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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., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)

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.

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, R 0 , 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 R 0 . 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 R 0 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., (Copyright © 2021 Elsevier B.V. All rights reserved.)

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., (Copyright © 2014 Elsevier B.V. All rights reserved.)