BGS Hosted Metadata
Cryptosporidium in upland water biota, United Kingdom (2012-2015)
These data show the presence/absence and identification of Cryptosporidium species from the results of a molecular survey of various upland river biota aquatic invertebrates, biofilms, mammal droppings and fish guts, gills and faeces. Samples were collected from various upland influenced sites from around Wales between 2012 and 2015 and were collected. Additionally, otter samples from UK-wide project were also tested. Sample collection was primarily undertaken by DURESS researchers at Cardiff University. Sample testing and analysis was performed at the Cryptosporidium Reference Unit, Public Health Wales Microbiology, Swansea. DNA was extracted using a commercially available kit (Gentra PureGene), Qiagen stool and tissue DNA kits for the fish and mammal samples. These data were collected to provide new information required for the production of a catchment pathogen model to inform ecosystems (dis)services analysis of land use change scenarios for the Diversity in Upland Rivers for Ecosystem Service Sustainability (DURESS) project, part of the NERC Biodiversity and Ecosystem Service Sustainability (BESS) BESS Programme. Full details about this dataset can be found at https://doi.org/10.5285/84242834-dc78-49a6-83cb-951edac65d18
Simple
- Date (Publication)
- 2017-09-14
- Date (Creation)
- 2015-07-31
- Citation identifier
- https://catalogue.ceh.ac.uk/id/84242834-dc78-49a6-83cb-951edac65d18
- Citation identifier
- doi: / 10.5285/84242834-dc78-49a6-83cb-951edac65d18
- Other citation details
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Chalmers, R.M., Robinson, G. (2017). Cryptosporidium in upland water biota, United Kingdom (2012-2015). NERC Environmental Information Data Centre 10.5285/84242834-dc78-49a6-83cb-951edac65d18
- Point of contact
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Organisation name Individual name Electronic mail address Role Public Health Wales Robinson, G.
Point of contact Public Health Wales Chalmers, R.M.
Author Public Health Wales Robinson, G.
Author NERC Environmental Information Data Centre Publisher NERC EDS Environmental Information Data Centre Custodian Public Health Wales Owner
- Maintenance and update frequency
- Not planned
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GEMET - INSPIRE themes, version 1.0
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Human Health and Safety
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GEMET - Concepts, version 4.1.3
- Keywords
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DURESS
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Diversity of Upland Rivers for Ecosystem Service Sustainability
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Cryptosporidium
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Biofilm
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- Access constraints
- Other restrictions
- Other constraints
- no limitations
- Use constraints
- Other restrictions
- Use constraints
- Other restrictions
- Other constraints
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© Public Health Wales
- Use constraints
- Other restrictions
- Other constraints
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If you reuse this data, you should cite: Chalmers, R.M., Robinson, G. (2017). Cryptosporidium in upland water biota, United Kingdom (2012-2015). NERC Environmental Information Data Centre https://doi.org/10.5285/84242834-dc78-49a6-83cb-951edac65d18
- Spatial representation type
- Text, table
- Language
- English
- Character set
- UTF8
- Topic category
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- Health
- Biota
- Begin date
- 2012-05-01
- End date
- 2015-07-31
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- Unique resource identifier
- OSGB 1936 / British National Grid
- Distribution format
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Name Version Comma-separated values (CSV)
- Distributor contact
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre
Distributor
- OnLine resource
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Protocol Linkage Name https://catalogue.ceh.ac.uk/datastore/eidchub/84242834-dc78-49a6-83cb-951edac65d18 Download the data
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/sd/84242834-dc78-49a6-83cb-951edac65d18.zip Supporting information
- Hierarchy level
- Dataset
- Other
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dataset
Conformance result
- Title
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Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services
- Date (Publication)
- 2010-12-08
- Statement
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Sample preparation methods included a newly developed means of testing whole aquatic invertebrates by grinding them up in Liquid Nitrogen and extracting DNA using a commercially available kit (Gentra PureGene), Qiagen stool and tissue DNA kits for the fish and mammal samples. Nested Image result for PCR (Polymerase chain reaction) PCR targeting Cryptosporidium small subunit rDNA was used to screen the samples for the presence of Cryptosporidium followed by identification of the species using sequencing or species-specific real-time PCRs. Where Cryptosporidium hominis or Cryptosporidium parvum were found, isolates were subtyped by sequencing part of a 60 kilodaltons (kDa) glycoprotein gene. Biota samples were collected by Cardiff University staff and transported to the Cryptosporidium Reference Unit, Swansea for testing. DNA from biofilm samples was extracted at Cardiff University. Invertebrates were pooled up to a maximum of 5 larvae per sample and ground in liquid nitrogen before DNA extracted using the Gentra PureGene DNA extraction kit (Qiagen). Fish gut and gill samples (collected from fish culled for food-web studies) were processed by extracting DNA using the QIAamp DNA Mini kit tissue protocol (Qiagen). Faecal samples from fish, collected by gently massaging the gut just above the anus and mammals, collected from the ground in the riparian zone on ad hoc basis had DNA extracted using QIAamp Fast DNA Stool Mini kit. Samples were screened for any Cryptosporidium DNA using a published nested polymerase chain reaction (PCR) targeting the small subunit rhibosomal DNA (rDNA). The presence of DNA from the two main Cryptosporidium species that cause human cryptosporidiosis (Cryptosporidium parvum and Cryptosporidium hominis) was also screened for using species-specific real-time PCRs targeting the Lib13 and A135 genes. Any C. hominis and C. parvum positive samples were subtyped by sequencing part of the 60kDa glycoprotein gene. The prevalence of Cryptosporidium was very low, which could indicate that the water in these upland rivers is not overly contaminated. However, caution must be taken as no water samples were tested as part of this project and the low prevalence may also be linked to the location of the sampling, the sample sizes, the analytical sensitivity of the testing method and/or the potential for the host species tested to actually carry or be infected by Cryptosporidium species. Results were entered into Excel spreadsheets and exported to comma separated value files for ingestion into the Environmental Information Data Centre.
Metadata
- File identifier
- 84242834-dc78-49a6-83cb-951edac65d18 XML
- Metadata language
- English
- Character set
- 8859 Part 1
- Hierarchy level
- Dataset
- Hierarchy level name
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dataset
- Date stamp
- 2025-11-13T16:26:59
- Metadata standard name
- UK GEMINI
- Metadata standard version
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2.3
- Metadata author
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre Point of contact
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