ILRI supervised theses and dissertations
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Item Framing livestock and climate change in eastern Africa: Ambiguity and knowledge brokering in science-policy interfaces(Thesis, 2024-10-08) Cramer, Laura K.Item Prévalence et quantification de campylobacter dans les fèces de poulets domestiques et facteurs de risque dans la région du centre nord (Burkina Faso)(Thesis, 2024-09-20) Abou, D.A.T.Campylobacter spp. représente l’un des principaux agents bactériens de maladies infectieuses d’origine alimentaire (MIOA) dans le monde. Le réservoir de cette bactérie est la volaille, qui en disséminant ce micro-organisme dans l’environnement contamine les autres animaux et les humains. L’objectif de notre étude était de déterminer le taux de portage de Campylobacter spp et sa concentration dans les fèces de poulets de ménages. Après une enquête auprès de 73 ménages de Boussouma, dans la région du centre Nord du Burkina Faso, un total de 292 poulets locaux a été collectés auprès de ces ménages entre octobre 2023 et janvier 2024. Ainsi, les fèces de ces poulets ont été analysés à l’aide de méthodes microbiologiques standard. Les résultats ont indiqué que 76,03% (222/292) des échantillons fécaux analysés, étaient positifs à Campylobacter spp et la charge au Campylobacter, variait entre 2×105 et 4,5×107 UFC/ g de fèces. Même si cette charge ne constitue pas un problème pour ces poulets (règlement CE 1495/2017), ce germe peut être transmis aux humains et aux autres animaux. Il serait donc nécessaire de mettre en place des mesures de biosécurité pour éviter la contamination des humains par Campylobacter spp. L’évaluation des pratiques d’élevages a permis de mettre en évidence le non confinement et le non traitement aux antibiotiques des poulets comme des facteurs de risque de contamination. Cette étude a permis de connaitre le portage aviaire de Campylobacter spp par les espèces locales de poulets en milieu rural et le niveau de concentration de ce germe dans les fèces de ces poulets de ménage.Item Connaissance de la chaine d'approvisionnement des vaccins de volailles et des défis associés à la vaccination contre la maladie de Newcastle dans le Centre-Nord du Burkina Faso en 2023(Thesis, 2024-12-20) Ouedraogo, S.E.La maladie de Newcastle (MN) représente un obstacle majeur au développement de l'aviculture traditionnelle au Burkina Faso, ce qui rend nécessaire une stratégie de vaccination efficace. Cette étude visait à comprendre la chaîne d'approvisionnement en vaccins contre la MN ainsi que les lacunes et les obstacles dans un cadre rural où l’aviculture joue un rôle important dans la génération de revenus pour les communautés, ainsi que dans la satisfaction de leurs besoins nutritionnels. L’étude a été réalisée à Boussouma, une commune de la région du Centre-Nord. Elle a impliqué une enquête auprès de 483 ménages élevant des poulets, des entretiens avec huit (08) acteurs de la chaîne d'approvisionnement en vaccins pour les volailles et huit (08) discussions de groupe réalisées dans quatre (04) villages, avec un total de 30 hommes et 32 femmes aviculteurs. Les données quantitatives ont été analysées avec le logiciel R tandis que les données qualitatives ont été analysées en utilisant une approche générale inductive. Les résultats ont montré que les vaccins contre la MN sont importés, et que des analyses de laboratoire ne sont généralement pas réalisés pour en contrôler la qualité. Les enquêtes menées ont révélé que les agents de santé animale communautaires responsables de la vaccination dans les villages sont insuffisants en nombre pour garantir une couverture adéquate. Bien que la majorité (80%) des éleveurs adoptent la vaccination, les conditionnements de grande capacité des vaccins restent un obstacle majeur car ils ne répondent pas aux besoins des petits éleveurs, entraînant des difficultés dans la distribution et l’utilisation des vaccins. Le maintien de la chaîne du froid est également un défi majeur pour les agents de santé animale, qui rencontrent des obstacles tels que de longues distances à parcourir, des pannes de réfrigérateurs, des coupures d’électricité et des problèmes d'électrification. La participation des éleveurs à la vaccination est affectée négativement par tous ces obstacles, qui se résument en insuffisance logistique et manque de contrôle qualité des vaccins sur le terrain. Ces résultats mettent ainsi en évidence des lacunes significatives dans la chaîne d'approvisionnement en vaccins contre la MN, soulignant la nécessité d'améliorations pour garantir la disponibilité et la qualité des vaccins dans les zones rurales.Item Mycotoxins in Kenyan poultry feeds: Occurrence and use of bentonite and fumonisin esterase as a sustainable mitigation strategy to reduce effects of aflatoxins and fumonisins in broiler chicken and layer hens production(Thesis, 2023-10-18) Ochieng, P.E.This doctoral thesis consists of six chapters. Chapter 1 is a general introduction of what mycotoxins are and their toxicological impacts on poultry, and this is based on a published review paper. Major mycotoxins covered in detail are AFs, FBs, DON, ZEN, OTA, and T-2/HT-2. Some of the frequently occurring and yet neglected mycotoxins are discussed as well, and their toxicities highlighted. These include BEA, ENNs, MON, AME, AOH and modified mycotoxins of ZEN and DON such as deoxynivalenol-3-glucoside and zearalenone-14-sulfate. Also in this chapter, co-occurrence of mycotoxins in feed and feed ingredients is presented and co-contamination by FBs and AFs in feed and feed ingredients from SSA is highlighted with their impact on chickens. Legislation on mycotoxins in poultry feeds are further explored in this chapter, with particular discussion of the regulatory and guidance limits in SSA. Techniques for detecting mycotoxins biological matrices are also presented and sample preparation, clean-up and detection, especially using LC-MS/MS highlighted. Moreover, mycotoxin mitigation strategies for poultry protection are discussed, with the post-harvest methods that employ clay-based compounds, such as bentonite, and fumonisin esterase noted. Lastly, the rationale of this doctoral study is highlighted and objectives of this thesis discussed, with specific objectives being i) To study the prevalence of mycotoxins in Kenyan poultry feeds; ii) To produce sufficient quantities of AFs and FBs in the laboratory to be used in subsequent long-term in vivo trials with broiler and layer chickens; iii) To evaluate the effects of feed contaminated with AFs or FBs, or their combination, on broiler chickens and laying hens’ health and productivity; iv) To evaluate the carry-over of AFs to chicken products in a single or concomitant FBs contamination; and v) To assess the efficacy and safety of bentonite and fumonisin esterase mycotoxin detoxifying agents (feed additives) to protect chickens against negative health and productivity effects of AFs and FBs, respectively, and carry-over of AFs to chicken products. Chapter 2 details a survey of mycotoxin contamination levels in poultry feeds and feed ingredients from Kenya. This study was carried out to give an overview of the mycotoxins levels in feeds sold in Kenya in order to use relevant field concentrations for in vivo trials with broiler and layer chickens. Both feed and feed ingredients had a high prevalence (above 70%) of Fusarium mycotoxins including total FBs (max. level of 14,346 μg/kg), DON (max. level 1,037 μg/kg) and ZEN (max. level 910 μg/kg). Total AFs (max. level 99 μg/kg) were detected in 93% of the feed samples and in 29% of feed ingredients. Low occurrences of OTA (19%), T-2 and HT-2 (4%) were observed in feed and feed ingredients. Neglected and modified mycotoxins including Aspergillus toxins, Fusarium metabolites, Alternaria toxins, Penicillium toxins were also found in the samples. All mycotoxins were detected below EU regulatory limits, except for AFB1, where 16% of the samples had concentrations above the EU and EAC regulatory limits of 20 μg/kg for AFB1 in poultry feeds. Co-occurrence of mycotoxins in the samples was observed with all 4 major mycotoxins (AFs, FBs, DON and ZEN) detected in 55% of the samples and co-occurrence of AFs with FBs observed in 61% of the samples. In chapter 3, methods for laboratory production of large quantities of AFs and FBs for use in long-term in vivo trials are presented. Factors that affect mycotoxin production such as type of substrate, temperature, light and fungal isolate were optimized to enable maximum production of these mycotoxins. The concentration of AFs and FBs in the culture materials were screened by ELISA methods and confirmed by LC-MS/MS methods. Highest yield of AFB1 (88,174 μg/kg of substrate) was obtained in maize kernels inoculated with three different A. flavus isolates and incubated at 29°C for 21 days. For FBs, the highest yield (1,043,806 μg/kg of substrate) was in cracked maize kernels inoculated with three different F. verticillioides isolates and incubated for 21 days at 22–25°C in a growth chamber with yellow light conditions. Sufficient amounts of AFB1 and FBs were produced in maize, which was then mixed with control feeds (with no added mycotoxins or detoxifiers) to prepare experimental diets for in vivo animal trials. Chapter 4 describes the effects of dietary AFB1 and FBs (FB1+FB2), alone or in combination on broiler chickens’ health and productivity as well as carry-over of AFs from feed to plasma, liver and muscle. Safety and efficacy of bentonite and fumonisin esterase to counteract the effects of AFB1 and FBs were also evaluated. Four hundred one day old chickens were fed 20 diets (20 birds/treatment) from 1 to 35 days of age. The diets were either control or AFB1 (60 or 220 μg/kg feed) or FBs (17.43 mg FB1+FB2/kg feed), alone or in combination, and with bentonite clay (AFs binder) and/or fumonisin esterase (FBs modifier) in selected diets. The results showed that the levels of AFs and FBs used in this study did not affect growth performance of the broiler chickens. Nevertheless, the FCR was poor in broilers fed high AFB1 only when compared to those fed both high AFB1 and FBs. Changes in serum TP and ALB were observed in birds fed FBs alone or in combination with AFB1. The relative heart weight of the birds was increased by dietary high AFB1 and FBs. The efficiency of the bentonite was demonstrated in that the binder reduced the effects of AFB1 on the heart, liver and spleen weights. In-house developed and validated UHPLC-MS/MS methods were used to assess the carry-over of AFs from feed to plasma, breast muscle and liver of the birds. Residues of AFB1 (max: 0.12 ± 0.03 μg/kg) were detected above the limit of quantification (LOQ) in liver only, and from birds fed diets contaminated with high AFB1 (220 μg/kg feed). Supplementing bentonite clay into these diets reduced the accumulation of AFB1 in the liver by up to 50%, although the differences were not significant. No AFs were detected in breast muscles of the broiler chickens whereas AFB1 was detected in plasma of birds fed high AFB1, but below the LOQ. Moreover, at the doses tested, both bentonite clay and fumonisin esterase were found to be safe and did not affect the growth and health of the broiler chickens. In chapter 5, four hundred 21-weeks old laying hens were used to study the effects of AFB1 and FBs, alone or in combination, on health and productivity of the laying hens as well as carry-over of AFs from feed to plasma, liver, muscle and eggs. The safety and efficacy of bentonite and fumonisin esterase to prevent or reduce effects of AFB1 and FBs, respectively, were also evaluated. The hens were fed either the control diet or with AFB1 (54.6 or 546 μg/kg feed) and/or FBs (7.9 mg/kg feed) for 28 days. In selected diets, bentonite clay or fumonisin esterase were added. After 28 days, the results showed that neither AFB1 nor FBs caused an effect on performance, except for egg production which was reduced in hens fed diets with high AFB1 (546 μg/kg feed). Changes in serum TP and ALB levels and relative weights of liver, spleen and gizzard in laying hens fed contaminated diets are discussed. Analysis of residues of AFs in liver, plasma, muscle and eggs using validated UHPLC-MS/MS methods showed that the highest residues of AFB1 (0.66 μg/kg) were present in liver samples of laying hens fed 546 μg AFB1/kg feed and 7.9 mg FBs/kg feed for 28 days. Furthermore, AFB1 was detected in eggs and plasma of layers fed AFB1 (546 μg/kg) alone or with FBs (7.9 mg/kg feed), whereas no AFs were detected in the breast muscles of the laying hens. The efficacy of the two mycotoxin detoxifying agents (bentonite and fumonisin esterase) to reduce or suppress the negative effects of AFs and FBs was demonstrated in this study. The bentonite binder was also found to be effective in reducing the accumulation of AFs in the liver of laying hens as well as carry-over of AFs into eggs. Furthermore, bentonite clay and fumonisin esterase at the doses tested were safe and had no effect on the health and productivity of the laying hens. In chapter 6, general discussion, relevance of the study, future perspectives and conclusion are presented. The general discussion highlights the mycotoxins of concern in SSA, particularly AFs and FBs and the need to evaluate their effects on animal health and productivity, as well as their carry-over to animal products. Use of laboratory produced mycotoxins in feeding trials are also outlined in the discussion. The parameters to include when assessing toxicological impacts of mycotoxins or potential mycotoxin detoxifiers on chickens are further presented. The parameters include blood biochemical changes, gross pathological changes, organ weights and safety of animal food products. Also, the importance of analysing fecal, Sa/So ratio and microbiota of the GIT to determine the efficacy and safety of a potential mycotoxin detoxifier are further highlighted. Safety of mycotoxins detoxifiers on animals as well as the effects of long-term use are further discussed. The relevance of the current doctoral thesis is discussed on the basis of its contribution towards safe feed and food and linked to the UN SDGs agenda for food security and safety aimed at ensuring provision of sufficient and nutritious food to everyone by 2030. In the section of future perspectives, the research gaps are highlighted for every chapter of this thesis and areas for future studies are suggested. These include collaborations as well as coordination among private and public sectors to ensure continuous monitoring of mycotoxins along the food chain. The need for capacity building for human resources and equipment are also noted. Robust methods for simultaneous detection of multiple mycotoxins in food and feed is suggested. The need to carry out more in vivo animal trials, especially in SSA, to assess effects of mycotoxins on animal health and productivity, and in particular the effects of co-contamination by multiple mycotoxins, under conditions similar to farming practices in SSA is advised. Hindrances to setting regulatory limits for different mycotoxins in feed and food, especially in SSA, are highlighted in this section, and the need to harmonize regulatory limits of mycotoxins in different commodities across regions and trading blocks is also suggested. Some of the sustainable post-harvest mitigation strategies currently being explored to ensure safety of animal feeds and animal food products are explored in this section, particularly those that are cost effective, efficient and readily available in SSA such as clay compounds. In the conclusion, this doctoral thesis provides evidence on effects of AFB1 or FBs or both, on health and productivity of broiler chickens and laying hens as well as transfer of AFB1 to poultry food products. Information on safety and efficacy of bentonite clay and fumonisin esterase to counteract the negative effects of AFB1 and FBs, respectively, is further provided. This thesis also advises on laboratory production of mycotoxins as a cost effective means of producing sufficient quantities of mycotoxins for long-term in vivo animal experiments. The need to continuously monitor for multi mycotoxins contamination of poultry feeds to prevent their effects on animal health and productivity as well as transfer to animal source foods is suggested to prevent the mycotoxins from entering the food chain.Item Prevalence of clinical and subclinical mastitis in smallholder dairy farms in Kiambu, Kenya(Thesis, 2023-12-29) Hansen, N.S.; Jensen, R.In Kenya, mastitis is a major challenge, causing production losses and excessive antibiotic use. Early detection and correct mastitis treatment are crucial for the cow's recovery, thus increasing animal health welfare and minimizing economic losses for the farmer. There is a general lack of proper diagnosis, relevant knowledge, and resources in smallholder dairy farms in Kenya, leading to self-diagnosis and treatment. This results in indiscriminate or unnecessary use of antibiotics, affecting the development of antimicrobial resistance (AMR), a major global public health issue. A simple, rapid, on-farm test accessible to farmers is needed to guide initial treatment decisions. This study investigates the current mastitis management and estimates the apparent prevalence (AP) of mastitis in smallholder dairy farms in the Githunguri sub-county in Kiambu, Kenya. The distribution of four specific mastitis pathogens is determined. This study further evaluated the California Mastitis Test (CMT) to detect mastitis and the Point of Cow test (POC-t) to detect bacteria in milk samples. Lastly, this study explores the POC-t’s adoptability by dairy farmers and animal health service providers (AHSPs) in Kenya. This was done by visiting 42 farms, administering mastitis management questionnaires, and collecting milk samples from 124 randomly selected cows. Smallholder dairy farmers generally know the importance of housing practices, but the results suggest opportunities for improvement regarding milking hygiene techniques and control methods of mastitis. This study found the APs of clinical mastitis based on CMT and clinical signs at 6.5% and 14.3% and the APs of subclinical mastitis based on CMT at 50.0% and 69.0% at the cow and farm levels, respectively. The APs of clinical mastitis based on somatic cell count (SCC) and clinical signs were 6.8% and 16.7%, and the APs of subclinical mastitis based on SCC were 63.6% and 90.0% at the cow and farm levels, respectively. Based on clinical signs alone, the APs were 8.0% and 14.3% for clinical mastitis at the cow and farm levels, respectively. Streptococcus agalactiae was the most isolated target pathogen in 94.9% of positive samples. The calculated sensitivity (Se), specificity (Sp), and accuracy (Ac) of the CMT were 58.2%, 96.9%, and 80.1%, respectively, and for POC-t, 47.5%, 79.1%, and 56.5%, respectively. There was an interest in using the POC-t among farmers and AHSPs. The findings suggest a need for additional POC testing in low- and middle-income countries as the POC-t can potentially support the development of treatment guidelines in Kenya.Item Connaissances des risques liés à la gestion du fumier sur la santé publique dans les ménages de la région de Sikasso au Mali(Thesis, 2023-11-22) Yena, A.S.L’élevage contribue à l’augmentation de la production des cultures vivrières et de rentes à travers la traction animale et la production de fumure. Malgré ces atouts, l’élevage peut avoir des impacts sanitaires et environnementaux négatifs liés notamment à la cohabitation entre l’animal et l’homme et à la mauvaise gestion des déchets tels que la fumure. En effet, les populations sont souvent exposées à des risques de santé à travers des pratiques comme la divagation des animaux, leur promiscuité avec les populations, leur entretien, le stockage et l’épandage du fumier. Que ce soit les parasites ou microbes, les mauvaises odeurs, la pollution de l’eau et des sols, la contribution à l’augmentation des gaz à effet de serre, la gestion du fumier au sein des ménages entraine de nombreuses nuisances. La présente étude avait alors pour objectif de déterminer les pratiques de gestion du fumier au niveau des ménages et identifier les risques potentiels générés par les pratiques de gestion du fumier sur la santé les communautés qui détiennent ces animaux. A cet effet, une enquête descriptive a été menée au sein de 300 ménages dans deux cercles au Mali, à savoir celui de Sikasso et de Koutiala. Les répondants au questionnaire étaient majoritairement des hommes (98,7%) analphabètes (54,3%). Parmi eux, 97,8% utilisaient un lieu de confinement pour la garde des animaux (petits ruminants et volaille). Ce sont les clôtures sans toit ou des attaches aux piquets qui ont le plus été rencontrées (50,8%). L’étude a permis de constater que certaines pratiques de gestion du fumier peuvent constituer des risques pour la santé publique et environnementale. Ce sont notamment : la garde des animaux au sein d’une clôture sans toit ou attachés à un piquet dans les concessions (50,8%), l’absence de plancher au sein des lieux de confinement (1,3%), le non ramassage du fumier des animaux en divagation (74,3%), l’utilisation des enfants (40,3%) et des femmes (33,3%) comme main d’oeuvre pour le nettoyage du lieu de confinement et l’entretien des animaux, le stockage en tas du fumier (80,1%) sans couverture, ni plancher étanche favorisant les risques de pollutions environnementales (90,8%), le défaut d’utilisation des équipements de protection individuelle lors de la manipulation du fumier. Malgré ces pratiques, l’étude a également permis de s’apercevoir qu’un très faible constat de maladies qui selon les répondants pourraient être dues à la gestion du fumier a été fait. À la lumière des résultats de cette étude et de la discussion relative à la thématique, des recommandations ont été formulées afin d’améliorer la gestion optimale du fumier. Notamment, la formation, le conseil, le suivi, les démonstrations sur les techniques de gestion du fumier auprès des agro-éleveurs et l’initiation d’autres études plus approfondies sur la thématiqueItem Farming in transition in East Africa: Financial risk taking and agricultural intensification(Thesis, 2023-01-19) Balchin, E.This thesis contributes to understandings of the intensification of livestock production in Busia County, Western Kenya. Livestock production here has been intensifying in the recent past, and became a key strategy in Kenya for meeting the growing demand for livestock source foods here whilst simultaneously raising smallholder farmers out of poverty. How smallholders juggle insufficient incomes with a variety of expenditure needs is rarely considered in the context of smallholder livestock production in great detail. This study utilises the Financial Diaries Methodology to harness a great depth of information from 15 smallholder livestock farmers in Busia to establish the ways in which they attempt to intensify their production, understand how they engage with financial providers to achieve this, and establish the risks they face in their production. Research took place between November 2018-Febuary 2020, with around 20 months spent in the field. The results from this study find that overall, the participants make a profit from their livestock production, save for those who are categorised as subsistence farmers. However, there is a great variation in the size of these profits, even when expenditure on inputs (the resources used in livestock production, such as feed and veterinary care) is similar. Dairy cattle in particular tend to be far more lucrative, whilst chickens often resulted in financial losses for all participants, particularly due to very high mortality levels that prevent significant rises in the number of chickens owned at households that can be sold. Additionally, inputs the participants invest in plays a significant role in the incomes derived. However, despite large profit margins, this often equates to low levels of income in terms of money. The participants never accessed finance specifically for livestock production needs, and expressed fear of taking loans. Thus, this study recommends that if individual farmers are to intensify, they require access to higher yielding livestock and to inputs in a way that will not cause them any further financial burdens, as well as access to livestock production education.Item Are animal breeding and digital technologies shifting gender norms and dynamics? The case of Tanzanian small-scale dairy farming households(Thesis, 2023-07-31) Okeke, I.I.Gender dynamics and norms are crucial for rural livelihoods and achieving food security. While norms related to ownership, management, product distribution, and sales methods are prevalent in dairy production, more research needs to be conducted in this area. This study hypothesized that innovative technologies introduced without considering gender dynamics and norms may limit the extent of transformative change. Using gender-sensitive mixed methods, this study investigated the potential implications of introducing technologies for intra-household dynamics and gender norms in dairyproducing communities. The African Asian Dairy Genetic Gains Programme (AADGG) has been introducing improved genetics, precise breeding techniques, and telemetric data recording technologies in smallholder dairy farms in Tanzania, and this served as the study case. Intra-household data were collected from 180 smallholder farmers surveys, gender-aggregated focus group discussions involving 80 farmers, and six expert interviews. Data were analyzed using content analysis, descriptive statistics, the percentage rate of change, and the coefficient of variation. Age, education, gender, household size, household role, and farming system practiced were found to be significant determinants of the adoption of digital dairy applications (DDAs). Introducing dairy breeding technologies reduced women’s control over milk incomes in two ways. First, improved breeds led to women and men participating in milking, previously carried out solely by women. The increased profitability of the dairy enterprise raised the outlook and status of some chores related to dairy farming. The shift, although linked with women’s economic empowerment and gender-equal distribution of household responsibility, resulted in the transfer of milk income from women to men in most cases. The transfer of milk income from women to men demonstrates a marked shift in women’s traditional roles, from exclusive homemakers in charge of the overall well-being of the household to dependents on their husbands for money to meet household nutritional and welfare needs. The study revealed that both male and female male and female dairy farmers are now venturing into and taking control of dairy breeding activities by the opposite gender. The situation shows that tasks and responsibilities in dairy breeding, traditionally assigned to either men or women, are now actively pursued and led by both genders. In the majority of survey responses (99.9%), the study showed that technological improvement led to milk increase. The milk increase did not, however, necessarily correspond to higher income for farmers during the wet seasons, as the milk market would easily oversaturate due to excessive supply, culminating in low prices. The study views this situation as perception-based low milk pricing because the majority of respondents interviewed for this study were “borderline educated farmers” (farmers with primary education) who might not be able to understand the economics of production (input and output). These farmers might be unable to calculate the labour input, time, and opportunity cost of producing milk in the wet season against the milk price. The shifting dynamics in gender norms may have positive and negative consequences on household food security, nutritional status, and general livelihoods. However, the severity within households depends on the dairy farmer’s household type and marital status. These findings suggest innovative technologies are more likely to have transformative outcomes if tailored to suit the needs of different gender groups, consider prevailing societal and gender norms, and be accompanied by requisite training on further innovations that would mitigate the consequences of the current innovations. Also, introducers of dairy breeding technologies should consider training farmers on dairy farming input, output recording, and basic profit and loss calculation to better understand milk prices in different production seasons.Item Mobilisation des acteurs autour de la lutte contre la résistance aux antimicrobiens au Sénégal selon l’approche One Health: Focus sur le partage de l'information comme l'un des leviers d'action majeurs dans la définition des politiques concertées(Thesis, 2023) Nganjui, C.; Muteba, D.; Tchiebue, G.La résistance aux antimicrobiens (RAM) constitue actuellement l’un des problèmes mondiaux majeurs de santé publique. La mise en œuvre des actions contre la RAM fait appel à une multiplicité d’acteurs. Le paysage de la RAM au Sénégal n’échappe pas à cette dynamique mondiale : depuis 2017, une plateforme « One health » a été créée avec en son sein des groupes thématiques dont celui de la RAM, fait d’une grande variété des parties prenantes censées coconstruire un ensemble des savoirs et matérialiser la lutte dans leurs secteurs respectifs. L’interconnexion entre ces parties prenantes est assurée, dans une large mesure, par le partage mutuel d’informations ressources à l’orientation des politiques et moyens de lutte. A travers les entretiens semi structurés et « focus groups », notre étude a montré que le partage, la gestion de l’information en rapport avec la RAM, restent sectoriels et ne pourrait donc pas encore, à ce stade, favo-riser une meilleure collaboration entre parties prenantes de la lutte contre la RAM au Sénégal. Graduellement, cette étude nous a permis d’évaluer la perception de la problématique de la RAM par les parties prenantes, de situer le rôle de chaque acteur dans les rouages des pratiques informationnelles exis-tantes autour de la RAM, de profiler la mise en place d’un modèle de diffusion de l’information entre par-ties prenantes de lutte contre la RAM au Sénégal.Item Evaluating implementation strategies for improved food safety in Vietnam(Thesis, 2023-04-28) Hai Hoang Tuan NgoPork is the most popular and consumed meat in Vietnam, and the preference among consumers for fresh and “warm” pork makes the traditional pork value chain dominate the pork industry. This thesis assessed microbial contamination in pork, then evaluated the technical and economic aspects of light-touch interventions in improving the safety of pork in the small-scale value chain. A total of 671 specimens of retailed pork were collected from traditional retail, modern retail, and food services to assess total bacterial count (TBC) and Salmonella prevalence. The results showed that 58% of samples were contaminated with Salmonella, and 93% of samples did not qualify for the Vietnamese standard of TBC in meat. The contamination of pork was not significantly different between the traditional and modern retail while hygiene practices were associated with lower microbial contamination. Subsequently, light-touch intervention packages were co-designed and implemented at ten small-scale slaughterhouses and 29 traditional pork shops. The packages consisted of providing tools and delivering training for participants. Results showed a reduction of TBC in pig carcasses (from 4.46 to 4.24 log10 colony forming units (CFU)/cm2, p = 0.09) and Salmonella prevalence in retailed pork (from 52% to 24% detection, p = 0.08). The upgraded pork shop was then introduced to local consumers in a Becker-DeGroot-Marschak auction game. Consumers showed a strong belief in the intervention at retail stage and were willing to pay 13,000 Vietnam Dong (VND), or 20% higher price, (p < 0.01) for each kilogram intervened pork compared to a typical one. This premium payment would cover the investment to upgrade most shops (varied from 421 to 4,146 VND/kg pork). Besides, consuming intervened pork was predicted to reduce annual risk of salmonellosis from 12% to 6%. This reduction could lead to a net benefit of 27,696,241 VND (95% CI: -546,816 – 117,515,493) for consumers and 207,788 VND (95% CI: -38,941 – 658,884) for pork sellers. This thesis provides a sustainable solution to improve pork safety across the small-scale value chain in Vietnam. An appropriate strategy to motivate these actors to implement the light-touch intervention could significantly improve the well-being of community.Item Epidemiology of selected respiratory diseases and their impacts on smallholder pig production systems in Lira District, Uganda(Thesis, 2023-01-11) Oba, PeterRespiratory diseases contribute significant economic losses to the swine industry globally. In Uganda, no detailed studies on pig respiratory pathogens have been undertaken previously. This doctoral thesis aimed to fill knowledge gaps on epidemiology of important respiratory pathogens, gastro-intestinal (GIT) parasites and their economic impacts on smallholder pig production systems in Uganda. The studies were conducted in Lira district from October 2018 to September 2019. Four respiratory pathogens of economic importance in pigs including porcine reproductive and respiratory syndrome virus (PPRSv), porcine circovirus type 2 (PCV2), Mycoplasma hyopneumoniae (M. hyo) and Actinobacillus pleuropneumoniae (App) were studied. The first study was a desk systematic review on status and gaps of research on swine respiratory pathogens in Africa. This was followed by three cross-sectional studies: prevalence and risk factors for respiratory co-infections, a slaughter slab survey which correlated serology to 4 selected respiratory pathogens and pneumonia lesions and identify PRRSv genotypes. Tissue and blood samples were collected from pigs and used for genotypying PRRSv and to determine exposure to respiratory pathogens using ELISA assays, respectively. A mixed effects model was fitted to quantify economic losses due to exposure of pigs to respiratory pathogens and GIT parasites. Results highlighted major knowledge, information gaps on epidemiology, and economic impacts of the 4 studied pathogens reported in pigs in Africa. We found that there was dual circulation of both PRRSv PRRSv-1 and PRRSv-2 in Lira district with type 1 more predominant. A high prevalence and severity of pneumonia forms (17.4 – 74.2%) in slaughtered pigs was observed. The model showed that a grower pig in a given farm exposed to PRRSv and Ascaris spp. infection had significantly lower average daily weight gain by 18.5 and 23.7 grams/pig/day respectively, compared to a similar unexposed pig. Monetary losses encountered by farmers due to PRRSv and Ascaris spp. infection amounted to USD 7.12 and USD 9.16 respectively, per pig during 200 days of fattening. In conclusion, these findings strengthened evidence of the role of housing, hygiene and biosecurity in reducing disease incidence in herds. The most important respiratory pathogens were PPRSv, App, Ascaris spp. and risk factors were use of murram as floor type, poor hygiene, biosecurity practices, and concurrent GIT parasite infestations. Associations between serology and lung lesions suggests their potential role in lung disease precipitation. Farmers should pay close attention to proper housing, hygiene, biosecurity, wastes management and parasite control and limiting contacts with outside pigs. The findings from this study shall inform national policy in Uganda.Item Item Evaluation du coût de production et de déploiement du vaccin thermostable contre la peste des petits ruminants au Mali(Thesis, 2022-11-15) Dembélé, E.Le Laboratoire Central Vétérinaire (LCV) de Bamako a, sur la base d’un protocole de l’Institut International de Recherche en Elevage (ILRI), mis au point un vaccin thermostable contre la Peste des Petits Ruminants (PPR). En prélude au déploiement de ce vaccin sur le terrain, cet institut en charge de la mise en œuvre du projet de diffusion à grande échelle au Mali, a initié une évaluation de son coût de production comparativement aux autres vaccins conventionnellement produits jusque-là contre la PPR par le LCV. Des entretiens ont été menés avec les chefs de section et les techniciens de recherche à chaque étape de la production du vaccin au sein du LCV. L’estimation des coûts des intrants des vaccins a été faite avec l’appui d’experts des sections de production et marketing. En outre, 34 mandataires de la région de Sikasso ont été interrogés sur le coût de déploiement des vaccins sur le terrain. La méthode de coût complet a été utilisée. Les résultats montrent que les coûts de production d’une dose ont été estimés à 80FCFA pour le vaccin Xerovac (thermostable), 80 FCFA pour le vaccin classique et 85 FCFA pour le vaccin selon le protocole ILRI (thermostable). De ces résultats, on retient qu’il y a seulement 5 FCFA de différence entre les coûts de production du vaccin selon le protocole ILRI et ceux des deux autres vaccins contre la PPR. Les coûts de déploiement des vaccins (classique, Xerovac et ILRI) contre la PPR du LCV jusqu’à la région de Sikasso ont été évalués à 55 FCFA/dose. En outre, le nombre de doses dans un lot varie d’un type de vaccin à un autre. Au-delà des coûts financiers, il semble nécessaire de développer et d’étendre un programme de vaccination et une meilleure collaboration entre l’Etat, le LCV et les réseaux de distribution. Des actions de sensibilisation des éleveurs sont toutes aussi indispensables pour améliorer la couverture vaccinale des petits ruminants contre la PPR. ABSTRACT IN ENGLISH: The Central Veterinary Laboratory (LCV) of Bamako has, on the basis of a protocol of the International Institute for Research in Livestock (ILRI), developed a thermostable vaccine against the Peste des Petits Ruminants (PPR). As a prelude to the deployment of this vaccine in the field, this institute in charge of the implementation of the large-scale dissemination project in Mali, initiated an evaluation of its production cost compared to the other vaccines conventionally produced until then against PPR by LCV. Interviews were conducted with section heads and research technicians at each stage of vaccine production within the LCV. Estimates of vaccine input costs were made with the support of experts from the production and marketing sections. We met with agents from the Sikasso region to calculate the cost of deployment. This is the full cost method that was used to get the results. The costs of producing a dose have been estimated at 80 FCFA for the Xerovac vaccine (thermostable), 80 FCFA for the conventional vaccine and 85 FCFA for the vaccine according to the ILRI protocol (thermostable). From these results, we note that there is only 5 FCFA difference between the costs of producing vaccine according to the ILRI protocol and those of the two other PPR vaccines. The costs of deploying LCV PPR vaccines (conventional, Xerovac and ILRI) to the Sikasso region have been estimated at 55 FCFA / dose. In addition, the number of doses in a batch varies from one type of vaccine to another. Beyond the financial costs, it seems necessary to develop and extend a vaccination program and better collaboration between the State, the LCV and the distribution networks. Actions to raise farmers' awareness are also essential to improve the vaccination coverage of small ruminants against PPR.Item Exploring the challenges to investigating antibiotic resistance along the pork value chain in Viet Nam and the benefits of the One Health approach(Thesis, 2018) Mitchell, M.E.V.Background Antibacterial resistance (ABR) is a global health crisis, which threatens the ability to treat diseases and complicate medical procedures. The Vietnamese government have recognised the multifaceted risk ABR poses to human health and the country’s sustainable development and are in the process of developing a surveillance system for ABR. However, the implementation of policies that require inter-sectoral collaboration can be challenging. This project aimed to explore the experiences of actors in the animal health and human health sector to elucidate their perspectives and experiences of investigations in addressing ABR along the pork-value-chain in Viet Nam. Methodology Using qualitative methodology, 11 semi-structured interviews were conducted with a total of 12 key informants working across the animal health (8; 2 men and 6 women) and human health (4; 3 men and 1 women) sector in Hanoi, Vietnam. Interviewees were purposively selected using the snowball effect. Two case studies were developed to guide the questionnaire with the interviewees. The questionnaire included 20 (human health) and 23 (animal health) open ended questions, split into 4 different sections: 1) background; 2) investigation process; 3) resources available; and, 4) inter-sectoral collaboration. The transcribed interview data was separated into sections and codebook was generated. Thematic analysis of each section was employed to generate themes to determine the challenges and constraints in investigations processes (section 1 – 3) and participant perspectives on the One Health (OH) approach to ABR surveillance (section 4). Results Two identified themes 1) public health systems and food systems; context and regulatory factors, 2) data availability; information and knowledge development factors, were identified to have emerged from the data from sections 1 – 3. Under these two major themes, three sub-themes 1) technical capacity, 2) financial capacity, 3) human resources were factored across both themes. Two major themes emerged from the analysis of section four; 1) communication and data availability factors influencing cross-sectoral collaboration, 2) harmonization of data and government policy and regulation development. Under both themes, two-subthemes were identified 1) relationship development and understandings increases the knowledge and understanding of ABR, 2) resources; fosters the environment of sharing resources, responsibility and understanding of ABR’. Key findings The key findings presented from this study suggest that, participants perceive that the use of antibiotics within animal food production is a key driver of antibiotic resistance in human health in Viet Nam; there is divergence of opinions on laboratory capacity by sector and profession; and there is insufficient data available and data sharing between sectors. The One Health approach to surveillance is seen to offer potential to strengthen data for policy decisions.Item Antimicrobial resistance analysis of non-typhoidal Salmonella in porcine from northern Vietnam(Thesis, 2018-09-15) Clark, E.Background Non-typhoidal Salmonella spp. (NTS) causing Salmonellosis remains a significant health burden in both developing and developed countries. Due to overcrowded hospitals and a lack of adequate diagnostic testing, Vietnam is a hotspot for drug resistance. Pork accounts for over 70% of total meat consumed within Vietnam, and contamination with NTS remains high. This study aimed to analyse the patterns of NTS serotypes and AMR of strains between 2014/5 to 2018 and also to determine whether the Colistin resistance seen in the 2014/5 study was caused by mcr-1. Methods To determine the presence of mcr-1, strains from a previous study, PigRISK 2014/5 were selected. The serotype was checked following the Kauffmann and White scheme, and Colistin antimicrobial resistance (AMR) performed using both disc diffusion and broth microdilution. Polymerase chain reaction (PCR) was used to determine the presence of mcr1. Samples representing 2018 were collected as part of the SafePORK study and processed for NTS isolation, serotyping and AMR for 12 antimicrobials. Results In the PigRISK strains, mcr-1 was not identified on either the chromosome or plasmid. From analysing serotypes and AMR between 2014/5 and 2018, a significant increase of NTS prevalence was observed from 44.7% to 78.6%. Antimicrobial resistance also remained high, and the number of strains showing multidrug resistance had increased between studies. Conclusion This study was limited to determining the presence of one gene causing Colistin resistance, further work is required to identify the exact cause of observed resistance. The collection of samples representing 2018 was limited to one province, one sample type and one section of the pork value chain. To aid comparison, it would be necessary to obtain a variety of samples. This study demonstrated why the control of antimicrobials within the agriculture sector is essential for preventing resistance, and subsequently transmission to humans.Item Aflatoxins: A food safety hazard in Kenyan dairy chains – prevalence, risks and assessment of a biocontrol solution(Thesis, 2020-12-16) Ahlberg, S.Aflatoxins continue to be a food safety problem globally, especially in developing regions. Prevalent food contaminating aflatoxins are B1 (AFB1) and M1 (AFM1). These are human carcinogens and have potentially severe health impacts. Almost all (99.5 %) milk samples from Nairobi were contaminated with AFM1, highlighting the urgent need to create functional solutions to improve food safety. Based on the aflatoxin levels and milk consumption, risks were calculated: cancer risk caused by AFM1 was lower among consumers purchasing from formal markets (0.003 cases per 100,000) than for low-income consumers (0.006 cases per 100,000) purchasing from informal markets. Overall cancer risk (0.004 cases per 100,000) from AFM1 alone was low. Because of AFM1 in milk, 2.1 % of children below three years in middle-income families, and 2.4 % in low-income families, could be stunted. Overall, 2.7 % of children could hypothetically be stunted due to AFM1 exposure from milk. Based on these results AFM1 levels found in milk could contribute to an average of -0.340 height for age z-score reduction in growth. The exposure to AFM1 from milk is 46 ng/day on average, but children bear higher exposure of 3.5 ng/kg bodyweight (bw)/day compared with adults, at 0.8 ng/kg bw/day. Aflatoxins are produced by Aspergillus flavus fungus, which is prevalent in soils. Certain strains of lactic acid bacteria (LAB) have been reported inhibiting fungal growth. 171 LAB strains were tested against aflatoxin producing A. flavus fungi. The three LAB strains showing the highest antifungal activity were identified as Lactobacillus plantarum. None of the strains was able to completely inhibit fungal growth under conditions favorable for fungi and suboptimal for LAB. The three indigenous LAB Lactobacillus strains and one Lactococcus strains were tested for their AFM1 binding abilities in different conditions and after different treatments along with two reference Lactobacillus strains. The binding of AFM1 by LAB strains varied between 11 to 100 % in the biocontrol solution analysis, being approximately at the level of 40 % throughout the analysis sets. A significant amount of effort and resources have been invested in an attempt to control aflatoxins. However, these efforts have not substantially decreased the prevalence nor dietary exposure to aflatoxins in developing countries. The growth reduction of aflatoxin producing fungi with LAB could be one potential option, but there are still major issues to solve prior to any practical applications. A different approach to control aflatoxins suggesting the usage of binding agents in foods and lactic acid bacteria (LAB) have been studied extensively for this purpose. However, when assessing the results comprehensively and reviewing the practicality and ethics of use, risks are evident, and concerns arise. In conclusion, there are too many issues with using LAB for aflatoxin binding for it to be safely promoted. Arguably, using binders in human food might even worsen food safety in the longer term. A more comprehensive food safety approach has to be taken to solve this ongoing crisis.Item Formative research for the development of a theory-based social behavior change communication plan for the More Milk in Tanzania (MoreMilkIT) project(Thesis, 2018-04-25) Kelly, J.Malnutrition is a problem throughout the world, disproportionately affecting impoverished, rural, and vulnerable populations.1 Tanzania is not spared the effects of malnutrition, as almost 90% of the population is located in rural regions2 and 30% of the population is classified as food insecure.3,4 Rural Tanzania relies heavily on livestock for nutritional and economic security.5 Research suggests that livestock keeping in East Africa holds potential for economic growth,6 that can be environmentally and culturally sensitive,7 with specific benefits to highly vulnerable populations such as women and children.8 The More Milk in Tanzania project seeks to use advanced value-chain development to improve livelihoods through focused livestock and dairy production and sale.9 This research was conducted as the formative research for a social behavior change communication (SBCC) plan to supplement the More Milk project implementation, specifically to improve maternal and child nutrition through animal sourced foods. Formative research was grounded in a combination of three theoretical frameworks, the COM-B model10 the Theoretical Domains Framework,11 and the Designing for Behavior Change methodology of a barrier analysis.12 The formative research was conducted in Masatu, Tanzania in the district of Handeni. A mixed-methods barrier analysis consisted of 51 doer/non-doer surveys, nine key informant interviews, and four focus groups. Doer/non-doer surveys measured characteristics and behavioral domains of mothers who did and did not complete selected behaviors. Behaviors of interest included those recommended by the WHO for adequate maternal nutrition for fetal development and infant and young child feeding practices.13-21 Qualitative data collection consisted of conversation about community issues, program participation, community eating habits, and perceptions of the selected maternal and child nutrition behaviors. Several key determinants of behavior were identified including, access to resources, such as time, money, and food, socially normalized support from important family members, such as husbands and older female relatives, and both perceived positive/negative consequences and barriers/facilitators to maternal and child nutrition behaviors. Major themes such as perceived insufficient milk and consumption discrepancies between pregnant and lactating women and infants and children also arose. Using these results, this research lays the groundwork for a theory-based SBCC plan to improve maternal and child nutrition.