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Identification of Rodent Species That Infest Poultry Houses in Mafikeng, North West Province, South Africa

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Identification of Rodent Species That Infest Poultry Houses in Mafikeng, North West Province, South Africa Hindawi International Journal of Zoology Volume 2019, Article ID 1280578, 8 pages https://doi.org/10.1155/2019/1280578 Research Article Identification of Rodent Species That Infest Poultry Houses in Mafikeng, North West Province, South Africa Tsepo Ramatla ,1 Nthabiseng Mphuthi,1 Kutswa Gofaone,1 MoetiO.Taioe,2 Oriel M. M. Thekisoe,3 and Michelo Syakalima1 1 Department of Animal Health, School of Agriculture, Faculty of Natural and Agricultural Science, Mafkeng Campus, North West University, Private Bag X2046, Mmabatho, 2735, South Africa 2CenterforConservationScience,NationalZoologicalGardensofSouthAfrica,SouthAfricanNationalBiodiversityInstitute, PO Box 754, Pretoria, 0001, South Africa 3Unit for Environmental Sciences and Management, North West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa Correspondence should be addressed to Tsepo Ramatla; [email protected] Received 1 November 2018; Accepted 25 March 2019; Published 18 April 2019 Academic Editor: Hynek Burda Copyright © 2019 Tsepo Ramatla et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Rodents cause serious adverse efects on farm production due to destruction of food, contamination of feed, and circulation of diseases. Te extent of damage or the diseases spread will depend on the type of rodents that invade the farm. Tis study was conducted in order to fnd out the species of rodents that infest poultry farms around Mafkeng, North West Province of South Africa.TestudywaspartofabroaderprojectthatwasinvestigatingSalmonella vectors in the poultry farms around the province. Te study trapped 154 rodents from selected farms and used the Cytochrome oxidase subunit 1 (COI) and the Cytochrome b (Cyt- b) barcoding genes for species identifcation. Two rodent pest species, namely, Rattus rattus (the black rat) and Rattus tanezumi (the Asian Rat/Asian House Rat) were identifed. A total of 99 (64.3%) were identifed as Rattus rattus and 55 (35.7%) were Rattus tanezumi. Between the two target genes, Cyt-b gene was only able to identify 40 (25.97%) of the total samples while COI was more efcient and amplifed all the samples and thus was a better target gene for this kind of identifcation. Te two rat species identifed are known vectors of serious diseases; thus their presence should be regarded as an indication of high risk for diseases. Despite having been detected in the country before, fnding R. tanezumi as the second largest rat species in the area was unexpected since this species is known to be indigenous to Asia. 1. Introduction mulium. Te genus has some of the most adaptable rodents in theworldandmostofthemhavetheiroriginsinAsiawhere Rodents are relatively small mammals belonging to the order they migrated from to other parts of the world following Rodentia that includes porcupines, rats, mice, squirrels and the development of agriculture which provided food and marmots [1]. Tey are famously known to cause huge losses shelter for their survival. Teir intricate association with tostoredfood,crops,andpropertyandalsototransmitmany farms makes them very important vectors of pathogens some pathogens that cause diseases of humans and animals [2]. of which are zoonotic. For instance, the brown rat is famous as Te house mouse (Mus musculus), roof rats (Rattus rattus), a carrier of gastrointestinal helminths and mites responsible and the brown rat (R. norvegicus) are the three main species for Plague, the black rat is a carrier of trematode species, of rodents usually found worldwide [3]. Te genus Rattus is cestode species, and Salmonella spp., and the Asian rat is a one of the most common rodents found in poultry houses source of gastrointestinal helminths [4–7]. worldwide. Identifying the rodent species in a farm set-up is, Te genus Rattus consists mainly of Black rat (R. rattus), therefore, important in determining the specifc rat species’ Norway rat (R. norvegicus), Asian rat (R. tanezumi), and R. risktodiseaseaswellasotheradverseefectsinafarm. 2 International Journal of Zoology MAFIKENG Figure 1: Map of Africa showing the Mafkeng sampling area in the North West Province of South Africa. ∘ Unfortunately, rodents are not very easy to distinguish by Molema district (Figure 1). Te city lies between 25 and 28 C ∘ the routine methods available that use physical attributes and South of the Equator and 22 and 28 C longitude east of so molecular identifcation has been ofering the best option the Greenwich meridian. It shares an international border for identifcation. Molecular identifcation can be achieved with the Republic of Botswana in the North and is 260 km byanumberofmethodsbutDNAbarcoding,whichisa West of Johannesburg. Mafkeng is built on the open veld taxonomic method that uses a short genetic marker in an at an elevation of 1500m along the banks of the Upper organism’s DNA to identify it to a particular species, has been Molopo River. Climatic conditions of the province difer found easy and particularly efective for this purpose [8]. Te signifcantly from West to East. Te Western region receives target gene used for barcoding is the COI gene which is a very less than 300 mm of rain per annum, the central region common gene among species and has been fairly conserved around 550 mm per annum, while the Eastern and South over generations [9, 10]. Another gene commonly used is the Eastern regions receive over 600 mm per annum [12]. Cytochrome b gene which is also a very good discriminatory gene for species identifcation [8, 11]. Tese two genes were, 2.2. Collection of Samples. Alistofpoultryfarmsinthe therefore, used in this study to identify rodents in poultry Mafkeng area was compiled using the Department of Agri- houses from selected farms around Mafkeng, North West culture records. A few farms in the north, south, east, and Province of South Africa. west were randomly selected, the farmers were approached, and those that agreed were included in the study. Rodents 2. Materials and Methods were captured using Sherman rat traps [13] baited with peanut butter plus cheese and placed where the rats regularly 2.1. Study Area. Te study was carried out in Mafkeng, visit. Te traps were checked each morning during three the North West Province of South Africa. Te North West consecutive days. Te target number of rats was between Province is referred to as one of the biggest agricultural 150 and 200 based on previous studies [2, 5]. Live rats production areas in South Africa, with some of the largest were euthanized humanely using chloroform inhalation [14]. cattle herds in the country found at Stellaland (Vryburg) Teir surface was disinfected with 70% ethyl alcohol before and mixed crop farming land. Te province is also the dissection. Dissection of the abdominal cavity was done using second largest chicken producer in South Africa at 21.3% afer a surgical blade, a pair of forceps, and kidneys were harvested ∘ Western Cape with 21.9% (SAPA, 2014). Te province has four and placed in 4 C until processing. Extra care was taken in districts, namely, Bojanala Platinum, Ngaka Modiri Molema, order to avoid cross-contamination by using new disposable Dr Ruth Segomotsi Mompati, and Dr Kenneth Kaunda. Tis utensils like scalpels, forceps, petri-dishes, and gloves for study was conducted around Mafkeng in Te Ngaka Modiri each sample. Afer collecting the samples, carcasses were International Journal of Zoology 3 placed in carcass containers located within designated carcass for Biotechnology Information (NCBI) to identify sequences refrigerators/freezers in the post mortem room and then with high similarity (38). One direction sequencing was done. incinerated. 2.7. Phylogenetic Analysis. Gene sequences obtained from all 2.3. DNA Extraction. DNA was extracted from tissues (kid- positively tested amplicons were edited using BioEdit [17] to ney) using a QIAamp DNA Blood and Tissue Kit [Qiagen, remove any degenerate base pairs and then saved as FASTA Hilden, Germany (No. 69504)]. Te procedure was per- format. To confrm sequences obtained from CO1 and Cyt- formed according to protocols provided by the manufactur- b analysis, the nucleotide basic local alignment search tool ∘ ers. Te DNA extracted was stored at −80 Cuntilanalysisby (BLASTn) was used. Only gene sequences with 97% to 100% PCR. similarity match score were considered as signifcant. Te phylogenetic tree was constructed to illustrate the evolutionary relationships among Rattus spp. Multiple align- 2.4. Evaluation of the Quantity and Quality of Isolated DNA. ments of the sequences were carried out by MAFFT program Te amount of DNA extracted from the samples was deter- 6.864 against corresponding nucleotide sequences retrieved mined by spectrophotometry with a NanoDrop ND-1000 sys- from Gen-Bank. Evolutionary distance matrices were gen- tem (NanoDrop Technologies, Inc., Wilmington, DE, USA). erated [18]. Te aligned Cyt-b sequences were used to con- Te purity of DNA was determined spectrophotometrically struct a phylogenetic tree as implemented in the MEGA 7 from the ratio of absorbance at 260 and 280 nm (A260/A280). package and the neighbor-joining (NJ) and distance matrix A ratio of between 1.7 and 2 indicates an excellent quality of methods were used [18]. A bootstrap confdence analysis was DNA. performed with 1000 replicates. A putative chimeric sequence was identifed using the Chimera Buster 1.0 sofware. Manip- 2.5. PCR for Amplifcation
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