Bacillus anthracis in South Africa, 1975–2013 : are some lineages vanishing?

DATA AVAILABITY STATEMENT: This publication contains all of the MLVA-31 allele profiles of the 319 strains that were examined. The sequenced B. anthracis strains’ nucleotide accession numbers, which have been uploaded to the sequence reads archive database under the bioproject PRJNA642997, are provided in this work.The anthrax-causing bacterium Bacillus anthracis comprises the genetic clades A, B, and C. In the northernmost part (Pafuri) of Kruger National Park (KNP), South Africa, both the common A and rare B strains clades occur. The B clade strains were reported to be dominant in Pafuri before 1991, while A clade strains occurred towards the central parts of KNP. The prevalence of B clade strains is currently much lower as only A clade strains have been isolated from 1992 onwards in KNP. In this study 319 B. anthracis strains were characterized with 31-loci multiplelocus variable-number tandem repeat analysis (MLVA-31). B clade strains from soil (n=9) and a Tragelaphus strepsiceros carcass (n=1) were further characterised by whole genome sequencing and compared to publicly available genomes. The KNP strains clustered in the B clade before 1991 into two dominant genotypes. South African strains cluster into a dominant genotype A.Br.005/006 consisting of KNP as well as the other anthrax endemic region, Northern Cape Province (NCP), South Africa. A few A.Br.001/002 strains from both endemic areas were also identified. Subclade A.Br.101 belonging to the A.Br.Aust94 lineage was reported in the NCP. The B-clade strains seems to be vanishing, while outbreaks in South Africa are caused mainly by the A.Br.005/006 genotypes as well as a few minor clades such as A.Br.001/002 and A.Br.101 present in NCP. This work confirmed the existence of the rare and vanishing B-clade strains that group in B.Br.001 branch with KrugerB and A0991 KNP strains.The National Research Foundation, Institute of Tropical Medicine FA3, and BE-2157/3 − 1 from the German Research Foundation (DFG) and the North-West University.https://bmcgenomics.biomedcentral.com/Veterinary Tropical DiseasesSDG-03:Good heatlh and well-beingSDG-15:Life on lan

Decision rules for determining terrestrial movement and the consequences for filtering high-resolution global positioning system tracks: a case study using the African lion ( Panthera leo )

The combined use of global positioning system (GPS) technology and motion sensors within the discipline of movement ecology has increased over recent years. This is particularly the case for instrumented wildlife, with many studies now opting to record parameters at high (infra-second) sampling frequencies. However, the detail with which GPS loggers can elucidate fine-scale movement depends on the precision and accuracy of fixes, with accuracy being affected by signal reception. We hypothesized that animal behaviour was the main factor affecting fix inaccuracy, with inherent GPS positional noise (jitter) being most apparent during GPS fixes for non-moving locations, thereby producing disproportionate error during rest periods. A movement-verified filtering (MVF) protocol was constructed to compare GPS-derived speed data with dynamic body acceleration, to provide a computationally quick method for identifying genuine travelling movement. This method was tested on 11 free-ranging lions (Panthera leo) fitted with collar-mounted GPS units and tri-axial motion sensors recording at 1 and 40 Hz, respectively. The findings support the hypothesis and show that distance moved estimates were, on average, overestimated by greater than 80% prior to GPS screening. We present the conceptual and mathematical protocols for screening fix inaccuracy within high-resolution GPS datasets and demonstrate the importance that MVF has for avoiding inaccurate and biased estimates of movement

Adaptation and diagnostic potential of a commercial cat interferon gamma release assay for the detection of Mycobacterium bovis infection in African lions (Panthera leo)

CITATION: Gumbo, R. et al. 2022. Adaptation and diagnostic potential of a commercial cat interferon gamma release assay for the detection of Mycobacterium bovis infection in African lions (Panthera leo). Pathogens, 11:765, doi:10.3390/pathogens11070765.The original publication is available at https://www.mdpi.comMycobacterium bovis (M. bovis) infection in wildlife, including lions (Panthera leo), has implications for individual and population health. Tools for the detection of infected lions are needed for diagnosis and disease surveillance. This study aimed to evaluate the Mabtech Cat interferon gamma (IFN-γ) ELISABasic kit for detection of native lion IFN-γ in whole blood samples stimulated using the QuantiFERON® TB Gold Plus (QFT) platform as a potential diagnostic assay. The ELISA was able to detect lion IFN-γ in mitogen-stimulated samples, with good parallelism, linearity, and a working range of 15.6–500 pg/mL. Minimal matrix interference was observed in the recovery of domestic cat rIFN-γ in lion plasma. Both intra- and inter-assay reproducibility had a coefficient of variation less than 10%, while the limit of detection and quantification were 7.8 pg/mL and 31.2 pg/mL, respectively. The diagnostic performance of the QFT Mabtech Cat interferon gamma release assay (IGRA) was determined using mycobacterial antigen-stimulated samples from M. bovis culture-confirmed infected (n = 8) and uninfected (n = 4) lions. A lion-specific cut-off value (33 pg/mL) was calculated, and the sensitivity and specificity were determined to be 87.5% and 100%, respectively. Although additional samples should be tested, the QFT Mabtech Cat IGRA could identify M. bovisinfected African lions.https://www.mdpi.com/2076-0817/11/7/765Publisher's versio

Fatal Tuberculosis in a Free-Ranging African Elephant and One Health Implications of Human Pathogens in Wildlife

Tuberculosis (TB) in humans is a global public health concern and the discovery of animal cases of Mycobacterium tuberculosis (Mtb) infection and disease, especially in multi-host settings, also has significant implications for public health, veterinary disease control, and conservation endeavors. This paper describes a fatal case of Mtb disease in a free-ranging African elephant (Loxodonta africana) in a high human TB burden region. Necropsy revealed extensive granulomatous pneumonia, from which Mtb was isolated and identified as a member of LAM3/F11 lineage; a common lineage found in humans in South Africa. These findings are contextualized within a framework of emerging Mtb disease in wildlife globally and highlights the importance of the One Health paradigm in addressing this anthroponotic threat to wildlife and the zoonotic implications

Dead-reckoning animal movements in R: a reappraisal using Gundog.Tracks

BackgroundFine-scale data on animal position are increasingly enabling us to understand the details of animal movement ecology and dead-reckoning, a technique integrating motion sensor-derived information on heading and speed, can be used to reconstruct fine-scale movement paths at sub-second resolution, irrespective of the environment. On its own however, the dead-reckoning process is prone to cumulative errors, so that position estimates quickly become uncoupled from true location. Periodic ground-truthing with aligned location data (e.g., from global positioning technology) can correct for this drift between Verified Positions (VPs). We present step-by-step instructions for implementing Verified Position Correction (VPC) dead-reckoning in R using the tilt-compensated compass method, accompanied by the mathematical protocols underlying the code and improvements and extensions of this technique to reduce the trade-off between VPC rate and dead-reckoning accuracy. These protocols are all built into a user-friendly, fully annotated VPC dead-reckoning R function; Gundog.Tracks, with multi-functionality to reconstruct animal movement paths across terrestrial, aquatic, and aerial systems, provided within the Additional file 4 as well as online (GitHub).ResultsThe Gundog.Tracks function is demonstrated on three contrasting model species (the African lion Panthera leo, the Magellanic penguin Spheniscus magellanicus, and the Imperial cormorant Leucocarbo atriceps) moving on land, in water and in air. We show the effect of uncorrected errors in speed estimations, heading inaccuracies and infrequent VPC rate and demonstrate how these issues can be addressed.ConclusionsThe function provided will allow anyone familiar with R to dead-reckon animal tracks readily and accurately, as the key complex issues are dealt with by Gundog.Tracks. This will help the community to consider and implement a valuable, but often overlooked method of reconstructing high-resolution animal movement paths across diverse species and systems without requiring a bespoke application

"Outroduction”: A Research Agenda on Collegiality in University Settings

Collegiality is the modus operandi of universities. Collegiality is central to academic freedom and scientific quality. In this way, collegiality also contributes to the good functioning of universities’ contribution to society and democracy. In this concluding paper of the special issue on collegiality, we summarize the main findings and takeaways from our collective studies. We summarize the main challenges and contestations to collegiality and to universities, but also document lines of resistance, activation, and maintenance. We depict varieties of collegiality and conclude by emphasizing that future research needs to be based on an appreciation of this variation. We argue that it is essential to incorporate such a variation-sensitive perspective into discussions on academic freedom and scientific quality and highlight themes surfaced by the different studies that remain under-explored in extant literature: institutional trust, field-level studies of collegiality, and collegiality and communication. Finally, we offer some remarks on methodological and theoretical implications of this research and conclude by summarizing our research agenda in a list of themes

Introducing a unique animal ID and digital life history museum for wildlife metadata

Funding: C.R. acknowledges funding from the Gordon and Betty Moore Foundation (GBMF9881) and the National Geographic Society (NGS-82515R-20). G.B., R.K., S.C.D. and D.E.-S. acknowledge funding from NASA. A.S. and F.I. acknowledge support from the European Commission through the Horizon 2020 Marie Skłodowska-Curie Actions Individual Fellowships (grant no. 101027534 and no. 101107666, respectively). S.C.D. acknowledges funding from NASA Ecological Forecasting Program Grant 80NSSC21K1182. A.M.M.S. was supported by an ARC DP DP210103091. This project is funded in part by the Gordon and Betty Moore Foundation through Grant GBMF10539 to M.W., as well as the Academy for the Protection of Zoo Animals and Wildlife e.V., Germany.1. Over the past five decades, a large number of wild animals have been individually identified by various observation systems and/or temporary tracking methods, providing unparalleled insights into their lives over both time and space. However, so far there is no comprehensive record of uniquely individually identified animals nor where their data and metadata are stored, for example photos, physiological and genetic samples, disease screens, information on social relationships. 2. Databases currently do not offer unique identifiers for living, individual wild animals, similar to the permanent ID labelling for deceased museum specimens. 3. To address this problem, we introduce two new concepts: (1) a globally unique animal ID (UAID) available to define uniquely and individually identified animals archived in any database, including metadata archived at the time of publication; and (2) the digital ‘home’ for UAIDs, the Movebank Life History Museum (MoMu), storing and linking metadata, media, communications and other files associated with animals individually identified in the wild. MoMu will ensure that metadata are available for future generations, allowing permanent linkages to information in other databases. 4. MoMu allows researchers to collect and store photos, behavioural records, genome data and/or resightings of UAIDed animals, encompassing information not easily included in structured datasets supported by existing databases. Metadata is uploaded through the Animal Tracker app, the MoMu website, by email from registered users or through an Application Programming Interface (API) from any database. Initially, records can be stored in a temporary folder similar to a field drawer, as naturalists routinely do. Later, researchers and specialists can curate these materials for individual animals, manage the secure sharing of sensitive information and, where appropriate, publish individual life histories with DOIs. The storage of such synthesized lifetime stories of wild animals under a UAID (unique identifier or ‘animal passport’) will support basic science, conservation efforts and public participation.Peer reviewe

“Outroduction” : a research agenda on collegiality In university settings

Collegiality is the modus operandi of universities. Collegiality is central to academic freedom and scientific quality. In this way, collegiality also contributes to the good functioning of universities’ contribution to society and democracy. In this concluding paper of the special issue on collegiality, we summarize the main findings and takeaways from our collective studies. We summarize the main challenges and contestations to collegiality and to universities, but also document lines of resistance, activation, and maintenance. We depict varieties of collegiality and conclude by emphasizing that future research needs to be based on an appreciation of this variation. We argue that it is essential to incorporate such a variation-sensitive perspective into discussions on academic freedom and scientific quality and highlight themes surfaced by the different studies that remain under-explored in extant literature: institutional trust, field-level studies of collegiality, and collegiality and communication. Finally, we offer some remarks on methodological and theoretical implications of this research and conclude by summarizing our research agenda in a list of themes

Integrating remote sensing data in an agent-based model applied to spatial epidemiology

info:eu-repo/semantics/nonPublishe

Update on the EPISTIS project

info:eu-repo/semantics/nonPublishe