, unbiased detection of microbes across diverse sample types, leading to exciting discoveries in infectious disease, microbiome, and viral research. However, analysis metagenomic data is often complex computationally resource-intensive. CZ ID a free, cloud-based genomic platform that enables researchers detect using data, identify antimicrobial resistance genes, generate consensus genomes. With ID, can upload raw sequencing find matches NCBI databases, get per-sample taxon metrics, perform variety analyses visualizations. The intuitive interface interactive visualizations make exploring interpreting results simple. Here, we describe expansion with new long read mNGS pipeline accepts Oxford Nanopore generated ( czid.org ). We report benchmarking standard mock microbial community dataset against Kraken2, widely used tool for analysis. evaluated ability this divergent viruses simulated datasets. also assessed limit spiked-in virus cell line as proxy clinical samples. Lastly, detected known novel previously characterized disease vector (mosquitoes)
Language: Английский
Citations
10
Molecular Systems Biology, Journal Year: 2023, Volume and Issue: 19(8)
Published: June 16, 2023
The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to future relationship planet. While the concept One Health describes how human health is inextricably linked health, many these complex interdependencies are still not well-understood. Here, we describe advent real-time genomic analyses can benefit it enable timely, in-depth ecosystem assessments. We introduce nanopore sequencing as only disruptive technology that currently allows for already being used worldwide improve accessibility versatility sequencing. showcase studies on zoonotic disease, food security, microbiome, emerging pathogens, their antimicrobial resistances, itself - from resource creation wildlife conservation monitoring biodiversity, invasive species, trafficking. stress why equitable access genomics in context will be paramount discuss related practical, legal, ethical limitations.
Language: Английский
Citations
23
Healthcare, Journal Year: 2024, Volume and Issue: 12(9), P. 922 - 922
Published: April 29, 2024
When we take into account how the boundaries between human, animal, and environmental health are inextricably linked increasingly intertwined, it comes as no surprise that One Health approach has assumed an unprecedented level of importance over past decade [...]
Language: Английский
Citations
6
ISME Communications, Journal Year: 2024, Volume and Issue: 4(1)
Published: Jan. 1, 2024
While the air microbiome and its diversity are essential for human health ecosystem resilience, comprehensive microbial monitoring has remained rare, so that little is known about microbiome's composition, distribution, or functionality. Here we show nanopore sequencing-based metagenomics can robustly assess in combination with active sampling through liquid impingement tailored computational analysis. We provide fast portable laboratory approaches profiling, which leverage to taxonomic composition of core a controlled greenhouse environment natural outdoor environment. long-read sequencing resolve species-level annotations specific functions de novo metagenomic assemblies despite low amount fragmented DNA used as an input sequencing. then apply our pipeline variability urban microbiome, using Barcelona, Spain, example; this randomized experiment gives first insights into presence highly stable location-specific microbiomes within city's boundaries, showcases robust assessments be achieved automatable, fast, technology.
Language: Английский
Citations
6
International Journal of Environmental Research and Public Health, Journal Year: 2024, Volume and Issue: 21(10), P. 1337 - 1337
Published: Oct. 9, 2024
The One Health concept underscores the interconnectedness of human, animal, and environmental health, necessitating an integrated, transdisciplinary approach to tackle contemporary health challenges. This perspective paper explores pivotal role genomics bioinformatics in advancing initiatives. By leveraging genomic technologies tools, researchers can decode complex biological data, enabling comprehensive insights into pathogen evolution, transmission dynamics, host-pathogen interactions across species environments (or ecosystems). These are crucial for predicting mitigating zoonotic disease outbreaks, understanding antimicrobial resistance patterns, developing targeted interventions promotion prevention. Furthermore, integrating data with epidemiological information enhances precision public responses. Here we discuss case studies demonstrating successful applications contexts, such as including integration, standardization, ethical considerations research. fostering collaboration among geneticists, bioinformaticians, epidemiologists, zoologists, scientists, harness full potential safeguard global health. necessity continued investment interdisciplinary education, research infrastructure, policy frameworks effectively employ these service a healthier planet.
Language: Английский
Citations
6
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: Sept. 28, 2023
A global genome database of all Earth's species diversity could be a treasure trove scientific discoveries. However, regardless the major advances in sequencing technologies, only tiny fraction have genomic information available. To contribute to more complete planetary database, scientists and institutions across world united under Earth BioGenome Project (EBP), which plans sequence assemble high-quality reference genomes for ~1.5 million recognized eukaryotic through stepwise phased approach. As initiative transitions into Phase II, where 150,000 are sequenced just four years, worldwide participation project will fundamental success. European node EBP, Reference Genome Atlas (ERGA) seeks implement new decentralised, accessible, equitable inclusive model producing genomes, inform EBP as it scales. embark on this mission, ERGA launched Pilot establish network Europe develop test first infrastructure its kind coordinated distributed production 98 from sample providers 34 countries. Here we outline process challenges faced during development pilot resources, explore effectiveness approach terms production, considering also equity inclusion. The outcomes lessons learned provide solid foundation while offering key learnings other transnational national resource projects.
Language: Английский
Citations
12
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: March 2, 2024
Abstract Avian influenza virus (AIV) currently causes a panzootic with extensive mortality in wild birds, poultry, and mammals, thus posing major threat to global health underscoring the need for efficient monitoring of its distribution evolution. Here, we utilized well-defined AIV strain systematically investigate characterization through rapid, portable nanopore sequencing by (i) benchmarking performance fully RNA extraction viral detection; (ii) comparing latest DNA approaches in-depth profiling; (iii) evaluating various computational pipelines consensus sequence creation phylogenetic analysis. Our results show that RNA-specific nanopores can accurately genomically profile from native while additionally detecting epigenetic modifications. We further identified an optimal laboratory bioinformatic pipeline reconstructing genomes data at rarefaction thresholds, which validated application real-world environmental samples livestock. Author Summary tested portable, easy-to-use technology obtain more information about potentially zoonotic avian virus, or AIV. has spread globally via migratory paths endangers domestic human populations given past evidence infections different animal species. here used novel genomic is based on explore virus; established optimized ways creating genome either directly converted DNA. then applied protocol dust were collected duck farm France during outbreak. showed able use resulting reconstruct relationship between responsible outbreak previously detected Altogether, how support surveillance pathogens recreating better understand evolution transmission these pathogens.
Language: Английский
Citations
5