Dataset Information

Anaplasma phagocytophilum and Other Anaplasma spp. in Various Hosts in the Mnisi Community, Mpumalanga Province, South Africa.

ABSTRACT: DNA samples from 74 patients with non-malarial acute febrile illness (AFI), 282 rodents, 100 cattle, 56 dogs and 160 Rhipicephalus sanguineus ticks were screened for the presence of Anaplasma phagocytophilum DNA using a quantitative PCR (qPCR) assay targeting the msp2 gene. The test detected both A. phagocytophilum and Anaplasma sp. SA/ZAM dog DNA. Microbiome sequencing confirmed the presence of low levels of A. phagocytophilum DNA in the blood of rodents, dogs and cattle, while high levels of A. platys and Anaplasma sp. SA/ZAM dog were detected in dogs. Directed sequencing of the 16S rRNA and gltA genes in selected samples revealed the presence of A. phagocytophilum DNA in humans, dogs and rodents and highlighted its importance as a possible contributing cause of AFI in South Africa. A number of recently described Anaplasma species and A. platys were also detected in the study. Phylogenetic analyses grouped Anaplasma sp. SA/ZAM dog into a distinct clade, with sufficient divergence from other Anaplasma species to warrant classification as a separate species. Until appropriate type-material can be deposited and the species is formally described, we will refer to this novel organism as Anaplasma sp. SA dog.

SUBMITTER: Kolo AO

PROVIDER: S-EPMC7698776 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Anaplasma phagocytophilum and Other Anaplasma spp. in Various Hosts in the Mnisi Community, Mpumalanga Province, South Africa.

Kolo Agatha O AO Collins Nicola E NE Brayton Kelly A KA Chaisi Mamohale M Blumberg Lucille L Frean John J Gall Cory A CA M Wentzel Jeanette J Wills-Berriman Samantha S Boni Liesl De L Weyer Jacqueline J Rossouw Jennifer J Oosthuizen Marinda C MC

Microorganisms 20201118 11

DNA samples from 74 patients with non-malarial acute febrile illness (AFI), 282 rodents, 100 cattle, 56 dogs and 160 Rhipicephalus sanguineus ticks were screened for the presence of Anaplasma phagocytophilum DNA using a quantitative PCR (qPCR) assay targeting the msp2 gene. The test detected both A. phagocytophilum and Anaplasma sp. SA/ZAM dog DNA. Microbiome sequencing confirmed the presence of low levels of A. phagocytophilum DNA in the blood of rodent ...[more]

PMID: 33217891

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Project description:BackgroundSouth Africa has a generalized and explosive HIV/AIDS epidemic with the largest number of people infected with HIV-1 in the world. Molecular investigations of HIV-1 diversity can help enhance interventions to contain and combat the HIV/AIDS epidemic. However, many studies of HIV-1 diversity in South Africa tend to be limited to the major metropolitan centers and their surrounding provinces. Hardly any studies of HIV diversity have been undertaken in Mpumalanga Province, and this study sought to investigate the HIV-1 diversity in this province, as well as establish the occurrence and extent of transmitted antiretroviral drug resistance mutations.MethodsHIV-1 gag p24, pol p10 and p66/p51, pol p31 and env gp41 gene fragments from 43 participants were amplified and sequenced. Quality control on the sequences was carried out using the LANL QC online tool. HIV-1 subtype was preliminary assigned using the REGA 3.0 and jpHMM online tools. Subtype for the pol gene fragment was further designated using the SCUEAL online tool. Phylogenetic analysis was inferred using the Maximum Likelihood methods in MEGA version 6. HIV-1 antiretroviral drug resistance mutations were determined using the Stanford database.ResultsPhylogenetic analysis using Maximum Likelihood methods indicated that all sequences in the study clustered with HIV-1 subtype C. The exception was one putative subtype BC unique recombinant form. Antiretroviral drug resistance mutations K103N and E138A were also detected, indicating possible transmission of anti-retroviral drug resistance mutations.ConclusionsThe phylogenetic analysis of the HIV sequences revealed that, by 2009, patients in the Bushbuckridge, Mpumalanga were predominantly infected with HIV-1 subtype C. However, the generalized, explosive nature of the HIV/AIDS epidemic in South Africa, in the context of extensive mobility by South Africans who inhabit rural areas, renders the continued molecular monitoring and surveillance of the epidemic imperative.

Project description:Pests and diseases are a major contributor to yield losses in sub-Saharan Africa, prompting smallholder farmers to seek cost-effective, accessible and ecologically friendly alternatives for crop protection. This study explored the management of pests and diseases affecting crops across eight selected villages in Ehlanzeni District, Mpumalanga Province, South Africa. A total of 120 smallholder farmers were purposefully selected utilising the snowball technique. Information on the management of plant pests and diseases was collected through interviews and focus group discussions using semi-structured interview schedules. Ethnobotanical indices, including relative frequency of citation (RFC), use-value (UV) and informant consensus factor (Fic), were used to quantify and rank the plants used for crop protection in the study area. Twenty-three plant species (16 naturalised exotics and seven indigenous plants) belonging to 16 families were used for managing pests (vertebrates and invertebrates) and diseases (fungal and bacterial related) affecting crops in the study area. The dominant (100%) crops cultivated by the participants were Allium cepa L., Mangifera indica L., Solanum lycopersicum L. and Zea mays L. The RFC value ranged from 0.08 to 0.83 and the three most popular plants for crop protection were Capsium annuum L. (0.83), A. cepa (0.63) and Dichrostachys cinerea (L.) Wight & Arn. (0.43). In terms of the UV, the five most promising plants used as biocontrol were Tulbaghia violacea (0.13), A. cepa (0.12), C. annuum L. (0.09), Solanum campylacanthum Hochst. Ex A.Rich.(0.09) and Pinus pinaster (0.08). Based on the Fic, four categories were established and dominated by fungal diseases (0.64). Furthermore, T. violacea and A. cepa were the most often mentioned plants used against fungal conditions. Other categories cited were bacterial diseases (0.3), invertebrate pests (0.11) and vertebrate pests (0.14), an indication that smallholder farmers had limited agreement or common knowledge about the plants used for their management. The preparation methods included maceration (38%), decoction (38%) and burning (24%). Foliar application (67%) and soil drenching (33%) were used for administering plant extracts during the management of crop pests and diseases. The study highlights the importance of botanicals and associated indigenous knowledge among smallholder farmers in Mpumalanga Province, South Africa. It is pertinent to explore the valorisation of these botanicals by generating empirical data on their biological efficacies and phytochemical profiles.

Dataset Information

Anaplasma phagocytophilum and Other Anaplasma spp. in Various Hosts in the Mnisi Community, Mpumalanga Province, South Africa.

Publications

<i>Anaplasma phagocytophilum</i> and Other <i>Anaplasma</i> spp. in Various Hosts in the Mnisi Community, Mpumalanga Province, South Africa.

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