Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus).

The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.

Phenotypic and genotypic characterization of acaricide resistance in Rhipicephalus microplus field isolates from South Africa and Brazil.

Rhipicephalus (Boophilus) microplus is one of the most successful ticks infesting cattle around the world. This highly-invasive species transmits cattle parasites that cause cattle fever leading to a high socio-economic burden. Tick eradication programs have often failed, due to the development of acaricide resistance. Here we characterize acaricide resistance in a large number of tick isolates from regions in South Africa (KwaZulu Natal, Mpumalanga, Western & Eastern Cape provinces) and two Brazilian regions. By means of Larval Packet Tests (LPT's) acaricide resistance was evaluated against five commonly used acaricides (chlorfenvinphos, fipronil, deltamethrin, amitraz, and ivermectin). Furthermore, the coding region containing the knock down resistance (kdr) mutation, known to result in pyrethroid resistance, was sequenced. Resistance to at least one acaricide class was reported in each of the five regions, and a high proportion of tick isolates exhibited multi-resistance to at least two acaricide classes (range: 22.2-80.0%). Furthermore, resistance ratios (RR) showed high spatial variation (intercontinental, as well as regional) but low regional spatial autocorrelation. Previous and current acaricide use correlated with current RR, and several combinations of acaricide RR were positively correlated. Moreover, fipronil resistance tended to be higher in farms with more intense acaricide use. The kdr-mutations provided the ticks a fitness advantage under the selection pressure of synthetic pyrethroids based on population (kdr-allele frequency) and individual level data (genotypes). The data show the threat of acaricide (multi-)resistance is high in Brazil and South Africa, but acaricide specific levels need to be assessed locally. For this purpose, gathering complementary molecular information on mutations that underlie resistance can reduce costs and expedite necessary actions. In an era of human-caused habitat alterations, implementing molecular data-driven programs becomes essential in overcoming tick-induced socio-economic losses.

Mitochondrial genome sequence comparisons indicate that the elephant louse Haematomyzus elephantis (Piaget, 1869) contains cryptic species.

The parvorder Rhynchopthirina contains three currently recognised species of lice that parasitize elephants (both African savanna elephant Loxodonta africana and Asian elephant Elephas maximus), desert warthogs (Phacochoerus aethiopicus) and Red River hogs (Potamochoerus porcus), respectively. The Asian elephant lice and the African savanna elephant lice are currently treated as the same species, Haematomyzus elephantis (Piaget, 1869), based on morphology despite the fact that their hosts diverged 8.4 million years ago. In the current study, we sequenced 23 mitochondrial (mt) genes of African savanna elephant lice collected in South Africa and analysed the sequence divergence between African savanna elephant lice and previously sequenced Asian elephant lice. Sequence comparisons revealed >23% divergence for the 23 mt genes as a whole and ~17% divergence for cox1 gene between African savanna and Asian elephant lice, which were far higher than the divergence expected within a species. Furthermore, the mt gene sequence divergences between these lice are 3.76-4.6 times higher than that between their hosts, the African savanna and Asian elephants, which are expected for the co-divergence and co-evolution between lice and their elephant hosts. We conclude that (1) H. elephantis (Piaget, 1869) contains cryptic species and (2) African savanna and Asian elephant lice are different species genetically that may have co-diverged and co-evolved with their hosts.

Comparing the minimum inhibitory and mutant prevention concentrations of selected antibiotics against animal isolates of Pasteurella multocida and Salmonella typhimurium.

Historically, the use of antibiotics was not well regulated in veterinary medicine. The emergence of antibiotic resistance (ABR) in pathogenic bacteria in human and veterinary medicine has driven the need for greater antibiotic stewardship. The preservation of certain antibiotic classes for use exclusively in humans, especially in cases of multidrug resistance, has highlighted the need for veterinarians to reduce its use and redefine dosage regimens of antibiotics to ensure efficacy and guard against the development of ABR pathogens. The minimum inhibitory concentration (MIC), the lowest concentration of an antibiotic drug that will prevent the growth of a bacterium, is recognised as a method to assist in antibiotic dosage determination. Minimum inhibitory concentrations sometimes fail to deal with first-step mutants in bacterial populations; therefore dosing regimens based solely on MIC can lead to the development of ABR. The mutant prevention concentration (MPC) is the minimum inhibitory antibiotic concentration of the most resistant first-step mutant. Mutant prevention concentration determination as a complementary and sometimes preferable alternative to MIC determination for veterinarians when managing bacterial pathogens. The results of this study focused on livestock pathogens and antibiotics used to treat them, which had a MIC value of 0.25 µg/mL for enrofloxacin against all 27 isolates of Salmonella typhimurium. The MPC values were 0.50 µg/mL, with the exception of five isolates that had MPC values of 4.00 µg/mL. The MPC test yielded 65.52% (18 isolates) Salmonella isolates with florfenicol MICs in the sensitive range, while 11 isolates were in the resistant range. Seventeen isolates (58.62%) of Pasteurella multocida had MIC values in the susceptible range and 41.38% (12 isolates) had an intermediate MIC value. Mutant prevention concentration determinations as done in this study is effective for the antibiotic treatment of bacterial infections and minimising the development of resistance. The MPC method can be used to better control to prevent the development of antibiotic drug resistance used in animals.

Carnivore Detection at the Domestic/Wildlife Interface within Mpumalanga Province, South Africa.

South African protected areas account for 8% of the total landmass according to World Bank indicators. Effective conservation of biodiversity in protected areas requires the development of specific reserve management objectives addressing species and disease management. The primary objective of the current study was to identify predictors of carnivore detection in an effort to inform carnivore species management plans on Andover and Manyeleti nature reserves in South Africa. A limited number of camera traps were placed randomly using a grid system. Species detection data were analysed using mixed-effects logistic regression and Spearman's correlation coefficients. Deterministic inverse distance weighted distribution maps were used to describe the spatial distribution of carnivore species. Camera traps identified similar species as traditional call-up surveys during the study and would be useful as an adjunct census method. Carnivore detection was associated with several variables, including the presence of specific prey species. The measured intra-and interspecies interactions suggested the risk of disease transmission among species, and vaccination for prevalent diseases should be considered to manage this risk.

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

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.

Amblyomma hebraeum is the predominant tick species on goats in the Mnisi Community Area of Mpumalanga Province South Africa and is co-infected with Ehrlichia ruminantium and Rickettsia africae.

BACKGROUND: In sub-Saharan Africa, Amblyomma ticks are vectors of heartwater disease in domestic ruminants, caused by the rickettsial pathogen Ehrlichia ruminantium. Immature tick stages often bite humans, whereby they act as vectors of tick-bite fever caused by Rickettsia africae. Moreover, Amblyomma ticks cause damage to livestock due to their feeding behaviour. In South Africa, we studied the abundance of Amblyomma hebraeum ticks on goats of emerging farmers in Mpumalanga Province. A selected number of A. hebraeum nymphs and adult ticks was tested for co-infection with E. ruminantium and R. africae. METHODS: A total of 630 indigenous goats, belonging to farmers in the Mnisi Community area, were examined for ticks in 2013 and 2014. All ticks were identified, and a selected number was tested by PCR with reverse line blot hybridisation. RESULTS: In total, 13,132 ticks were collected from goats distributed over 17 different households. Amblyomma hebraeum was the predominant species, followed by R. microplus. Rhipicephalus appendiculatus, R. simus and R. zambeziensis were also identified. Amblyomma hebraeum was present throughout the year, with peak activity of adults in summer (November) and nymphs in winter (July). The ratio between adults and nymphs ranged from 1:2.7 in summer to 1:55.1 in winter. The mean prevalence of infection for E. ruminantium by PCR/RLB in adult ticks was 17.4% (31/178), whereas 15.7% (28/178) were infected with R. africae. In pooled nymphs, 28.4% were infected with E. ruminantium and 38.8% carried R. africae infection. Co-infections of E. ruminantium and R. africae in adult and pooled nymphal ticks were 3.9% (7/178) and 10% (14.9), respectively. Lameness of goats due to predilection of ticks for the interdigital space of their feet was observed in 89% of the households. CONCLUSIONS: Goats act as important alternative hosts for cattle ticks, which underscored the necessity to include goats in control programs. It is suggested to use acaricide-impregnated leg-bands as a sustainable method to kill ticks and prevent lameness in goats. The challenge of goats by considerable numbers of E. ruminantium-infected ticks is a major obstacle for upgrading the indigenous goat breeds. Humans may be at risk to contract tick-bite fever in this area.

Rabies Vaccination of 6-Week-Old Puppies Born to Immunized Mothers: A Randomized Controlled Trial in a High-Mortality Population of Owned, Free-Roaming Dogs.

To achieve global elimination of human rabies from dogs by 2030, evidence-based strategies for effective dog vaccination are needed. Current guidelines recommend inclusion of dogs younger than 3 months in mass rabies vaccination campaigns, although available vaccines are only recommended for use by manufacturers in older dogs, ostensibly due to concerns over interference of maternally-acquired immunity with immune response to the vaccine. Adverse effects of vaccination in this age group of dogs have also not been adequately assessed under field conditions. In a single-site, owner-blinded, randomized, placebo-controlled trial in puppies born to mothers vaccinated within the previous 18 months in a high-mortality population of owned, free-roaming dogs in South Africa, we assessed immunogenicity and effect on survival to all causes of mortality of a single dose of rabies vaccine administered at 6 weeks of age. We found that puppies did not have appreciable levels of maternally-derived antibodies at 6 weeks of age (geometric mean titer 0.065 IU/mL, 95% CI 0.061-0.069; n = 346), and that 88% (95% CI 80.7-93.3) of puppies vaccinated at 6 weeks had titers ≥0.5 IU/mL 21 days later (n = 117). Although the average effect of vaccination on survival was not statistically significant (hazard ratio [HR] 1.35, 95% CI 0.83-2.18), this effect was modified by sex (p = 0.02), with the HR in females 3.09 (95% CI 1.24-7.69) and the HR in males 0.79 (95% CI 0.41-1.53). We speculate that this effect is related to the observed survival advantage that females had over males in the unvaccinated group (HR 0.27; 95% CI 0.11-0.70), with vaccination eroding this advantage through as-yet-unknown mechanisms.

Sero-Epidemiological Study of Selected Zoonotic and Abortifacient Pathogens in Cattle at a Wildlife-Livestock Interface in South Africa.

A cross sectional sero-epidemiological study was conducted on cattle in a communal farming area adjacent to Kruger National Park at a wildlife-livestock interface in South Africa. A total of 184 cattle were screened for exposure to 5 abortifacient or zoonotic pathogens, namely Coxiella burnetii, Toxoplasma gondii, Chlamydophila abortus, Neospora caninum, and Rift Valley fever virus (RVFV) using enzyme-linked immunosorbent assays. In addition, the virus neutralization test was used to confirm the presence of antibodies to RVFV. The seroprevalence of C. burnetii, T. gondii, C. abortus, N. caninum, and RVFV antibodies was 38.0%, 32.6%, 20.7%, 1.6%, and 0.5%, respectively, and varied between locations (p < 0.001). Seroprevalence of C. burnetii and T. gondii was highly clustered by location (intraclass correlation coefficient [ICC] = 0.57), and that of C. abortus moderately so (ICC = 0.11). Seroprevalence was not associated with sex or age for any pathogen, except for C. abortus, for which seroprevalence was positively associated with age (p = 0.01). The predominant mixed infections were C. burnetii and T. gondii (15.2%) and C. burnetii, T. gondii, and C. abortus (13.0%). The serological detection of the five abortifacient pathogens in cattle indicates the potential for economic losses to livestock farmers, health impacts to domestic animals, transmission across the livestock-wildlife interface, and the risk of zoonotic transmission. This is the first documentation of T. gondii infection in cattle in South Africa, while exposure to C. burnetii, C. abortus, and N. caninum infections is being reported for the first time in cattle in a wildlife-livestock interface in the country.

The first report of Escherichia fergusonii isolated from non-human primates, in Africa.

The aim of this study was to determine the resistance phenotypes of selected enteric bacteria isolated from non-human primates at a wildlife-human interface. Bacterial isolates from faecal samples of non-human primates at two wildlife rehabilitation centres in South Africa were screened for the presence of Escherichia coli. The biochemical characterisation of E. coli and E. coli-like bacteria revealed both adonitol positive and sorbitol negative strains - a unique characteristic of Escherichia fergusonii and Escherichia coli K99. Further tests were carried out to identify the isolates, namely growth on Simmons citrate agar supplemented with 2% adonitol and biochemical tests based on their ability to ferment cellobiose and d-arabitol. Antimicrobial sensitivity was determined with microbroth dilution tests employing microtitre plates with 21 different antimicrobial drugs. Molecular characterisation was done with a duplex polymerase chain reaction (PCR) assay that targeted the yliE and EFER_1569 genes. E. fergusonii strains were confirmed by the presence of a 233 bp segment of the yliE gene and a 432 bp segment of the EFER_1569 gene. Twenty-three E. coli-like bacteria were confirmed as E. fergusonii based on the confirmatory tests and they were in 100% agreement. Approximately 87% of them were resistant to polymyxins B and E (colistin) as well as the carbapenem group with occasional resistance to amikacin. This is the first reported isolation and identification of E. fergusonii strains in non-human primates. The findings point to E. fergusonii as a possible emerging pathogen of zoonotic importance.