Occurrence

FBIP: Cataloguing zoonotic tick-borne bacterial pathogen strain diversity in wild rodent species in rural South Africa

Latest version published by South African National Biodiversity Institute on 30 September 2020 South African National Biodiversity Institute
The aim of the study is, therefore, to catalogue the tick-borne bacterial pathogen strain diversity present in wild rodent species in the Mnisi community that could impact human health by using a metagenomics approach.
Publication date:
30 September 2020
License:
CC-BY 4.0

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 108 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

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Data as a DwC-A file download 108 records in English (7 kB) - Update frequency: unknown
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Metadata as an RTF file download in English (9 kB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Oosthuizen M (2020): FBIP: Cataloguing zoonotic tick-borne bacterial pathogen strain diversity in wild rodent species in rural South Africa. v1.0. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip2&v=1.0

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is South African National Biodiversity Institute. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: eb8708e4-5788-4c44-89c9-ef54e4423086.  South African National Biodiversity Institute publishes this resource, and is itself registered in GBIF as a data publisher endorsed by South African Biodiversity Information Facility.

Keywords

Occurrence; Specimen

Contacts

Who created the resource:

Marinda Oosthuizen
Professor
University of Pretoria
Faculty of Veterinary Science, Arnold Theiler Building, Room 2.20-3, Hatfied Campus, Soutpan Road (M35)
0110 Pretoria
Gauteng
ZA
0125298390

Who can answer questions about the resource:

Marinda Oosthuizen
Professor
University of Pretoria
Faculty of Veterinary Science, Arnold Theiler Building, Room 2.20-3, Hatfied Campus, Soutpan Road (M35)
0110 Pretoria
Gauteng
ZA
0125298390

Who filled in the metadata:

Marinda Oosthuizen
Professor
University of Pretoria
Faculty of Veterinary Science, Arnold Theiler Building, Room 2.20-3, Hatfied Campus, Soutpan Road (M35)
0110 Pretoria
Gauteng
ZA
0125298390

Who else was associated with the resource:

Distributor
Mahlatse Kgatla
FBIP Data Specialist
SANBI
2 Cussonia Avenue, Brummeria
0184 Pretoria
Gauteng
ZA
0128435196
http://fbip.co.za/contact/

Geographic Coverage

South Africa (Mpumalanga)

Bounding Coordinates South West [-24.827, 31.33], North East [-24.617, 32.371]

Taxonomic Coverage

Catalogue the tick-borne bacterial pathogen strain diversity present in wild rodent species

Genus  Anaplasma (Bacteria),  Mastomys (Rodents)

Temporal Coverage

Start Date / End Date 2012-04-01 / 2016-04-05

Project Data

The aim of the study is, therefore, to catalogue the tick-borne bacterial pathogen strain diversity present in wild rodent species in the Mnisi community that could impact human health by using a metagenomics approach.

Title FBIP: Cataloguing zoonotic tick-borne bacterial pathogen strain diversity in wild rodent species in rural South Africa
Identifier FBIS170330225236
Funding Foundational Biodiversity Information Programme
Study Area Description South Africa (Mpumalanga)

The personnel involved in the project:

Principal Investigator
Marinda Oosthuizen

Sampling Methods

-Ethical clearance through the Animal Ethics Committee (AEC) of the University of Pretoria was obtained (V046-14 and V030-14). -302 rodent blood samples across three habitat types (urban/periurban, communal rangelands, adjacent protected rangeland areas) in Mnisi has already been collected. Further Trapping will be done using Sherman-type traps; five sites will be pre-selected per habitat type; 50 traps will be used/site for up to 5 consecutive days. Traps will be baited with peanut butter, oats and marmite, checked twice/day. We aim to trap at least 15-20 individuals of 10 main species of rodents in each of the habitat types (n=600). Targeted species will be euthanized, blood will be collected immediately after euthanasian by cardiocentesis. Carcasses will be placed individually in sealed plastic bags and frozen.

Study Extent South Africa (Mpumalanga) in Mnisi
Quality Control NA

Method step description:

  1. -Apart from identifying rodent species by means of the Stuarts’ Field Guide to Mammals of Southern Africa (Stuart & Stuart, 2001), species verification will be done using sequence analysis of the mitochondrial gene Cytochrome Oxidase I (COI) -Catalogue the occurrence of the tick-borne bacterial pathogens present in wild rodent species by DNA analysis of the rodent microbiome. -Establish the genetic diversity of A. phagocytophilum strains by using specific gene markers.

Additional Metadata