a ILRI Health of Animals, People and Ecosystems theme outputs (2025–)
Permanent URI for this collectionhttps://hdl.handle.net/10568/169325
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Item Gender roles in ruminant disease management in Uganda: Implications for the control of peste des petits ruminants and Rift Valley fever(Journal Article, 2025-04-25) Namatovu, Jane; Lule, Peter; Asindu, Marsy; Campbell, Zoë A.; Tumusiime, Dan; Kiara, Henry K.; Bett, Bernard K.; Roesel, Kristina; Ouma, Emily A.; Osman, Nussieba A.There is a distinct division of tasks and roles between men and women in livestock management in the different ruminant production systems in Uganda. Division of roles can influence disease control and prevention. This qualitative study asks what men and women do to prevent or control diseases that affect them and their livestock and what factors influence the choice of disease control measures taken. Discussants represented three production systems (pastoral, agro-pastoral, and mixed crop livestock), selected for the high prevalence of two livestock diseases (peste des petits ruminants and Rift Valley fever). Sex-disaggregated focus group discussions with livestock keepers and key informant interviews with veterinarians and other experts were conducted in six districts in the western, northeastern, and eastern regions of Uganda. Gendered livestock management roles strategically positioned men, women, girls, and boys to observe different clinical manifestations of disease. Livestock keepers mostly reported within-farm prevention and control methods, for which they presumably had more control than between-farm or community-level methods. While livestock keepers embraced disease control options such as the use of drugs, spraying acaracides, and the use of traditional herbs, many had concerns and misconceptions about vaccination as a preventive measure. Although women had fewer concerns about vaccine side effects, they still faced constraints, such as mistrust of animal health workers, limited decision-making powers, domestic workload, and inability to access vaccination points. The study findings can guide appropriate, gender-responsive interventions tailored by production system for controlling ruminant diseases in Uganda.Item Systems thinking for hygiene in settings with high risk of infectious disease transmission(Journal Article, 2025) Freeman, M.C.; Crocker, J.; Chipungu, J.; Bagwan, J.; Dione, Michel M.; Dreibelbis, R.; Dumlao, M.C.; Faruque, A.S.G.; Flint-O'Kane, M.; Gautam, O.P.; Lakhe, N.A.; Muga, R.; Muralidharan, A.; Ndiaye, I.; Sarr, M.Hygiene is critical for controlling infectious disease and delivering well-being. During the pandemic phase of COVID-19, there was widespread awareness of the importance of hygiene for disease control, and demand was high for action to improve access to hygiene materials. However, those efforts have faltered, and, in general, interventions to improve hygiene at scale have shown limited success in delivering sustained behaviour change and health impact. We convened experts in hygiene across sectors (for example, health, education and agriculture) and disciplines (for example, academia, policy and practice) in Dakar, Senegal, to discuss the critical barriers and opportunities for researching, developing and implementing systems-level hygiene interventions and promote learning across sectors, with a focus on systems approaches. We report what is needed to achieve catalytic improvements in hygiene in low-income settings and the Global South, with an emphasis on ‘hygienic systems’ that target all relevant hygiene moments—a set of associated behaviours at a given time and place with high pathogen exposure risk—and their enabling conditions and pre-conditions. This focus beyond individual behaviours will require removing silos across sectors and ministries, the generation of relevant evidence for policymakers and the localization of guidance.Item Antimicrobial resistance in community-acquired enteric pathogens amongst children ≤10-years in low- and middle-income countries: a systematic review and meta-analysis(Journal Article, 2025-04-28) Okumu, Noah O.; Muloi, Dishon M.; Moodley, Arshnee; Watson, J.; Kiarie, Alice; Ochieng, Linnet; Wasonga, Joseph O.; Mutisya, Christine; Alumasa, Lorren; Ngeranwa, J.J.N.; Cumming, O.; Cook, Elizabeth A.J.Introduction: Antimicrobial resistance (AMR) is a global health priority. This systematic review summarizes the prevalence of AMR in enteric pathogens originating from the community, specifically among ≤10-year-old children in low-and middle-income countries (LMICs). In addition, it presents the proportions of pooled resistance in Campylobacter spp., Escherichia coli, Shigella spp., and Salmonella spp. (CESS) to clinically relevant antibiotics. Methods: Six online repositories, namely PubMed, Medline, Web of Science, Cochrane Library, CABI, and EMBASE were searched for articles published between January 2005 and September 2024. Random-effects meta-analysis models were constructed to estimate the pooled AMR proportions for CESS pathogens, and a subgroup analysis by region was also carried out. Results: A total of 64 publications from 23 LMICs met our inclusion criteria. The pooled estimates of E. coli AMR for clinically important antibiotics were as follows: sulfamethoxazole/trimethoprim (SXT) 71% [95%CI: 57–82%]; ampicillin (AMP) 56% [95%CI: 44–67%]; ciprofloxacin (CIP) 10% [95%CI: 5–20%]; and ceftriaxone (CRO) 8% [95%CI: 2–31%]. The proportions of AMR detected in Shigella spp. were AMP 76% [95%CI: 60–87%]; nalidixic acid (NA) 9% [95%CI: 2–31%]; CIP 3% [95%CI: 0–15%]; and CRO 2% [95%CI: 0–19%]. The proportions of Salmonella spp. AMR were AMP 55% [95%CI: 35–73%] and SXT 25% [95%CI: 15–38%]. The proportions of Campylobacter spp. AMR were erythromycin (ERY) 33% [95%CI: 12–64%] and CIP 27% [95%CI: 8–61%]. There was high variability in the regional subgroup analysis, with high interstudy and regional heterogeneity I2 ≥ 75%. Conclusion: Our results shed light on drug-resistant enteric bacterial pathogens in young children, providing evidence that CESS pathogens are becoming increasingly resistant to clinically important antimicrobials. Regional differences in resistance patterns between these community isolates highlight the need for strong national and regional surveillance to detect regional variations and inform treatment and appropriate antibiotic stewardship programs. The limitations of our findings include high regional variability, significant interstudy heterogeneity, and underrepresentation of certain LMICs.Item Genetic estimates and genome-wide association studies of antibody response in Tanzanian dairy cattle(Journal Article, 2025-04-24) Hernandez-Castro, L.E.; Cook, Elizabeth A.J.; Matika, O.; Mengele, I.J.; Motto, S.K.; Bwatota, S.F.; Zirra-Shallangwa, B.; Pong-Wong, R.; Prendergast, J.; Mrode, Raphael A.; Toye, Philip G.; Komwihangilo, D.M.; Lyatuu, E.; Karani, Benedict E.; Nangekhe, Gertrude; Okeyo Mwai, Ally; Shirima, G.M.; Bronsvoort, B.M. de C.Identifying the genetic determinants of host defence against infectious pathogens is central to enhancing disease resilience and therapeutic efficacy in livestock. Here, we investigated immune response heritability to important infectious diseases affecting smallholder dairy cattle using variance component analysis. We also conducted genome-wide association studies (GWAS) to identify genetic variants that may help understand the underlying biology of these health traits. By assessing 668,911 single-nucleotide polymorphisms (SNPs) genotyped in 2,045 crossbred cattle sampled from six regions of Tanzania, we identified high levels of interregional admixture and European introgression, which may increase infectious disease susceptibility relative to indigenous breeds. Heritability estimates were low to moderate, ranging from 0.03 (SE ± 0.06) to 0.44 (SE ± 0.07), depending on the health trait. GWAS results revealed several loci associated with seropositivity to the viral diseases Rift Valley fever and bovine viral diarrhoea, the protozoan parasites Neospora caninum and Toxoplasma gondii, and the bacterial pathogens Brucella sp., Leptospira hardjo, and Coxiella burnetii. The identified quantitative trait loci mapped to genes involved in immune defence, tumour suppression, neurological processes, and cell exocytosis. We propose that our results provide a basis for future understanding of the cellular pathways contributing to general and taxon-specific infection responses, and for advancing selective breeding and therapeutic target design.Item Prevalence of Shiga toxin-producing Escherichia coli, Salmonella, and Campylobacter species among diarrheal patients from three major hospitals in Ethiopia(Journal Article, 2025-04-21) Teshale, A.M.; Abegaz, W.E.; Azmeraye, B.M.; Degefaw, D.; LaPolt, D.; Bonger, Z.; Kalayu, A.A.; Tigabu, E.; Gazu, Lina; Yimer, G.; Abate, E.; Tsige, E.; Tasew, G.; Dessie, Y.; Biks, G.; Barkley, J.A.; Garsow, A.V.; Beckiewicz, A.; Alonso, Silvia; Kowalcyk, B.Diarrheal illness remains a major global health challenge, causing millions of deaths annually. Non-typhoidal Salmonella (NTS), Shiga toxin-producing Escherichia coli (STEC), and Campylobacter species (CAMPY) significantly contribute to this burden. Given the limited information on these pathogens in Ethiopia, this study aimed to estimate their prevalence among diarrhea patients in Ethiopia and identify risk factors for infection. A cross-sectional study was conducted from October 2021 to November 2022 in three hospitals in Ethiopia (Addis Ababa, Gondar, and Harar). Sociodemographic characteristics, clinical signs and symptoms were collected from study participants using a structured questionnaire. Stool samples were tested for NTS, STEC, and CAMPY using standardized methods. The prevalence of targeted pathogens was estimated overall and by study sites. Univariable and multivariable logistic regression were used to identify associated factors. A total of 2,331 patients were enrolled. The overall prevalence of NTS, STEC (stx only), STEC (stx + eae), and CAMPY was 1.29% (95%CI: 0.91, 1.84), 12.56% (95%CI: 11.29, 13.98), 3.43% (95%CI: 2.77, 4.25), and 4.46% (95%CI: 4.61, 8.00), respectively. Harar had the highest prevalence of all the pathogens compared to Addis Ababa and Gondar. Odds of NTS in Harar were over 10 (AOR: 10.43: 95%CI: 2.95, 69.20) and 3.5 times (AOR: 3.57: 95%CI: 1.50, 9.90) higher than that in Addis Ababa and Gondar, respectively. Odds of STEC (stx only) in the dry (AOR: 1.97: 95%CI: 1.37, 2.90) and long rainy (AOR: 1.80: 95%CI: 1.20, 2.69) seasons were nearly twice the odds in the short rainy season. Odds of CAMPY infection decreased by 3.29% (AOR: 0.97: 95%CI: 0.95, 0.98) with every one-year increase in age. Moreover, the odds of CAMPY infection for rural residents (AOR: 1.93, 95%CI: 1.15, 3.19) were nearly twice that of urban residents. This is the first study to estimate the prevalence of NTS, STEC, and CAMPY simultaneously across all age groups and diverse regions in Ethiopia, revealing significant variations. Results can be used to understand the burden of disease, inform clinical management and risk mitigation strategies to reduce illness in Ethiopia.Item Disturbance and disease(Journal Article, 2025-04-18) Lambin, E.F.; Anugwom, E.; Prist, P.R.; Agha, S.; White, S.; Grace, Delia; Khan, S.A.; Fèvre, Eric M.; Gottdenker, N.; Murray, K.The world has witnessed an alarming rise in the emergence of infectious diseases, posing profound challenges to public health, ecological balance, and global well-being. Displacement of people and the destabilization of ecosystems create conditions that significantly amplify the risk of disease outbreaks. In this Voices, we ask: how has anthropogenic environmental disturbance impacted the likelihood of disease outbreaks?Item Fully phased population-prevalent East African cattle BoLA-I alleles determined using PacBio HiFi long-read sequencing represent five novel specificities with distinctive peptide binding potential(Journal Article, 2025-04-17) Obara, I.; Sandro, A.; Elati, K.; Conneley, T.; Nielsen, M.; Githaka, Naftaly W.; Nanteza, A.; Bishop, Richard P.; Nijhof, A.Due to factors such as lower biosecurity, greater wildlife/farm animal interfaces, and environmental challenges, cattle in sub-Saharan Africa are exposed to more diverse and intensive bacterial, viral and protozoan pathogen challenges than cattle in Europe and other high-income regions of the world. Classical class I genes of the major histocompatibility complex (MHC) contribute to protection from diseases caused by these pathogens by refining a huge pool of potential pathogen-derived peptide ligands into a smaller ensemble for presentation to CD8+ T cells. Knowledge of population-prevalent MHC alleles is therefore critical for evidence-based approaches to vaccine design and improved understanding of pathogen resistance. Whereas variation in MHC molecules is understood in most detail for European Bos taurus, the alleles expressed by Africa's cattle remain poorly defined. We have leveraged recent improvements in the accuracy of PacBio high-fidelity (HiFi) circular consensus sequencing (CCS) and adapted stringent sequence filtering algorithms to identify hundreds of as yet uncharacterised fully phased BoLA-I alleles from multiple populations of African taurine (Ankole) and indicine (Zebu) cattle in East Africa. The analysis highlights a convergence of population-prevalent class I MHC allelic repertoires in taurine and indicine cattle, likely due to the similar pathogen-driven selective pressures. Our analysis of the anchor residue accommodating pockets of these prevalent alleles revealed extremely high levels of polymorphism, which contrast with Holstein alleles that exhibit a more limited repertoire of MHC specificity-determining pocket residues, potentially constraining the breadth of peptide presentation. However, in the context of considerable sequence and physicochemical variation in the pocket-forming residues, it was possible to discern overlaps in the predicted peptide binding spectrum. Interrogation of potential differences in peptide binding specificities with European B. taurus alleles revealed that the fully phased African cattle class I MHC alleles represent five novel specificities. We envisage that this novel finding will find broad application in assessing potentially achievable vaccination coverages of future pathogen-encoded vaccine candidates against important intracellular pathogens. One aim of future research should be to leverage recent improvements in the sensitivity of mass spectrometry combined with immunoprecipitation of peptides bound to African cattle MHC to search directly for T-cell epitopes in the context of the inferred ‘supertype’ diversity.Item Livestock for sustainable food system(Presentation, 2025-03-15) Unger, Fred; Hung Nguyen-Viet; Baltenweck, Isabelle; Whitbread, Anthony M.; Tarawali, Shirley A.Item Biosecurity measures and effects on health performance and antibiotic use in semi-intensive broiler farms in Uganda(Journal Article, 2025-06) Ayebare, Dreck; Mbatidde, Irene; Kemunto, Naomi P.; Muloi, Dishon M.; Ibayi, Eugine L.; Nielsen, S.S.; Ndoboli, Dickson; Roesel, Kristina; Tenhagen, B.-A.; Moodley, ArshneeBackground: Effective biosecurity measures prevent the spread of pathogens, thereby reducing the need for antibiotic use on livestock farms. However, quantitative data on these practices and health outcomes in semi-intensive broiler farms in low-income settings is limited. A longitudinal study in Wakiso, Uganda, aimed to evaluate biosecurity practices, health performance, and antibiotic use in such farms. Methods: The FarmUSE survey tool was used to collect data from 19 farms over two production cycles. A biosecurity risk assessment tool was used to quantify biosecurity. Blood samples (n = 342) were collected and analyzed using the ProFLOK® assay to assess antibody responses to vaccines for Newcastle disease (NCD), Infectious Bronchitis (IB), and Infectious bursal disease (IBD). Results: Median biosecurity scores were 26.3 % for external measures, 55.6 % for internal measures, and an overall score of 38.5 %. Sixteen farms reported respiratory signs, and 12 had gastrointestinal issues, with median mortality rates of 2.9 % in the first cycle and 4.6 % in the second. Antibiotic use was reported by 84 % and 77 % of farms in the first and second cycles, respectively. The most used antibiotics were tetracyclines, fluoroquinolones, and macrolides, with the highest usage occurring during the brooding phase. Good antibody responses were reported in only 10.5 % of flocks for NCD and 16 % for IBD, while all farms had poor responses against IB. Conclusion: Recurrent clinical signs could be attributed to insufficient biosecurity and inadequate vaccination outcomes, resulting in high antibiotic usage despite low mortality rates. Improving diagnostic access and strengthening the vaccine supply chain are essential. Identifying feasible and cost-effective biosecurity practices for semi-intensive broiler farms can enhance health outcomes, reduce antibiotic use, and boost productivity.Item Operationalizing regional One Health initiatives in Southeast Asia: Ways forward(Journal Article, 2025-06) Lam, Steven; Sinh Dang-Xuan; Unger, Fred; Meeyam, T.; Phuc Pham-Duc; Wacharapluesadee, S.; Hung Nguyen-VietOperationalizing One Health initiatives that link human, animal, and environmental health at the regional level is key for jointly addressing infectious diseases that can cross borders. This work is urgently needed in Southeast Asia, a recognized hotspot for emerging animal and human infectious diseases that have the potential to spread globally. As such, our objective is to identify action items to advance regional One Health efforts in Southeast Asia. We organized a 1.5-day workshop that convened 34 experts from government, national research institutes, universities, and international organizations spanning seven countries in Southeast Asia. Group discussions and prioritization exercises were conducted which led to 12 action items, serving as ideas for resourcing, operationalizing, and implementing One Health efforts in Southeast Asia. Participants also emphasized the importance of sustained funding, a collective voice, and a willingness among members to be bold in their collective efforts. Given the heightened focus on zoonotic risks in Southeast Asia, harnessing this momentum by operationalizing regional efforts could establish a solid foundation to draw on when facing future global health threats.Item A novel Nobecovirus in an Epomophorus wahlbergi bat from Nairobi, Kenya(Journal Article, 2025-04-12) VanAcker, M.C.; Ergunay, K.; Webala, P.W.; Kamau, M.; Mutura, J.; Lebunge, R.; Ochola, G.O.; Bourke, B.P.; McDermott, E.G.; Achee, N.L.; Jiang, L.; Grieco, J.P.; Keter, E.; Musanga, A.; Murray, S.; Stabach, J.A.; Craft, M.E.; Fèvre, Eric M.; Linton, Y.-M.; Hassell, JamesMost human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, we obtained fecal swabs from two fruit bat species—Eidolon helvum (n = 6) and Epomophorus wahlbergi (n = 43) (family Pteropodidae)—in peridomestic habitats in Nairobi, Kenya, and used metagenome sequencing to detect microorganisms. A near-complete genome of a novel virus assigned taxonomically to the Coronaviridae family Betacoronavirus genus and Nobecovirus subclade was characterized from E. wahlbergi. Phylogenetic analysis indicates this unique Nobecovirus clade shares a common ancestor with Eidolon/Rousettus Nobecovirus subclades isolated from Madagascar, Kenya, and Cameroon. Recombination was detected across open reading frames, except the spike protein, in all BOOTSCAN analyses, indicating intra-host coinfection and genetic exchange between genome regions. Although Nobecoviruses are currently bat-specific and are not known to be zoonotic, the propensity of coronaviruses to undergo frequent recombination events and the location of the virus alongside high human and livestock densities in one of East Africa’s most rapidly developing cities justifies continued surveillance of animal viruses in high-risk urban landscapes.Item Three serotypes of dengue virus circulated in hospitalized adult patients in an endemic metropolitan city of Northern Vietnam(Journal Article, 2025) Thang Nguyen-Tien; Ling, J.; Tung Duy Dao; Anh Ngoc Bui; Huy Quang Nguyen; Vuong Nghia Bui; Long Pham Thanh; Lindeborg, M.; Strömdahl, S.; Cuong Do Duy; Luat Le Xuan; Hung Nguyen-Viet; Grace, Delia; Lundvist, Å.; Lindahl, Johanna F.Item Building the future One Health workforce in Eastern and Southern Africa: Gaps and opportunities(Journal Article, 2025-01) Yussuf, Buke; Richards, Shauna; Grace, Delia; Mutie, Ianetta; Caron, A.; De Nys, H.; Goregena, B.; Kgosimore, M.; Kimaro, E.; Qekwana, N.; Tadesse, Y.; Knight-Jones, Theodore J.D.; Mutua, Florence K.The Quadripartite comprised of the Food and Agriculture Organization (FAO), World Health Organization (WHO), World Organisation for Animal Health (WOAH), the United Nations Environment Program (UNEP), and the One Health High Level Expert Panel collectively support enhancing the One Health (OH) capacities of the workforce addressing OH issues; however, competencies for this workforce are not generally agreed upon, applied uniformly, or always relevant in the global South. The objectives of this study were to (1) develop an inventory of OH education offered by higher education institutes in Eastern and Southern Africa, and (2) define OH competencies relevant for OH training in Eastern and Southern Africa. A survey in 11 Eastern and Southern African countries was conducted with OH key informants purposively selected from higher education institutes offering OH education (n = 1–3/higher education institutes). Snowball sampling was used to identify additional higher education institutes/individuals. Results were validated by OH country representatives. Data were collected using questionnaires, and descriptive statistics were used to present the results. Forty-two questionnaires were completed from 29 higher education institutes, and 166 OH education interventions were reported with 69% being courses contributing to a degree, 21% as degree/diploma awarding, and the remainder were missing data (n = 16). Masters were the most common OH degree program of which the highest number of students taught were from public health/OH, food safety, and applied epidemiology. There are many OH educational courses and activities on offer in Eastern and Southern Africa; however, their total breadth is difficult to assess due to limited awareness of the availability of OH education not only between higher education institutes in a country but also even within a higher education institute between faculties. Numerous cross-cutting and technical competencies were considered essential to work in OH; however, this level of expertise is rarely logistically possible to provide in any single degree program. For OH education to be consistently applied, competency frameworks that are relevant to a region are necessary. Technical competencies are important from a disciplinary context; however, necessary cross-cutting competencies should be a focus in developing the future OH workforce.Item Wild meat is eaten by millions, but puts billions at risk – how to manage the trade(Blog Post, 2025-04-09) Grace, Delia; Hung Nguyen-Viet; Staal, Steven J.Item One Health teacher training in Meru Province sub-counties of Buuri East, Buuri West and Tigania East, Kenya(Report, 2025-03-30) Richards, Shauna; Yussuf, Buke; Omutoko, J.L.; Walton, C.; Mutahi, J.M.Item Amhara public-private partnership approach: Experience sharing(Presentation, 2025-03-27) Sinshaw, W.Item VSF Germany experience: Public-private partnership (PPP) in animal health(Presentation, 2025-03-27) Sisay, A.Item The Donkey Sanctuary: Experiences in implementing public-private partnerships(Presentation, 2025-03-27) Haile, T.Item Somali public-private partnership approach: Experience sharing(Presentation, 2025-03-27) Yusuf, A.