Identification

Title

Cryptosporidium in upland water biota, United Kingdom (2012-2015)

Abstract

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

Resource type

dataset

Resource locator

https://catalogue.ceh.ac.uk/datastore/eidchub/84242834-dc78-49a6-83cb-951edac65d18

name: Download the data

description: Download a copy of this data

function: download

https://data-package.ceh.ac.uk/sd/84242834-dc78-49a6-83cb-951edac65d18.zip

name: Supporting information

description: Supporting information available to assist in re-use of this dataset

function: information

Unique resource identifier

code

https://catalogue.ceh.ac.uk/id/84242834-dc78-49a6-83cb-951edac65d18

codeSpace

doi:

Dataset language

eng

Spatial reference system

code identifying the spatial reference system

Classification of spatial data and services

Topic category

health

biota

Keywords

Keyword set

keyword value

Human Health and Safety

originating controlled vocabulary

title

GEMET - INSPIRE themes, version 1.0

reference date

date type

publication

effective date

2008-06-01

Keyword set

keyword value

Cryptosporidium

Fish

Invertebrates

Mammals

Biofilm

DURESS

Diversity of Upland Rivers for Ecosystem Service Sustainability

Geographic location

West bounding longitude

-6.452

East bounding longitude

1.768

North bounding latitude

55.812

South bounding latitude

49.864

Temporal reference

Temporal extent

Begin position

2012-05-01

End position

2015-07-31

Dataset reference date

date type

publication

effective date

2017-09-14

date type

creation

effective date

2015-07-31

Frequency of update

notPlanned

Quality and validity

Lineage

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.

Conformity

Conformity report

specification

title

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

reference date

date type

publication

effective date

2010-12-08

degree

explanation

Data format

name of format

Comma-separated values (CSV)

version of format

Constraints related to access and use

Constraint set

Limitations on public access

Constraint set

Limitations on public access

Constraint set

Limitations on public access

Constraint set

Limitations on public access

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

owner

Metadata on metadata

Metadata point of contact

organisation name

Environmental Information Data Centre

full postal address

Lancaster Environment Centre, Library Avenue, Bailrigg

Lancaster

LA1 4AP

email address

info@eidc.ac.uk

responsible party role

pointOfContact

Metadata date

2021-06-25T18:33:35

Metadata language

eng