Highlights d Isolated Caenorhabditis bovis from ear of a cow at livestock market in rural Kenya d Sequenced genome using the Oxford Nanopore MinION in nearby field laboratory d C. bovis genome is 40% smaller than C. elegans and encodes 7,000 fewer genes d Most closely related to a species isolated from carrion

Campylobacteriosis is a leading foodborne zoonosis worldwide, and is frequently associated with handling and consumption of poultry meat. Various studies indicate that Campylobacter causes a substantial human disease burden in low to middle-income countries, but data regarding the organism’s epidemiology in countries like Kenya are scarce. In sub-Saharan Africa, 3.8 million deaths of children under-5 years of age are reported annually. Of those, 25% are caused by diarrheal diseases, and Campylobacter is one of the most frequently isolated bacteria from diarrheic children. With the growth of urban conglomerates, such as Kenya’s capital, Nairobi, changes in diets, food production systems, and retailing dynamics, it is likely that exposure and susceptibility to this pathogen will change. Therefore, the importance of Campylobacter disease burden in Kenya may increase further. The objectives of this study were: 1) to determine the prevalence of Campylobacter spp. in Nairobi’s small-scale chicken farms and meat retailers, and 2) to identify potential risk factors associated with its presence in those sites. The prevalence data provides the first detailed baseline for this pathogen in the urban Kenyan context. The risk factors provide context-specific insights for disease managers. A cross-sectional study of broiler, indigenous chicken farms, and chicken meat retailers, was conducted in a peri-urban, low to middle-income area (Dagoretti), and a very-low income informal settlement (Kibera) of Nairobi. Chicken faeces were collected using one pair of boot socks per farm, and 3 raw chicken meat samples were purchased per retailer. Samples were cultured for viable Campylobacter spp. using mCCDA, followed by blood agar plates in aerobic/microaerobic conditions for prevalence calculations. A questionnaire-based survey on sanitary, sourcing and selling practices was conducted at each site for risk factor identification using logistic regression analyses. A total of 171 farm premises and 53 retailers were sampled and interviewed. The prevalence results for Campylobacter spp. were between 33 to 44% for broiler and indigenous chicken farms, 60% and 64% for retailers, in Dagoretti and Kibera, respectively. Univariable logistic regression showed an association between Campylobacter spp. presence and the easiness of cleaning the display material used by the retailer. Restricting access to the flock was also associated with the pathogen’s presence. Multivariable logistic regression identified the selling of defrosted meat as a retailer risk factor (OR: 4.69; 95% CI: 1.31–19.97), calling for more investigation of the reported repetitive freezing-thawing processes and cold chain improvement options. At the farm-level, having a pen floor of material not easy to clean was found to increase the risk (OR: 2.31; 95%CI: 1.06–5.37). The relatively high prevalence of Campylobacter spp. across different areas and value chain nodes indicates a clear human exposure risk. The open nature of both small-scale broiler and indigenous chicken production...

Surveillance of diseases in Kenya and elsewhere in East Africa is currently carried out by both human and animal health sectors. However, a recent evaluation highlighted the lack of integration between these sectors, leading to disease under-reporting and inefficiencies. This project aimed to develop an integrated and cost-effective surveillance and reporting system for 15 zoonotic diseases piloted in the counties of Bungoma, Busia, and Kakamega in western Kenya. Specifically, in this paper we describe the operational aspects of such a surveillance system. Interviews were carried out with key informants, and this was followed by field visits to identify sentinel sites and liaise with relevant stakeholders. Based on this information, a sampling strategy comprising 12 sentinel sites, 4 in each county, was developed. Each sentinel site comprised of a livestock market, 1–2 neighboring slaughter houses/slabs, and a hospital in the vicinity; each of the 12 sites, comprising 12 × 3 = 36 sampling locations, was visited every 4 weeks for 20 cycles. At each site, animal or patient sampling included a clinical examination and collection of blood, feces, and nasal swabs; in slaughtered animals, mesenteric lymph nodes, hydatid cysts, and flukes were also collected. At the end of each field visit, data on staff involved and challenges encountered were recorded, while biological samples were processed and tested for 15 zoonotic diseases in the field laboratory in Busia, Kenya. Public engagement sessions were held at each sentinel site to share preliminary results and provide feedback to both stakeholders and study participants. A livestock market visit lasted just over 3 h, and the most common challenge was the frequent refusals of animal owners to participate in the study. At the slaughterhouses, visits lasted just under 4 h, and challenges included poorly engaged meat inspectors or slaughter processes that were too quick for sampling. Finally, the hospital visits lasted around 4 h, and the most frequent challenges included low patients turn-out, frequent staff turn-over leading to poor institutional memory, and difficulty in obtaining patient stool samples. Our experiences have highlighted the importance of engaging with local stakeholders in the field, while also providing timely feedback through public engagement sessions, to ensure on-going compliance.

Demand for dairy products in sub-Saharan Africa, is expected to triple by 2050, while limited increase in supply is predicted. This poses significant food security risk to low income households. Understanding how the dairy food system operates is essential to identify mitigation measures to food insecurity impact. This study aims to determine the structure and functionality of Nairobi's dairy system using a value chain mapping approach.Primary data were gathered through focus group discussions and key informant interviews with dairy value chain stakeholders in Nairobi to obtain qualitative information on people and products in the chains while describing their interactions and flows. Qualitative thematic analysis combined with flowcharts created by participants enabled identification of key food system segments and the development of chain profiles (or flow-diagrams) which together form Nairobi's dairy system.Seven chain profiles forming Nairobi's dairy value chain were identified. These were found to be dominated by small-scale individuals who operate largely independently. Our profiles for the urban and peri-urban farming systems were structurally similar in their downstream networks, obtaining inputs from similar sources. Upstream, the urban systems were shorter, supplying mostly to immediate neighbours or based on own consumption, while the peri urban systems supplied to a wider network and showed some affiliations to producers' associations. Two distinct profiles characterize the milk flow from traders belonging either to a Dairy Traders Association (DTA) or those not belonging to this association (non-DTA). DTA traders sell mainly to fixed retailers and non-DTA traders to mobile retailers (hawkers or roadside vendors). Profiles associated with medium and large cooperatives were driven by networks of collection centres, but with medium-sized cooperatives selling half of their production to large processing companies, and large cooperatives only to fixed retailers. Large processing companies' profiles indicated distribution of high volumes and value addition processing. They reported strategic milk collection arrangements with suppliers on long, medium - or short - term contracts and with well-established product distribution channels.We have identified numerous inter-linkages across dairy chain profiles in Nairobi's complex system, demonstrating significant interdependency among the stakeholders. Therefore, enhancing the system's efficiency requires a holistic, system-wide approach and any policy interventions should consider every segment of the value chain. This study provides a methodological approach for organizations and policy makers to understand and address structural and functional vulnerabilities within food systems more broadly. The insights from this study are relevant to other rapidly growing cities in the region.

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