Biphasic MERS-CoV Incidence in Nomadic Dromedaries with Putative Transmission to Humans, Kenya, 2022-2023.

Middle East respiratory syndrome coronavirus (MERS-CoV) is endemic in dromedaries in Africa, but camel-to-human transmission is limited. Sustained 12-month sampling of dromedaries in a Kenya abattoir hub showed biphasic MERS-CoV incidence; peak detections occurred in October 2022 and February 2023. Dromedary-exposed abattoir workers (7/48) had serologic signs of previous MERS-CoV exposure.

Mapping Nairobi's dairy food system: An essential analysis for policy, industry and research.

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.

Mapping of beef, sheep and goat food systems in Nairobi - A framework for policy making and the identification of structural vulnerabilities and deficiencies.

Nairobi is a large rapidly-growing city whose demand for beef, mutton and goat products is expected to double by 2030. The study aimed to map the Nairobi beef, sheep and goat systems structure and flows to identify deficiencies and vulnerabilities to shocks. Cross-sectional data were collected through focus group discussions and interviews with people operating in Nairobi ruminant livestock and meat markets and in the large processing companies. Qualitative and quantitative data were obtained about the type of people, animals, products and value adding activities in the chains, and their structural, spatial and temporal interactions. Mapping analysis was done in three different dimensions: people and product profiling (interactions of people and products), geographical (routes of animals and products) and temporal mapping (seasonal fluctuations). The results obtained were used to identify structural deficiencies and vulnerability factors in the system. Results for the beef food system showed that 44-55% of the city's beef supply flows through the 'local terminal markets', but that 54-64% of total supply is controlled by one 'meat market'. Numerous informal chains were identified, with independent livestock and meat traders playing a pivotal role in the functionality of these systems, and where most activities are conducted with inefficient quality control and under scarce and inadequate infrastructure and organisation, generating wastage and potential food safety risks in low quality meat products. Geographical and temporal analysis showed the critical areas influencing the different markets, with larger markets increasing their market share in the low season. Large processing companies, partly integrated, operate with high quality infrastructures, but with up to 60% of their beef supply depending on similar routes as the informal markets. Only these companies were involved in value addition activities, reaching high-end markets, but also dominating the distribution of popular products, such as beef sausages, to middle and low-end market. For the small ruminant food system, 73% of the low season supply flows through a single large informal market, Kiamaiko, located in an urban informal settlement. No grading is done for these animals or the meat produced. Large companies were reported to export up to 90% of their products. Lack of traceability and control of animal production was a common feature in all chains. The mapping presented provides a framework for policy makers and institutions to understand and design improvement plans for the Nairobi ruminant food system. The structural deficiencies and vulnerabilities identified here indicate the areas of intervention needed.

Human brucellosis in Baringo County, Kenya: Evaluating the diagnostic kits used and identifying infecting Brucella species.

Human brucellosis diagnosis has been a challenge in Brucella-endemic areas. In Kenya, diagnosis is usually carried out using Febrile Brucella Antigen agglutination test (FBAT) whose performance is not well documented. This paper reports on the sensitivity and specificity of the FBAT used for brucellosis diagnosis on blood samples/serum collected in three healthcare facilities in Baringo County, Kenya, and on Brucella species present in the study area. The FBAT test results at the hospitals were used to guide patient management. Patients who visited the hospital's laboratory with a clinician's request for brucellosis testing also filled a questionnaire to assess knowledge and attitudes associated with transmission of the disease in the study area. The remaining serum samples were tested again using FBAT and Rose Bengal Plate Test (RBPT) within a month of blood collection at the University Nairobi Laboratory. The two rapid tests were then compared, with respect to brucellosis diagnostic sensitivity and specificity. To identify infecting Brucella species, a proportion 43% (71/166) of the blood clots were analyzed by multiplex polymerase chain reaction (PCR) using specific primers for B. abortus, B. melitensis, B. ovis and B. suis. Out of 166 serum samples tested, 26.5% (44/166) were positive using FBAT and 10.2% (17/166) positive using RBPT. The sensitivity and specificity of FBAT compared to RBPT was 76.47% and 71.19%, respectively while the positive and negative predictive values were 29.55% and 96.72%, respectively. The FBAT showed higher positivity then RBPT. The difference in sensitivity and specificity of FBAT and RBPTs was relatively low. The high FBAT positivity rate would be indication of misdiagnosis; this would lead to incorrect treatment. Brucella abortus was detected from 9.9% (7/71) of the blood clots tested; no other Brucella species were detected. Thus human brucellosis, in Baringo was mainly caused by B. abortus.

Social-technical interventions to reduce antimicrobial resistance in agriculture: evidence from poultry Farmer Field Schools in Ghana and Kenya.

OBJECTIVES: To assess the feasibility of the Farmer Field School approach to address the complex problem of antimicrobial resistance in agriculture, specifically within small-to-medium-scale layer poultry systems in Ghana and Kenya. Impact was assessed across three domains relevant to the emergence and selection of antimicrobial resistance, including infection, prevention, and control practices, engagement with animal health professionals, and knowledge, attitudes, and practices on antimicrobial use and antimicrobial resistance. METHODS: Farmer Field Schools were held in Ghana (N = 2) and Kenya (N = 3) across an eight-month period with an average of 18 participants in each school. After completion, a quantitative evaluation survey was administered to participants and a sample of non-participants (Ghana; N = 97) (Kenya; N = 103). Logistic and ordinary least squares regression were used to assess differences between participants and non-participants on the three domains. RESULTS: Participation in a layer poultry Farmer Field School in Ghana and Kenya is associated with self-reported reductions in antibiotic use, particularly for prevention, an increased investment in farm infection, prevention, and control practices, including the use of footbaths and personal protective equipment, and enhanced engagement with animal health professionals. CONCLUSIONS: Antimicrobial resistance is a complex problem driven by a wide range of practices and multiple stakeholders. To holistically address these factors requires the use of complex intervention approaches. The Farmer Field School approach offers a complex intervention methodology that can reduce the emergence and spread of antimicrobial resistance in agricultural systems through targeting the variety of on-farm and off-farm factors that drive resistance.

Assessment of Milk Quality and Food Safety Challenges in the Complex Nairobi Dairy Value Chain.

Food networks present varying food safety concerns because of the complexity of interactions, production, and handling practices. We investigated total bacteria counts (TBCs) and total coliform counts (TCCs) in various nodes of a Nairobi dairy value chain and identified practices that influence food safety. A value chain analysis framework facilitated qualitative data collection through 23 key informant interviews and 20 focus group discussions. Content thematic analysis identified food safety challenges. Cow milk products (N = 290) were collected from farms (N = 63), collection centers (N = 5), shops/kiosks (N = 37), milk bars (N = 17), roadside vendors (N = 14), restaurants (N = 3), milk vending machines (N = 2), mobile traders (N = 2) and a supermarket (N = 1). Mean values of colony-forming units for TBC and TCC were referenced to East African Standards (EAS). Logistic regression analysis assessed differences in milk acceptability based on EAS. The raw milk from farms and collection centers was relatively within acceptable EAS limits in terms of TBC (3.5 × 105 and 1.4 × 106 respectively) but TCC in the milk from farms was 3 times higher than EAS limits (1.5 × 105). Compared to farms, the odds ratio of milk acceptability based on TBC was lower on milk bars (0.02), restaurants (0.02), roadside vendors (0.03), shops/kiosks (0.07), and supermarkets (0.17). For TCC, the odds that milk samples from collection centers, milk bars, restaurants, roadside vendors, and shops/kiosks were acceptable was less than the odds of samples collected from farms (0.18, 0.03, 0.06, 0.02, and 0.12, respectively). Comparison of raw milk across the nodes showed that the odds of milk samples from restaurants, roadside vendors, and shops/kiosks being acceptable were less than the odds of samples collected the farm for TBC (0.03, 0.04, and 0.04, respectively). For TCC, the odds of raw milk from collection centers, restaurants, roadside vendors, milk bars, and shops/kiosks being acceptable were lower than the odds of acceptability for the farm samples (0.18, 0.12, 0.02, 0.04, and 0.05, respectively). Practices with possible influence on milk bacterial quality included muddy cowsheds, unconventional animal feed sources, re-use of spoilt raw milk, milk adulteration, acceptance of low-quality milk for processing, and lack of cold chain. Therefore, milk contamination occurs at various points, and the designing of interventions should focus on every node.

Understanding Antimicrobial Use Contexts in the Poultry Sector: Challenges for Small-Scale Layer Farms in Kenya.

The poultry sector contributes significantly to Kenya's food and economic security. This contribution is expected to rise dramatically with a growing population, urbanization, and preferences for animal-source foods. Antimicrobial resistance is putting the poultry sector in Kenya-and worldwide-at risk of production losses due to the failure of medicines for animal (and human) health. The emergence and spread of antimicrobial resistance has been linked to overuse and misuse of antimicrobials in poultry and other sectors. Previous studies have documented poultry farmer antimicrobial use but without systematic consideration of the contexts (i.e., drivers) as important targets for behavior change, particularly in low- and middle-income countries. To improve understanding of antimicrobial use patterns in poultry systems, we conducted a mixed-methods knowledge, attitudes, and practices study of 76 layer farms in Kiambu County; Kenya. We found that commonly used antibiotics were often labeled for prophylactic, growth promotion, and egg production improvement purposes. Antimicrobial use was also motivated by the presence of diseases/disease symptoms, most of which could instead be managed through infection prevention measures. The results suggest that improving vaccination and biosecurity practices on farms and engaging with drug-makers to ensure proper labeling and marketing of antimicrobial drugs may represent important areas of opportunity for social behavior change communication and/or behavioral science interventions (i.e., nudges) to reduce disease burdens and promote prudent antimicrobial use. We conclude our findings with suggestions for further research into the behavioral insights at play in these scenarios to fuel future intervention development.

Risk factors for acute human brucellosis in Ijara, north-eastern Kenya.

Brucellosis is an important zoonotic disease globally, with particularly high burdens in pastoral settings. While the zoonotic transmission routes for Brucella spp. are well known, the relative importance of animal contact, food-handling and consumption practices can vary. Understanding the local epidemiology of human brucellosis is important for directing veterinary and public health interventions, as well as for informing clinical diagnostic decision making. We conducted a cross-sectional study in Ijara District Hospital, north-eastern Kenya. A total of 386 individuals seeking care and reporting symptoms of febrile illness were recruited in 2011. Samples were tested for the presence of Brucella spp. using a real-time PCR (RT-PCR) and results compared to those from the test for brucellosis used at Ijara District Hospital, the febrile Brucella plate agglutination test (FBAT). A questionnaire was administered to all participants and risk factors for brucellosis identified using logistic regression with an information theoretic (IT) approach and least absolute shrinkage and selection (LASSO). Sixty individuals were RT-PCR positive, resulting in a prevalence of probable brucellosis of 15.4% (95% CI 12.0-19.5). The IT and LASSO approaches both identified consuming purchased milk as strongly associated with elevated risk and boiling milk before consumption strongly associated with reduced risk. There was no evidence that livestock keepers were at different risk of brucellosis than non-livestock keepers. The FBAT had poor diagnostic performance when compared to RT-PCR, with an estimated sensitivity of 36.6% (95% CI 24.6-50.1) and specificity of 69.3% (95% CI 64.0-74.3). Brucellosis is an important cause of febrile illness in north-eastern Kenya. Promotion of pasteurisation of milk in the marketing chain and health messages encouraging the boiling of raw milk before consumption could be expected to lead to large reductions in the incidence of brucellosis in Ijara. This study supports the growing evidence that the FBAT performs very poorly in the diagnosis of brucellosis.

The Impacts of Animal Health Service Providers on Antimicrobial Use Attitudes and Practices: An Examination of Poultry Layer Farmers in Ghana and Kenya.

International organizations and governments have argued that animal health service providers can play a vital role in limiting antimicrobial resistance by promoting the prudent use of antimicrobials. However, there is little research on the impact of these service providers on prudent use at the farm level, especially in low- and middle-income countries where enforcement of prudent-use regulations is limited. Here, we use a mixed-methods approach to assess how animal health-seeking practices on layer farms in Ghana (n = 110) and Kenya (n = 76) impact self-reported antimicrobial usage, engagement in prudent administration and withdrawal practices and perceptions of antimicrobial resistance. In general, our results show that the frequency of health-seeking across a range of service providers (veterinarians, agrovets, and feed distributors) does not significantly correlate with prudent or non-prudent use practices or the levels of antimicrobials used. Instead, we find that patterns of antimicrobial use are linked to how much farmers invest in biosecurity (e.g., footbaths) and the following vaccination protocols. Our results emphasize that more research is required to understand the interactions between animal health service providers and farmers regarding antimicrobial use and antimicrobial resistance. Addressing these gaps will be crucial to inform antimicrobial stewardship training, curriculums and, guidelines whose ultimate purpose is to limit the selection and transmission of antimicrobial resistance.

Risk factors for serological evidence of MERS-CoV in camels, Kenya, 2016-2017.

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging viral disease and dromedary camels are known to be the source of human spill over events. A cross-sectional epidemiological surveillance study was carried out in Kenya in 2017 to, 1) estimate MERS-CoV antibody seropositivity in the camel-dense counties of Turkana, Marsabit, Isiolo, Laikipia and Nakuru to identify, and 2) determine the risk factors associated with seropositivity in camels. Blood samples were collected from a total of 1421 camels selected using a multi-stage sampling method. Data were also collected from camel owners or herders using a pre-tested structured questionnaire. The sera from camel samples were tested for the presence of circulating antibodies to MERS-CoV using the anti-MERS-CoV IgG ELISA test. Univariate and multivariable statistical analysis were used to investigate factors potentially associated with MERS-CoV seropositivity in camels. The overall seropositivity in camel sera was 62.9 %, with the highest seropositivity recorded in Isiolo County (77.7 %), and the lowest seropositivity recorded in Nakuru County (14.0 %). When risk factors for seropositivity were assessed, the "Type of camel production system" {(aOR = 5.40(95 %CI: 1.67-17.49)}, "Age between 1-2 years, 2-3 years and above 3 years" {(aOR = 1.64 (95 %CI: 1.04-2.59}", {(aOR = 3.27 (95 %CI: 3.66-5.61)}" and {(aOR = 6.12 (95 %CI: 4.04-9.30)} respectively and "Sex of camels" {(aOR = 1.75 (95 %CI: 1.27-2.41)} were identified as significant predictors of MERS-CoV seropositivity. Our studies indicate a high level of seropositivity to MERS-CoV in camels in the counties surveyed, and highlights the important risk factors associated with MERS-CoV seropositivity in camels. Given that MERS-CoV is a zoonosis, and Kenya possesses the fourth largest camel population in Africa, these findings are important to inform the development of efficient and risk-based prevention and mitigation strategies against MERS-CoV transmission to humans.