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Awesome Parasite

A curated list of host-parasite information

Here you can see meta information about this topic like the time we last updated this page, the original creator of the awesome list and a link to the original GitHub repository.

Last Update: Dec. 2, 2020, 12:07 p.m.

Thank you ecohealthalliance & contributors
View Topic on GitHub:
ecohealthalliance/awesome-parasite

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Databases

The CDC-curated arbovirus information including dates of first isolation and wildlife hosts.

A collective management database for museum specimens. See below for specific collections. Data includes locality and collection dates, and is downloadable for any registered accounts.

Extensive database with 8,510 host species associations of parasites with complex life cycles (acanthocephalans, cestodes, and nematodes). Includes life‐history data such as development time and body size for each life cycle stage of the parasites.

A database that pulls organism associations from NCBI sequences and PubMed. See database and brief analysis in Wardeh et al. 2015.

A species interaction repository that can be searched by 'parasite of', 'pathogen of', or 'host of'.

A database of the parasites of wild ungulates (artiodactyls and perissodactyls), carnivores, and primates.

A rodent virus database curated from Genbank with host traits.

A database of avian blood parasites from the Plasmodium, Haemoproteus and Leucocytozoon genera including select host and vector information. See database description by Bensch et al. 2009.

Collation of fish host and parasites datasets from several Canadain liminological sites, including information on prevalence and intensity. Part of a larger database of species interactions in food webs and plant relationships.

A database of parasitic worms extracted from the scientific literature maintained by London Natural History Museum. Compilation started in 1922 by Dr H.A. Baylis, with curation through 2003 by LNHM staff. Wells et al. 2018 provides a broad analysis of this database, and you can access data through the R package helminthR.

Conservation assessments of macroparasitic invertebrates.

A database with information on specific genes of fungal, Oomycete and bacterial pathogens that affect pathogenicity. Focused on agricultural and medical pathogens of importance.

Field data from the USAID PREDICT project 2008-2019, a global emerging virus surveillance program. This data is downloadable if you have a healthmap account.

A human-curated database of 12,212 host-pathogen associations: 2,595 bacterial and viral pathogens infecting 2,656 vertebrate host species across 90 host orders. It also contains a mitochondrial genome phylogeny for the host species. Currently, analysis is hosted on BioRxiv.

A synthesis of host-virus associations from genomes posted in NCBI/RefSeq and GenBank.

Museums & Collections

scientific institution with the largest helminth collection in Latin America with nearly 40,000 specimens. The institute also houses several other open-access catalogues of protozoa and medically important vector species.

Collection of mammalian ecto- and endo- parasites primarily focused on the Rocky Mountain and Great Plains regions of the United States. Accessible through Arctos.

Specimen collection focused "on the helminth parasites of mammals of the Nearctic and Neotropical regions stressing studies of the phylogeny and diversity of parasites of Rodentia, Marsupialia, Xenarthra, and Chiroptera." The archive site for the American Society of Parasitologists. Accessible through Arctos.

Swedish Museum with collection of >10,000 flatworms, >2,000 nematodes, and select other parasite groups. Accessible through GBIF.

Museum in Tokyo, Japan focused on human parasites with over 60,000 specimens. Data is not digitized, though the museum's founder, Dr. S. Yamaguti, described many of the specimens in 10 volumes of Systema Helminthum. Collections primarily from Japan, Indonesia and Hawaii.

Helminth collection with more than 30,000 occurences of helminths with particular focus in tropical regions. Accessible through GBIF.

Specimen collection of parasites amphibians, reptiles, birds, and mammals. Particular focus on parasites of small mammals in high altidude locations and Sevilleta Long Term Ecological Research Station in New Mexico, and parasites of seabirds in the artic and Antartica. Accessible through Arctos.

Nearly 70,000 vouchered specimens of mites from around the globe starting from 1864. Information includes host species, collection gps points, collection location (e.g. ear), and collection method. Can also be accessed through GBIF.

Downloadable excel document of nearly 50,000 specimens of helminths primarily from Australian vertebrates. Most specimens are Platyhelminths, Acanthocephala, or Nematoda from mammals, birds, or Elasmobranchii. Some specimens are included in the LNHM database and accessible through helminthR.

Museum focused on human food-borne outbreaks, with each exhibit being a different historical outbreak. Part of The Northwest Center for Foodborne Outbreak Management, Epidemiology, and Surveillance.

Specimen collection maintained by USDA that focuses on agriculturally important helminths and protozoans from North America. Accessible through Arctos.

Citizen Science Projects

This is a UK collaborative project between the Zoological Society of London (ZSL), the British Trust for Ornithology (BTO), Froglife and the Royal Society for the Protection of Birds (RSPB) that historically has been running since the 1980's (previously as Garden Bird Health initiative and Frog Mortality Project). Citizens can submit sickness and mortality reports, as well as animal wildlife samples, for wild birds, amphibians, reptiles, and hedgehogs.

A citizen science project running since 2006 to test adult monarch butterflies from the U.S. and Canada for the protozoan parasite Ophryocystis elektroscirrha. Participants submit spore samples collected from adult abdomems with tape for laboratory assessment at University of Georgia.

Reporting Systems

A web platform that provides infectious disease outbreak alerts for humans and animals.

An early warning of outbreaks of emerging and re-emerging diseases. Sources of information include media reports, official reports, online summaries, local observers, and others. EIDR-Connect parses ProMed reports into disease outbreak events, curated by disease experts.

An interactive map of human bloodborne or foodborne outbreaks in the past two years. Targeted to practitioners and clinicians.

Wildlife Health Information Sharing Partnership event reporting system managed by USGS National Wildlife Health Center. Events of North American wildlife mortality (death) and morbidity (illness) involving five or more individuals are reported.

The OIE archive of country alerts and regular reports of certain pathogens. They also have some nice interfaces to show disease distribution and timelines.

Taxonomy

Aggregation and synonymization of taxonomy for animals, bacteria, protozoa, and viruses that synthesizes 56 taxonomy sources.

The viral taxonomy authority with excellent archives and open reports.

Online database that provides taxonomic information for wild hosts. You can use the R package rredlist and the API to access the data directly.

The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases, both parasites and hosts.

Scientific Journals

AJTMH publishes a broad range of papers covering topics in tropical medicine. Their archive is open-access after a 12-month embargo.

Open-access scientific journal of the Polish Parasitological Society, formerly Wiadomości Parazytologiczne, that publishes issues quarterly. Open archives start from 2002.

Open-access journal of the European Food Safety Authority with yearly reports of food-borne outbreaks and cases of zoonotic agents and antibiotic resistance emergence in humans and animals.

Open-access scientific journal of the Slovak Academy of Sciences that publishes quarterly since 1959. Articles relate to human, veterinary and plant helminthology.

JWD provides many open-access articles on new parasite expansions or discoveries.

23 open access volumes (1971-2001) of the scientific journal of the Austrian Society for Tropical Medicine and Parasitology.

Open access journal associated with the Société Française de Parasitologie. Focuses on both animal and human parasites.

31 open-access volumes (1960-1998) of Parasitologia Hungarica, a scientific journal hosted by the Hungarian Natural History Museum.