Genome Sequences of Foot-and-Mouth Disease Virus SAT1 Strains Purified from Coinfected Cape Buffalo in Kenya.

Nearly complete genomes of 49 novel foot-and-mouth disease virus (FMDV) SAT1 strains acquired from oropharyngeal fluid samples from asymptomatic African Cape buffalo in Kenya in 2016 were determined. Sequences were from primary passage or plaque-purified dually SAT1/SAT2-infected samples. These sequences are important for elucidation of the molecular epidemiology of persistent and subclinical FMDV infections.

Genome Sequences of Foot-and-Mouth Disease Virus SAT2 Strains Purified from Coinfected Cape Buffalo in Kenya.

Foot-and-mouth disease virus (FMDV) SAT2 sequences were acquired from Cape buffalo in Kenya in 2016, from either primary passage (n = 38) or plaque purification of dually SAT1/SAT2-infected samples (n = 61). All samples were derived from asymptomatic animals. These sequences contribute to our understanding of FMDV diversity in reservoirs and during subclinical FMDV infections.

Factors influencing usage of antimicrobial drugs among pastoralists in Kenya.

Agricultural use of antimicrobials in food animal production may contribute to the global emergence of antimicrobial resistance (AMR). However, considerable gaps exist in research on the use of antimicrobial drugs (AMDs) in food animals in small-scale production systems in low- and middle-income countries, despite the minimal regulation of antimicrobials in such regions. The aim of this study was to identify factors that may influence AMD use in livestock among pastoral communities in Kenya. We collected data related to household and herd demographics, herd health, and herd management from 55 households in the Maasai Mara ecosystem, Kenya, between 2018 and 2019. We used multi-model logistic regression inference (supervised machine learning) to ascertain trends in AMD use within these households. AMD use in cattle was significantly associated with AMD use in sheep and goats (p = 0.05), implying that decisions regarding AMD use in cattle or sheep and goats were interdependent. AMD use in sheep and goats was negatively associated with vaccination against the foot and mouth disease (FMD) virus in cattle (OR = 0.06, 95% CI 0.01-0.67, p = 0.02). Less AMD use was observed for vaccine-preventable diseases like contagious ecthyma when households had access to state veterinarians (OR = 0.06, p = 0.05, 95% CI 0.004-0.96). Overall, decisions to use AMDs were associated with vaccine usage, occurrence of respiratory diseases, and access to animal health advice. This hypothesis-generating study suggests that applying community-centric methods may be necessary to understand the use of AMDs in pastoral communities.

Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya.

African buffalo are the natural reservoirs of the SAT serotypes of foot-and-mouth disease virus (FMDV) in sub-Saharan Africa. Most buffalo are exposed to multiple FMDV serotypes early in life, and a proportion of them become persistently infected carriers. Understanding the genetic diversity and evolution of FMDV in carrier animals is critical to elucidate how FMDV persists in buffalo populations. In this study, we obtained oropharyngeal (OPF) fluid from naturally infected African buffalo, and characterized the genetic diversity of FMDV. Out of 54 FMDV-positive OPF, 5 were co-infected with SAT1 and SAT2 serotypes. From the five co-infected buffalo, we obtained eighty-nine plaque-purified isolates. Isolates obtained directly from OPF and plaque purification were sequenced using next-generation sequencing (NGS). Phylogenetic analyses of the sequences obtained from recombination-free protein-coding regions revealed a discrepancy in the topology of capsid proteins and non-structural proteins. Despite the high divergence in the capsid phylogeny between SAT1 and SAT2 serotypes, viruses from different serotypes that were collected from the same host had a high genetic similarity in non-structural protein-coding regions P2 and P3, suggesting interserotypic recombination. In two of the SAT1 and SAT2 co-infected buffalo identified at the first passage of viral isolation, the plaque-derived SAT2 genomes were distinctly grouped in two different genotypes. These genotypes were not initially detected with the NGS from the first passage (non-purified) virus isolation sample. In one animal with two SAT2 haplotypes, one plaque-derived chimeric sequence was found. These findings demonstrate within-host evolution through recombination and point mutation contributing to broad viral diversity in the wildlife reservoir. These mechanisms may be critical to FMDV persistence at the individual animal and population levels, and may contribute to the emergence of new viruses that have the ability to spill-over to livestock and other wildlife species.

Strengthening global health security by improving disease surveillance in remote rural areas of low-income and middle-income countries.

The COVID-19 pandemic has underscored the need to strengthen national surveillance systems to protect a globally connected world. In low-income and middle-income countries, zoonotic disease surveillance has advanced considerably in the past two decades. However, surveillance efforts often prioritise urban and adjacent rural communities. Communities in remote rural areas have had far less support despite having routine exposure to zoonotic diseases due to frequent contact with domestic and wild animals, and restricted access to health care. Limited disease surveillance in remote rural areas is a crucial gap in global health security. Although this point has been made in the past, practical solutions on how to implement surveillance efficiently in these resource-limited and logistically challenging settings have yet to be discussed. We highlight why investing in disease surveillance in remote rural areas of low-income and middle-income countries will benefit the global community and review current approaches. Using semi-arid regions in Kenya as a case study, we provide a practical approach by which surveillance in remote rural areas can be strengthened and integrated into existing systems. This Viewpoint represents a transition from simply highlighting the need for a more holistic approach to disease surveillance to a solid plan for how this outcome might be achieved.

Livestock Presence Influences the Seroprevalence of Crimean Congo Hemorrhagic Fever Virus on Sympatric Wildlife in Kenya.

Crimean Congo Hemorrhagic Fever (CCHF) is an emerging tick-borne zoonotic viral disease with the potential of causing public health emergencies. However, less is known about the role of wildlife and livestock in spreading the virus. Therefore, we aimed to assess how the interactions between African buffalo (Syncerus caffer) and cattle may influence the seroprevalence of CCHF across livestock-wildlife management systems in Kenya. The study included archived sera samples from buffalo and cattle from wildlife only habitats (Lake Nakuru National Park and Solio conservancy), open wildlife-livestock integrated habitats (Maasai Mara ecosystem and Meru National Park), and closed wildlife-livestock habitats (Ol Pejeta Conservancy) in Kenya. We analyzed 191 buffalo and 139 cattle sera using IDvet multispecies, double-antigen IgG enzyme-linked immunosorbent assay (ELISA). The seroprevalence toward Crimean Congo hemorrhagic fever virus (CCHFV) was significantly higher for buffalo compared to cattle (75.3% and 28.1%, respectively, p < 0.001). We obtained the highest seroprevalence among buffalo of 92.1% in closed wildlife only systems compared to 28.8% and 46.1% prevalence in closed-integrated and open-integrated systems, respectively. The regression coefficients were all negative for cattle compared to buffalo in both closed-integrated and open-integrated compared to wildlife only system. Our results show that CCHFV circulates among the diverse animal community in Kenya in spatially disconnected foci. The habitat overlap between cattle and buffalo makes cattle a "bridge species" or superspreader host for CCHFV and increases transmission risks to humans. The effect of animal management system on prevalence is depended on tick control on the cattle and not the animal per se. We conclude that buffalo, a host with a longer life span than livestock, is a reservoir and may serve as a sentinel population for longitudinal surveillance of CCHFV.

Animal movement in a pastoralist population in the Maasai Mara Ecosystem in Kenya and implications for pathogen spread and control.

Livestock movements are important drivers for infectious disease transmission. However, paucity of such data in pastoralist communities in rangeland ecosystems limits our understanding of their dynamics and hampers disease surveillance and control. The aim of this study was to investigate animal movement networks in a pastoralist community in Kenya, and assess network-based strategies for disease control. We used network analysis to characterize five types of between-village animal movement networks. We then evaluated implications of these networks for disease spread and control by quantifying topological changes in the network associated with targeted and random removal of nodes. To construct these networks, data were collected using standardized questionnaires (N = 165 households) from communities living within the Maasai Mara Ecosystem in southwestern Kenya. Our analyses show that the Maasai Mara National Reserve (MMNR), a protected wildlife area, was critical for maintaining village connectivity in the agistment network (dry season grazing), with MMNR-adjacent villages being highly utilized during the dry season. In terms of disease dynamics, the network-based basic reproduction number, R0, was sufficient to allow disease invasion in all the five networks, and removal of villages based on degree or betweenness was not efficient in reducing R0. However, we show that villages with high degree or betweenness may play an important role in maintaining network connectivity, which may not be captured by assessment of R0 alone. Such villages may function as potential "firebreaks." For example, targeted removal of highly connected village nodes was more effective at fragmenting each network than random removal of nodes, indicating that network-based targeting of interventions such as vaccination could potentially disrupt transmission pathways in the ecosystem. In conclusion, this work shows that animal movements have the potential to shape patterns of disease transmission in this ecosystem, with targeted interventions being a practical and efficient measure for disease control.

The role of African buffalo in the epidemiology of foot-and-mouth disease in sympatric cattle and buffalo populations in Kenya.

Quantitative knowledge on the contribution of African buffalo to the epidemiology of foot-and-mouth disease virus (FMDV) in East Africa is lacking, and this information is essential for the design of control programs in the region. The objective of this study was to investigate the epidemiology of FMDV in buffalo, including the role of buffalo in the circulation of FMDV in livestock populations. We collected blood and oropharyngeal fluids from 92 wild buffalo and 98 sympatric cattle in central Kenya and sequenced the virus' VP1 coding region. We show that FMDV has a high seroprevalence in buffalo (~77%) and targeted cattle (~93%). In addition, we recovered 80 FMDV sequences from buffalo, all of which were serotype SAT1 and SAT2, and four serotype O and A sequences from sympatric cattle. Notably, six individual buffalo were co-infected with both SAT1 and SAT2. Amongst sympatric buffalo and cattle, the fact that no SAT1 or 2 sequences were found in cattle suggests that transmission of FMDV from buffalo to sympatric cattle is rare. Similarly, there was no evidence that serotype O and A sequences found in cattle were transmitted to buffalo. However, viruses from FMDV outbreaks in cattle elsewhere in Kenya were closely related to SAT1 and SAT2 viruses found in buffalo in this study, suggesting that FMDV in cattle and buffalo do not constitute independently evolving populations. We also show that fine-scale geographic features, such as rivers, influence the circulation of FMDV in buffalo and that social segregation amongst sympatric herds may limit between-herd transmission. These results significantly advance our understanding of the ecology and molecular epidemiology of FMDV at wildlife-livestock interfaces in East Africa and will help to inform the design of control and surveillance strategies for this disease in the region.

Foot-and-Mouth Disease Virus Serotype A Genome Sequence from Kenya in 2016.

We report the genome sequence of a foot-and-mouth disease virus (FMDV) serotype A topotype Africa isolate collected from bovine vesicular epithelium from Kenya in 2016. This novel sequence updates the knowledge of FMDV diversity in eastern Africa and has important implications for FMDV epidemiology and molecular analyses.

Genome Sequences of Foot-and-Mouth Disease Virus SAT1 and SAT2 Strains from Kenya in 2014 to 2016.

Here, we report the near-complete genomes of three Southern African Territories 1 (SAT1) serotype strains and one SAT2 serotype strain of foot-and-mouth disease virus (FMDV) recently isolated from Kenya. Viral isolates were obtained from bovine epithelial tissues collected in 2014 and 2016 following outbreaks of foot-and-mouth disease (FMD). These near-complete genome sequences provide a critical update of Kenyan FMDV molecular epidemiology.

First Report of Near-Complete Genome Sequences of Foot-and-Mouth Disease Virus Serotype O Strains from Kenya.

This is the first report of two near-complete genome sequences of foot-and-mouth disease virus (FMDV) serotype O from Kenya. The viruses were isolated from bovine epithelium collected in 2014 and 2016 from local FMD outbreaks. These full-genome sequences are critical for improving the understanding of regional FMDV molecular epidemiology.

Capture, immobilization, and Global Positioning System collaring of olive baboons (Papio anubis) and vervets (Chlorocebus pygerythrus): Lessons learned and suggested best practices.

As the value of Global Positioning System (GPS) technology in addressing primatological questions becomes more obvious, more studies will include capturing and collaring primates, with concomitant increased risk of adverse consequences to primate subjects. Here we detail our experiences in capturing, immobilizing, and placing GPS collars on six olive baboons (Papio anubis) in four groups and 12 vervet monkeys (Chlorocebus pygerythrus) in five groups in Kenya. We captured baboons with cage traps and vervets with box traps, immobilized them, and attached GPS collars that were to be worn for 1 year. Adverse consequences from the trapping effort included incidental death of two nonsubjects (an adult female and her dependent infant), temporary rectal prolapse in one baboon, superficial wounds on the crown of the head in two vervets, and failure to recapture/remove collars from two baboons and two vervets. Obvious negative effects from wearing collars were limited to abrasions around the neck of one vervet. A possible, and if so, serious, adverse effect was greater mortality for collared adult female vervets compared with known uncollared adult female vervets, largely due to leopard (Panthera pardus) predation. Collared animals could be more vulnerable to predation because trapping favors bolder individuals, who may also be more vulnerable to predation, or because collars could slow them down or make them more noticeable to predators. Along with recommendations made by others, we suggest that future studies diversify trapping bait to minimize the risk of rectal prolapse, avoid capturing the first individuals to enter traps, test the movement speeds of collared versus noncollared animals, include a release system on the collars to avoid retrapping failure, and publish both positive and negative effects of capturing, immobilizing, and collaring.

Phylogeographical and cross-species transmission dynamics of SAT1 and SAT2 foot-and-mouth disease virus in Eastern Africa.

Understanding the dynamics of foot-and-mouth disease virus (FMDV), an endemic and economically constraining disease, is critical in designing control programmes in Africa. This study investigates the evolutionary epidemiology of SAT1 and SAT2 FMDV in Eastern Africa, as well as between cattle and wild African buffalo. Bayesian phylodynamic models were used to analyse SAT1 and SAT2 VP1 gene segments collected between 1975 and 2016, focusing on the SAT1 and SAT2 viruses currently circulating in Eastern Africa. The root state posterior probabilities inferred from our analyses suggest Zimbabwe as the ancestral location for SAT1 currently circulating in Eastern Africa (p = 0.67). For the SAT2 clade, Kenya is inferred to be the ancestral location for introduction of the virus into other countries in Eastern Africa (p = 0.72). Salient (Bayes factor >10) viral dispersal routes were inferred from Tanzania to Kenya, and from Kenya to Uganda for SAT1 and SAT2, respectively. Results suggest that cattle are the source of the SAT1 and SAT2 clades currently circulating in Eastern Africa. In addition, our results suggest that the majority of SAT1 and SAT2 in livestock come from other livestock rather than wildlife, with limited evidence that buffalo serve as reservoirs for cattle. Insights from the present study highlight the role of cattle movements and anthropogenic activities in shaping the evolutionary history of SAT1 and SAT2 in Eastern Africa. While the results may be affected by inherent limitations of imperfect surveillance, our analysis elucidates the dynamics between host species in this region, which is key to guiding disease intervention activities.

Assessing Transmission of Antimicrobial-Resistant Escherichia coli in Wild Giraffe Contact Networks.

There is growing evidence that anthropogenic sources of antibiotics and antimicrobial-resistant bacteria can spill over into natural ecosystems, raising questions about the role wild animals play in the emergence, maintenance, and dispersal of antibiotic resistance genes. In particular, we lack an understanding of how resistance genes circulate within wild animal populations, including whether specific host characteristics, such as social associations, promote interhost transmission of these genes. In this study, we used social network analysis to explore the forces shaping population-level patterns of resistant Escherichia coli in wild giraffe (Giraffa camelopardalis) and assess the relative importance of social contact for the dissemination of resistant E. coli between giraffe. Of 195 giraffe sampled, only 5.1% harbored E. coli isolates resistant to one or more tested antibiotics. Whole-genome sequencing on a subset of resistant isolates revealed a number of acquired resistance genes with linkages to mobile genetic elements. However, we found no evidence that the spread of resistance genes among giraffe was facilitated by interhost associations. Giraffe with lower social degree were more likely to harbor resistant E. coli, but this relationship was likely driven by a correlation between an individual's social connectedness and age. Indeed, resistant E. coli was most frequently detected in socially isolated neonates, indicating that resistant E. coli may have a selective advantage in the gastrointestinal tracts of neonates compared to other age classes. Taken together, these results suggest that the maintenance of antimicrobial-resistant bacteria in wild populations may, in part, be determined by host traits and microbial competition dynamics within the host.IMPORTANCE Antimicrobial resistance represents a significant threat to human health, food security, and the global economy. To fully understand the evolution and dissemination of resistance genes, a complete picture of antimicrobial resistance in all biological compartments, including natural ecosystems, is required. The environment and wild animals may act as reservoirs for anthropogenically derived resistance genes that could be transferrable to clinically relevant bacteria of humans and domestic animals. Our study investigated the possible transmission mechanisms for antimicrobial-resistant bacteria within a wild animal population and, more broadly, contributes to our understanding of how resistance genes are spread and maintained in natural ecosystems.

Measuring The Impact Of Cash Transfers And Behavioral 'Nudges' On Maternity Care In Nairobi, Kenya.

Many patients in low-income countries express preferences for high-quality health care but often end up with low-quality providers. We conducted a randomized controlled trial with pregnant women in Nairobi, Kenya, to analyze whether cash transfers, enhanced with behavioral "nudges," can help women deliver in facilities that are consistent with their preferences and are of higher quality. We tested two interventions. The first was a labeled cash transfer (LCT), which explained that the cash was to help women deliver where they wanted. The second was a cash transfer that combined labeling and a commitment by the recipient to deliver in a prespecified desired facility as a condition of receiving the final payment (L-CCT). The L-CCT improved patient-perceived quality of interpersonal care but not perceived technical quality of care. It also increased women's likelihood of delivering in facilities that met standards for routine and emergency newborn care but not the likelihood of delivering in facilities that met standards for obstetric care. The LCT had fewer measured benefits. Women preferred facilities with high technical and interpersonal care quality, but these quality measures were often negatively correlated within facilities. Even with cash transfers, many women still used poor-quality facilities. A larger study is warranted to determine whether the L-CCT can improve maternal and newborn outcomes.

Corrigendum to "Exposure of vaccinated and naive cattle to natural challenge from buffalo-derived Theileria parva" [Int. J. Parasitol. Parasites Wildl. 4(2) (2015) 244-251].

[This corrects the article DOI: 10.1016/j.ijppaw.2015.04.006.].

Exposure of vaccinated and naive cattle to natural challenge from buffalo-derived Theileria parva.

Integrative management of wildlife and livestock requires a clear understanding of the diseases transmitted between the two populations. The tick-borne protozoan parasite Theileria parva causes two distinct diseases in cattle, East Coast fever and Corridor disease, following infection with parasites derived from cattle or buffalo, respectively. In this study, cattle were immunized with a live sporozoite vaccine containing three T. parva isolates (the Muguga cocktail), which has been used extensively and successfully in the field to protect against cattle-derived T. parva infection. The cattle were exposed in a natural field challenge site containing buffalo but no other cattle. The vaccine had no effect on the survival outcome in vaccinated animals compared to unvaccinated controls: nine out of the 12 cattle in each group succumbed to T. parva infection. The vaccine also had no effect on the clinical course of the disease. A combination of clinical and post mortem observations and laboratory analyses confirmed that the animals died of Corridor disease. The results clearly indicate that the Muguga cocktail vaccine does not provide protection against buffalo-derived T. parva at this site and highlight the need to evaluate the impact of the composition of challenge T. parva populations on vaccine success in areas where buffalo and cattle are present.

The influence of body mass index, age and sex on inflammatory disease risk in semi-captive Chimpanzees.

Obesity and ageing are emerging issues in the management of captive primates, including Chimpanzees, Pan troglodytes. Studies on humans show that obesity and old age can independently increase the risk of inflammatory-associated diseases indicated by elevated levels of pro-inflammatory cells and proteins in the blood of older or obese compared to levels in younger or non-obese individuals. In humans, sex can influence the outcomes of these risks. Health management of these problems in chimpanzee populations requires an understanding of similarities and differences of factors influencing inflammatory disease risks in humans and in chimpanzees. We examined the relationship between age, sex and Body Mass Index (BMI) with hematological biomarkers of inflammatory disease risk established for humans which include the neutrophil to lymphocyte ratio (NLR), and neutrophil, white blood cell (WBC), platelet microparticle and platelet counts. We found that higher values of NLR, neutrophil count and platelet microparticle count were associated with higher BMI values and older age indicating increased inflammation risk in these groups; a similar pattern to humans. There was a strong sex by age interaction on inflammation risk, with older males more at risk than older females. In contrast to human studies, total WBC count was not influenced by BMI, but like humans, WBC and platelet counts were lower in older individuals compared to younger individuals. Our findings are similar to those of humans and suggest that further insight on managing chimpanzees can be gained from extensive studies of ageing and obesity in humans. We suggest that managing BMI should be an integral part of health management in captive chimpanzee populations in order to partially reduce the risk of diseases associated with inflammation. These results also highlight parallels in inflammation risk between humans and chimpanzees and have implications for understanding the evolution of inflammation related diseases in apes.

Mixed-host aggregations and helminth parasite sharing in an East African wildlife-livestock system.

Parasitic infections transmitted between livestock and wildlife pose a significant risk to wildlife conservation efforts and constrain livestock productivity in tropical regions of the world. Gastrointestinal helminths are among the most ubiquitous parasites, and many parasites within this taxon can readily infect a wide range of host species. Factors shaping bidirectional transmission of parasites in wildlife-livestock systems are understudied. In this study, we investigate the prevalence and diversity of helminth infections in an East African community of wild and domestic ungulates. We also identify pairs of host species between which transmission may be possible based on shared parasite taxa, and explore the role of multi-host aggregations in shaping patterns of parasite sharing. Helminth taxa detected included Trichostrongylus, Trichuris, Paramphistomum, Skrjabinema, Strongyloides, Strongylus spp., and other strongyle-type nematodes. We found that nearly 50% of individuals harbored at least one species of helminth, but certain species, such as zebra and impala, exhibited higher prevalence than others. High canopy feeders, like giraffe, had lower prevalence than hosts feeding at medium and low foraging heights. For helminths, patterns of parasite sharing likely emerge from shared space use, which is mediated in part by mixed-species aggregations. The frequency with which host species associated together in mixed-species aggregations was positively correlated with the number of parasite taxa shared. We suggest that variation among species in their tendency to form mixed-species aggregations creates heterogeneity in transmission opportunities, and consequently, parasite sharing across ungulate species. These results enhance our understanding of the role of spatiotemporal relationships among host species in shaping parasite communities in mixed wildlife-livestock grazing systems.