Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology

The infection cycle of Marteilia pararefringens in blue mussels Mytilus edulis in a heliothermic marine oyster lagoon in Norway

(2022) M Bøgwald et al.   DISEASES OF AQUATIC ORGANISMS

Temporal variations of Microsporidia diversity and discovery of new host–parasite interactions in a lake ecosystem

(2022) Marina Chauvet et al.   ENVIRONMENTAL MICROBIOLOGY

The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments

(2022) Quentin Mauvisseau et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Best practices in metabarcoding of fungi: From experimental design to results

(2022) Leho Tedersoo et al.   MOLECULAR ECOLOGY

Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions

(2022) Kaushar Kagzi et al.   Molecular Ecology Resources

Passive sampling of environmental DNA in aquatic environments using 3D‐printed hydroxyapatite samplers

(2022) Héloïse Verdier et al.   Molecular Ecology Resources

Systematic review and meta‐analysis: Water type and temperature affect environmental DNA decay

(2022) Philip D. Lamb et al.   Molecular Ecology Resources

Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment

(2022) Aaron Pomerantz et al.   Nature Protocols

Discovery of the parasite Marteilia cocosarum sp. nov. In common cockle (Cerastoderma edule) fisheries in Wales, UK and its comparison with Marteilia cochillia

(2022) Ilze Skujina et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

eDNAssay : A machine learning tool that accurately predicts qPCR cross‐amplification

(2022) John A. Kronenberger et al.   Molecular Ecology Resources

Using haematophagous fly blood meals to study the diversity of blood‐borne pathogens infecting wild mammals

(2022) Solomon Mwakasungula et al.   Molecular Ecology Resources

Genomic sequence capture of Plasmodium relictum in experimentally infected birds

(2022) Vincenzo A. Ellis et al.   Parasites & Vectors

A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method

(2022) Hang Cheng et al.   BRIEFINGS IN BIOINFORMATICS

Environmental DNA in human and veterinary parasitology - Current applications and future prospects for monitoring and control

(2022) M.E. Sengupta et al.   Food and Waterborne Parasitology

Biosensors Based on Isothermal DNA Amplification for Bacterial Detection in Food Safety and Environmental Monitoring

(2021) Sandra Leonardo et al.   SENSORS

Freshwater monitoring by nanopore sequencing

(2021) Lara Urban et al.   eLife

Network Analysis: Ten Years Shining Light on Host–Parasite Interactions

(2021) Rogini Runghen et al.   TRENDS IN PARASITOLOGY

The rise of the syndrome – sub‐optimal growth disorders in farmed shrimp

(2021) Rajendran Kooloth Valappil et al.   Reviews in Aquaculture

The Promise and Pitfalls of Environmental DNA and RNA Approaches for the Monitoring of Human and Animal Pathogens from Aquatic Sources

(2021) Jessica A Farrell et al.   BIOSCIENCE

High-throughput sequencing of the kelp Alaria (Phaeophyceae) reveals epi-endobiotic associations, including a likely phaeophycean parasite

(2021) Trevor T. Bringloe et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Beyond taxonomy: Validating functional inference approaches in the context of fish‐farm impact assessments

(2021) Olivier Laroche et al.   Molecular Ecology Resources

Environmental RNA: A Revolution in Ecological Resolution?

(2021) Matthew C. Yates et al.   TRENDS IN ECOLOGY & EVOLUTION

Early detection of salmonid alphavirus in seawater from marine farm sites of Atlantic salmon Salmo salar

(2021) LV Bernhardt et al.   DISEASES OF AQUATIC ORGANISMS

Trade‐offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on “Environmental DNA: What's behind the term?” by Pawlowski et al., (2020)

(2021) Naiara Rodriguez‐Ezpeleta et al.   MOLECULAR ECOLOGY

pr2‐primers: An 18S rRNA primer database for protists

(2021) Daniel Vaulot et al.   Molecular Ecology Resources

Improved high throughput protocol for targeting eukaryotic symbionts in metazoan and eDNA samples

(2021) Diana Minardi et al.   Molecular Ecology Resources

Seasonal host and ecological drivers may promote restricted water as a viral vector

(2021) Anisha Dayaram et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Non‐invasive surveys of mammalian viruses using environmental DNA

(2021) Niccolò Alfano et al.   Methods in Ecology and Evolution

Field-Deployable Recombinase Polymerase Amplification Assay for Specific, Sensitive and Rapid Detection of the US Select Agent and Toxigenic Bacterium, Rathayibacter toxicus

(2021) Mohammad Arif et al.   Biology-Basel

Extracellular DNA in Environmental Samples: Occurrence, Extraction, Quantification, and Impact on Microbial Biodiversity Assessment

(2021) Sakcham Bairoliya et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Parasite DNA detection in water samples enhances crayfish plague monitoring in asymptomatic invasive populations

(2021) Natalie Sieber et al.   BIOLOGICAL INVASIONS

High‐throughput sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds

(2021) Andrew G. Briscoe et al.   Molecular Ecology Resources

Moore swab performs equal to composite and outperforms grab sampling for SARS-CoV-2 monitoring in wastewater

(2021) Mohammad Rafiee et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Pathogens and disease vectors/hosts monitoring in aquatic environments: Potential of using eDNA/eRNA based approach

(2021) Mohan Amarasiri et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Bridging the gap: aquatic parasites in the One Health concept

(2021) Christian Selbach et al.   TRENDS IN PARASITOLOGY

Revealing the composition of the eukaryotic microbiome of oyster spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS)

(2021) Kevin Xu Zhong et al.   Microbiome

Pathogens co-transported with invasive non-native aquatic species: implications for risk analysis and legislation

(2021) Rachel Foster et al.   NeoBiota

Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity

(2021) Maria Frolova et al.   Life-Basel

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities

(2020) John Beaulaurier et al.   GENOME RESEARCH

Validation of environmental DNA sampling for determination of Ceratonova shasta (Cnidaria: Myxozoa) distribution in Plumas National Forest, CA

(2020) Christine A. Richey et al.   PARASITOLOGY RESEARCH

Are migratory waterfowl vectors of seagrass pathogens?

(2020) Damian Michael Menning et al.   Ecology and Evolution

Detection and Serotyping of Salmonella and Escherichia coli in Wheat Flour by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple Displacement Amplification and Real-Time Sequencing

(2020) Fereidoun Forghani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Nucleic acid amplification free biosensors for pathogen detection

(2020) Yanju Chen et al.   BIOSENSORS & BIOELECTRONICS

Rapid and accurate species identification for ecological studies and monitoring using CRISPR‐based SHERLOCK

(2020) Melinda R. Baerwald et al.   Molecular Ecology Resources

Effects of parasite concentrations on infection dynamics and proliferative kidney disease pathogenesis in brown trout ( Salmo trutta )

(2020) Nicole Strepparava et al.   Transboundary and Emerging Diseases

An Optimized Metabarcoding Method for Mimiviridae

(2020) Florian Prodinger et al.   Microorganisms

Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems

(2020) Luca Carraro et al.   Nature Communications

msocc: Fit and analyse computationally efficient multi‐scale occupancy models in r

(2020) Christian Stratton et al.   Methods in Ecology and Evolution

Pooled samples and eDNA-based detection can facilitate the “clean trade” of aquatic animals

(2020) Jesse L. Brunner   Scientific Reports

An eDNA/eRNA‐based approach to investigate the life cycle of non‐cultivable shellfish micro‐parasites: the case of Bonamia ostreae , a parasite of the European flat oyster Ostrea edulis

(2020) Nicolas Mérou et al.   Microbial Biotechnology

Validation of an eDNA-based method for the detection of wildlife pathogens in water

(2020) N Sieber et al.   DISEASES OF AQUATIC ORGANISMS

Survival of viral haemorrhagic septicaemia virus (VHSV) and infectious haematopoietic necrosis virus (IHNV) in the environment and dried on stainless steel

(2020) C. Joiner et al.   Transboundary and Emerging Diseases

iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

(2020) Zahir Ali et al.   VIRUS RESEARCH

A non-lethal method for detection of Bonamia ostreae in flat oyster (Ostrea edulis) using environmental DNA

(2020) Louise von Gersdorff Jørgensen et al.   Scientific Reports

Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana

(2019) Steve Hamner et al.   International Journal of Environmental Research and Public Health

A next generation sequencing approach for targeted Varroa destructor (Acari: Varroidae) mitochondrial DNA analysis based on honey derived environmental DNA

(2019) Valerio Joe Utzeri et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Ancient pathogen genomics as an emerging tool for infectious disease research

(2019) Maria A. Spyrou et al.   NATURE REVIEWS GENETICS

Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain

(2019) Carolyn E. Riddell et al.   PeerJ

The application of CRISPR‐Cas for single species identification from environmental DNA

(2019) Molly‐Ann Williams et al.   Molecular Ecology Resources

Improving risk assessment of the emergence of novel influenza A viruses by incorporating environmental surveillance

(2019) Kim M. Pepin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Can Environmental RNA Revolutionize Biodiversity Science?

(2019) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

The Pathobiome in Animal and Plant Diseases

(2019) David Bass et al.   TRENDS IN ECOLOGY & EVOLUTION

Can environmental DNA be used for aquatic biosecurity in the aquarium fish trade?

(2019) A. Trujillo-González et al.   BIOLOGICAL INVASIONS

Spatial and temporal disease dynamics of the parasite Hematodinium sp. in shore crabs, Carcinus maenas

(2019) Charlotte E. Davies et al.   Parasites & Vectors

Non-destructive method for detecting Aphanomyces astaci, the causative agent of crayfish plague, on the individual level

(2019) Dora Pavić et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Simultaneous detection of invasive signal crayfish, endangered white-clawed crayfish and the crayfish plague pathogen using environmental DNA

(2018) Chloe Victoria Robinson et al.   BIOLOGICAL CONSERVATION

Design standards for experimental and field studies to evaluate diagnostic accuracy of tests for infectious diseases in aquatic animals

(2018) E Laurin et al.   JOURNAL OF FISH DISEASES

Catching the fish with the worm: a case study on eDNA detection of the monogenean parasite Gyrodactylus salaris and two of its hosts, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)

(2018) Johannes C. Rusch et al.   Parasites & Vectors

Parasitism and the Biodiversity-Functioning Relationship

(2018) André Frainer et al.   TRENDS IN ECOLOGY & EVOLUTION

Opportunistic but Lethal: The Mystery of Paramoebae

(2018) Barbara F. Nowak et al.   TRENDS IN PARASITOLOGY

Usefulness of environmental DNA for detecting Schistosoma mansoni occurrence sites in Madagascar

(2018) Marcello Otake Sato et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Investigating diversity of pathogenic microbes in commercial bait trade water

(2018) Andrew R. Mahon et al.   PeerJ

eDNA-based crayfish plague detection as practical tool for biomonitoring and risk assessment of A. astaci-positive crayfish populations

(2018) Claudia Wittwer et al.   BIOLOGICAL INVASIONS

Smell of Infection: A Novel, Noninvasive Method for Detection of Fish Excretory-Secretory Proteins

(2018) Rebecca J. Pawluk et al.   JOURNAL OF PROTEOME RESEARCH

Seasonal dynamics and potential drivers of ranavirus epidemics in wood frog populations

(2018) Emily M. Hall et al.   OECOLOGIA

Estimating species distribution and abundance in river networks using environmental DNA

(2018) Luca Carraro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parasitic protozoan interactions with bacterial microbiome in a tropical fish farm

(2018) Giana Bastos Gomes et al.   AQUACULTURE

Detection and characterisation of haplosporidian parasites of the blue mussel Mytilus edulis, including description of the novel parasite Minchinia mytili n. sp.

(2018) GM Ward et al.   DISEASES OF AQUATIC ORGANISMS

Adsorption of norovirus and ostreid herpesvirus type 1 to polymer membranes for the development of passive samplers

(2017) F. Vincent-Hubert et al.   JOURNAL OF APPLIED MICROBIOLOGY

ednaoccupancy : An r package for multiscale occupancy modelling of environmental DNA data

(2017) Robert M. Dorazio et al.   Molecular Ecology Resources

Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest

(2017) Constanze Hoffmann et al.   NATURE

Persistence, impacts and environmental drivers of covert infections in invertebrate hosts

(2017) Inês Fontes et al.   Parasites & Vectors

Temperature-related parasite infection dynamics: the case of proliferative kidney disease of brown trout

(2017) NICOLE STREPPARAVA et al.   PARASITOLOGY

A novel copro-diagnostic molecular method for qualitative detection and identification of parasitic nematodes in amphibians and reptiles

(2017) Lucas G. Huggins et al.   PLoS One

Integrated field, laboratory, and theoretical study of PKD spread in a Swiss prealpine river

(2017) Luca Carraro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Equine behavioral enrichment toys as tools for non-invasive recovery of viral and host DNA

(2017) Peter A. Seeber et al.   ZOO BIOLOGY

Risk of waterborne virus spread - review of survival of relevant fish and crustacean viruses in the aquatic environment and implications for control measures

(2017) Birgit Oidtmann et al.   Reviews in Aquaculture

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

(2017) Joanne B. Emerson et al.   Microbiome

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

(2017) Frédéric Mahé et al.   Nature Ecology & Evolution

Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

(2017) Xavier Pochon et al.   PLoS One

Quantitative detection of viable helminth ova from raw wastewater, human feces, and environmental soil samples using novel PMA-qPCR methods

(2016) P. Gyawali et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Development and application of an eDNA method to detect and quantify a pathogenic parasite in aquatic ecosystems

(2015) J. R. Huver et al.   ECOLOGICAL APPLICATIONS

Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils

(2015) Glade Dlott et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Detection of viable bacterial pathogens in a drinking water source using propidium monoazide-quantitative PCR

(2015) Avid Banihashemi et al.   JOURNAL OF WATER SUPPLY RESEARCH AND TECHNOLOGY-AQUA

Diverse Applications of Environmental DNA Methods in Parasitology

(2015) David Bass et al.   TRENDS IN PARASITOLOGY

Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis

(2015) Mohammad Mohiuddin et al.   Frontiers in Microbiology

Mikrocytids Are a Broadly Distributed and Divergent Radiation of Parasites in Aquatic Invertebrates

(2014) Hanna Hartikainen et al.   CURRENT BIOLOGY

Quantification of viable Giardia cysts and Cryptosporidium oocysts in wastewater using propidium monoazide quantitative real-time PCR

(2014) José L. Alonso et al.   PARASITOLOGY RESEARCH

The Relationship between the Distribution of Common Carp and Their Environmental DNA in a Small Lake

(2014) Jessica J. Eichmiller et al.   PLoS One

Policy, phylogeny, and the parasite

(2014) Grant D. Stentiford et al.   TRENDS IN PARASITOLOGY

Contribution to the understanding of the cycle of the protozoan parasite Marteilia refringens

(2013) I. ARZUL et al.   PARASITOLOGY

Reservoirs of Cyprinid herpesvirus 3 (CyHV-3) DNA in sediments of natural lakes and ponds

(2011) Mie N. Honjo et al.   VETERINARY MICROBIOLOGY