The evolution of Kenya’s animal health surveillance system and its potential for efficient detection of zoonoses

Introduction: Animal health surveillance systems in Kenya have undergone significant changes and faced various challenges throughout the years.Methods: In this article, we present a comprehensive overview of the Kenya animal health surveillance system (1944 to 2024), based on a review of archived documents, a scoping literature review, and an examination of past surveillance assessments and evaluation reports.Results: The review of archived documents revealed key historical events that have shaped the surveillance system. These include the establishment of the Directorate of Veterinary Services in 1895, advancements in livestock farming, the implementation of mandatory disease control interventions in 1944, the growth of veterinary services from a section to a ministry in 1954, the disruption caused by the Mau Mau insurrection from 1952 to 1954, which led to the temporary halt of agriculture in certain regions until 1955, the transition of veterinary clinical services from public to private, and the progressive privatization plan for veterinary services starting in 1976. Additionally, we highlight the development of electronic surveillance from 2003 to 2024. The scoping literature review, assessments and evaluation reports uncovered several strengths and weaknesses of the surveillance system. Among the strengths are a robust legislative framework, the adoption of technology in surveillance practices, the existence of a formal intersectoral coordination platform, the implementation of syndromic, sentinel, and community-based surveillance methods, and the presence of a feedback mechanism. On the other hand, the system’s weaknesses include the inadequate implementation of strategies and enforcement of laws, the lack of standard case definitions for priority diseases, underutilization of laboratory services, the absence of formal mechanisms for data sharing across sectors, insufficient resources for surveillance and response, limited integration of surveillance and laboratory systems, inadequate involvement of private actors and communities in disease surveillance, and the absence of a direct supervisory role between the national and county veterinary services.Discussion and recommendations: To establish an effective early warning system, we propose the integration of surveillance systems and the establishment of formal data sharing mechanisms. Furthermore, we recommend enhancing technological advancements and adopting artificial intelligence in surveillance practices, as well as implementing risk-based surveillance to optimize the allocation of surveillance resources

Socio‐ecological drivers of vertebrate biodiversity and human‐animal interfaces across an urban landscape

Urbanization can have profound impacts on the distributional ecology of wildlife and livestock, with implications for biodiversity conservation, ecosystem services and human health. A wealth of studies have assessed biotic responses to urbanization in North America and Europe, but there is little empirical evidence that directly links human activities to urban biodiversity in the tropics. Results from a large-scale field study conducted in Nairobi, Kenya, are used to explore the impact of human activities on the biodiversity of wildlife and livestock with which humans co-exist across the city. The structure of sympatric wildlife, livestock and human populations are characterized using unsupervised machine learning, and statistical modelling is used to relate compositional variation in these communities to socio-ecological drivers occurring across the city. By characterizing landscape-scale drivers acting on these interfaces, we demonstrate that socioeconomics, elevation and subsequent changes in habitat have measurable impacts upon the diversity, density and species assemblage of wildlife, livestock and humans. Restructuring of wildlife and livestock assemblages (both in terms of species diversity and composition) has important implications for the emergence of novel diseases at urban interfaces, and we therefore use our results to generate a set of testable hypotheses that explore the influence of urban change on microbial communities. These results provide novel insight into the impact of urbanization on biodiversity in the tropics. An understanding of associations between urban processes and the structure of human and animal populations is required to link urban development to conservation efforts and risks posed by disease emergence to human health, ultimately informing sustainable urban development policy

Genomic epidemiology of Escherichia coli:Antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

BackgroundLivestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism.MethodsWe conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock.ResultsWe detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households.ConclusionsFindings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control

Population genomics of <i>Escherichia coli</i> in livestock-keeping households across a rapidly developing urban landscape

Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance

The Genome of Caenorhabditis bovis

The free-living nematode Caenorhabditis elegans is a key laboratory model for metazoan biology. C. elegans has also become a model for parasitic nematodes despite being only distantly related to most parasitic species. All of the ∼65 Caenorhabditis species currently in culture are free-living, with most having been isolated from decaying plant or fungal matter. Caenorhabditis bovis is a particularly unusual species that has been isolated several times from the inflamed ears of Zebu cattle in Eastern Africa, where it is associated with the disease bovine parasitic otitis. C. bovis is therefore of particular interest to researchers interested in the evolution of nematode parasitism. However, as C. bovis is not in laboratory culture, it remains little studied. Here, by sampling livestock markets and slaughterhouses in Western Kenya, we successfully reisolated C. bovis from the ear of adult female Zebu. We sequenced the genome of C. bovis using the Oxford Nanopore MinION platform in a nearby field laboratory and used the data to generate a chromosome-scale draft genome sequence. We exploited this draft genome sequence to reconstruct the phylogenetic relationships of C. bovis to other Caenorhabditis species and reveal the changes in genome size and content that have occurred during its evolution. We also identified expansions in several gene families that have been implicated in parasitism in other nematode species. The high-quality draft genome and our analyses thereof represent a significant advancement in our understanding of this unusual Caenorhabditis species

Epidemiology of Clinically Relevant Antimicrobial Resistance at the Wildlife-Livestock-Human Interface in Nairobi

Background Antimicrobial resistance (AMR) represents one of the great challenges facing global health security in the modern era. Wildlife species, particularly those that utilise urban environments, are an important but understudied component of AMR epidemiology. This study investigated AMR overlap between sympatric wildlife, humans, livestock and their shared environment across the developing city of Nairobi, Kenya. We use these data to examine the role of urban wildlife in the spread of clinically relevant AMR. Methods 99 households across Nairobi were randomly selected on the basis of socioeconomic stratification. A detailed survey was administered to household occupants, and samples (n=2102) were collected from the faeces of 75 wildlife species inhabiting household compounds (n=849), 13 livestock species (n=656) and humans (n=333), and from the external environment (n=288). E. coli, our sentinel organism, was cultured, and a single isolate from each sample tested for sensitivity to 13 antibiotics. Diversity of AMR phenotypes were compared between urban wildlife, humans, livestock and the environment, to investigate whether wildlife are a net source for antimicrobial resistance in Nairobi. Generalised linear mixed models were used to determine whether the prevalence of AMR phenotypes and multi-drug resistant (MDR) E. coli carriage in urban wildlife is this linked to variation in ecological traits, such as foraging behaviour, and to determine household-level risk factors for sharing of AMR between humans, wildlife and livestock. Findings E. coli were isolated from 485 samples collected from wildlife, between September 2015 and September 2016. Wildlife carried a low prevalence of pan-susceptible E. coli isolates [9.3% (45/485) susceptible to all antibiotics tested] and a high prevalence of clinically relevant multi-drug resistance (MDR) [52% (252/485)], which varied between taxa and by foraging traits. Multiple isolates resistant to at least one agent in seven or more of the nine antimicrobial classes tested for, and a single isolate resistant to all antibiotics tested for in the study, were also present. The phenotypic diversity of AMR-E. coli in wildlife was lower than in livestock, humans and the environment. Within household perimeters, statistical models identified two “interfaces” for AMR exchange; i) between rodents/seed-eating birds, humans and their rubbish, and ii) between seed-eating birds, cattle and bovine manure. Interpretation Urban wildlife carry a high burden of clinically relevant AMR-E. coli in Nairobi, exhibiting resistance to drugs considered critically important for human medicine by the World Health Organisation. Identifiable traits of the wildlife contribute to this exposure. However, compared to humans, livestock and the environment, low phenotypic diversity in wildlife is consistent with the hypothesis that they are a net ‘sink’ rather than source of clinically relevant resistance. Wildlife that interact closely with humans, livestock and their waste within households, are exposed to more AMR phenotypes, and could therefore act as conduits for the dissemination of clinically relevant AMR to the wider environment. These results provide novel insight into the broader epidemiology of AMR in complex urban environments, characteristic of lower-middle income countries

Antimicrobial Resistance in Slaughterhouses, Kenya

Slaughterhouses are hotspots for the transmission of antimicrobial-resistant pathogens. We conducted stakeholder discussions on antimicrobial-resistant pathogens within the slaughterhouse setting. Butchers were described as powerful stakeholders; challenges included limited funding and staff, inadequate infrastructure, and limited laboratory capacity. Slaughterhouse workers understood that their work increased their risk for exposure

Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

Background Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism. Methods We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock. Results We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households. Conclusions Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control

Epidemiological connectivity between humans and animals across an urban landscape

Urbanization is predicted to be a key driver of disease emergence through human exposure to novel, animal-borne pathogens. However, while we suspect that urban landscapes are primed to expose people to novel animal-borne diseases, evidence for the mechanisms by which this occurs is lacking. To address this, we studied how bacterial genes are shared between wild animals, livestock, and humans (n = 1,428) across Nairobi, Kenya—one of the world’s most rapidly developing cities. Applying a multilayer network framework, we show that low biodiversity (of both natural habitat and vertebrate wildlife communities), coupled with livestock management practices and more densely populated urban environments, promotes sharing of Escherichia coli –borne bacterial mobile genetic elements between animals and humans. These results provide empirical support for hypotheses linking resource provision, the biological simplification of urban landscapes, and human and livestock demography to urban dynamics of cross-species pathogen transmission at a landscape scale. Urban areas where high densities of people and livestock live in close association with synanthropes (species such as rodents that are more competent reservoirs for zoonotic pathogens) should be prioritized for disease surveillance and control. </jats:p