Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya

Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization

Pastoral production is associated with increased peste des petits ruminants seroprevalence in northern Tanzania across sheep, goats and cattle

Peste des petits ruminants virus (PPRV) causes a contagious disease of high morbidity and mortality in small ruminant populations globally. Using cross-sectional serosurvey data collected in 2016, our study investigated PPRV seroprevalence and risk factors among sheep, goats and cattle in 20 agropastoral (AP) and pastoral (P) villages in northern Tanzania. Overall observed seroprevalence was 21.1% (95% exact confidence interval (CI) 20.1–22.0) with 5.8% seroprevalence among agropastoral (95% CI 5.0–6.7) and 30.7% among pastoral villages (95% CI 29.3–32.0). Seropositivity varied significantly by management (production) system. Our study applied the catalytic framework to estimate the force of infection. The associated reproductive numbers (R0) were estimated at 1.36 (95% CI 1.32–1.39), 1.40 (95% CI 1.37–1.44) and 1.13 (95% CI 1.11–1.14) for sheep, goats and cattle, respectively. For sheep and goats, these R0 values are likely underestimates due to infection-associated mortality. Spatial heterogeneity in risk among pairs of species across 20 villages was significantly positively correlated (R2: 0.59–0.69), suggesting either cross-species transmission or common, external risk factors affecting all species. The non-negligible seroconversion in cattle may represent spillover or cattle-to-cattle transmission and must be investigated further to understand the role of cattle in PPRV transmission ahead of upcoming eradication efforts

Analysing livestock network data for infectious disease control: an argument for routine data collection in emerging economies

Livestock movements are an important mechanism of infectious disease transmission. Where these are well recorded, network analysis tools have been used to successfully identify system properties, highlight vulnerabilities to transmission, and inform targeted surveillance and control. Here we highlight the main uses of network properties in understanding livestock disease epidemiology and discuss statistical approaches to infer network characteristics from biased or fragmented datasets. We use a ‘hurdle model’ approach that predicts (i) the probability of movement and (ii) the number of livestock moved to generate synthetic ‘complete’ networks of movements between administrative wards, exploiting routinely collected government movement permit data from northern Tanzania. We demonstrate that this model captures a significant amount of the observed variation. Combining the cattle movement network with a spatial between-ward contact layer, we create a multiplex, over which we simulated the spread of ‘fast’ (R0 = 3) and ‘slow’ (R0 = 1.5) pathogens, and assess the effects of random versus targeted disease control interventions (vaccination and movement ban). The targeted interventions substantially outperform those randomly implemented for both fast and slow pathogens. Our findings provide motivation to encourage routine collection and centralization of movement data to construct representative networks. This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’. This theme issue is linked with the earlier issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’

Assessing the impact of tailored biosecurity advice on farmer behaviour and pathogen presence in beef herds in England and Wales

The term ‘biosecurity’ encompasses many measures farmers can take to reduce the risk of pathogen incursion or spread. As the best strategy will vary between settings, veterinarians play an important role in assessing risk and providing advice, but effectiveness requires farmer acceptance and implementation. The aim of this study was to assess the effectiveness of specifically-tailored biosecurity advice packages in reducing endemic pathogen presence on UK beef suckler farms. One hundred and sixteen farms recruited by 10 veterinary practices were followed for three years. Farms were randomly allocated to intervention (receiving specifically-tailored advice, with veterinarians and farmers collaborating to develop an improved biosecurity strategy) or control (receiving general advice) groups. A spreadsheet-based tool was used annually to attribute a score to each farm reflecting risk of entry or spread of bovine viral diarrhoea virus (BVDV), bovine herpesvirus-1 (BHV1), Mycobacterium avium subsp. paratuberculosis (MAP), Leptospira interrogans serovar hardjo (L. hardjo) and Mycobacterium bovis (M. bovis). Objectives of these analyses were to identify evidence of reduction in risk behaviours during the study, as well as evidence of reductions in pathogen presence, as indications of effectiveness. Risk behaviours and pathogen prevalences were examined across study years, and on intervention compared with control farms, using descriptive statistics and multilevel regression. There were significant reductions in risk scores for all five pathogens, regardless of intervention status, in every study year compared with the outset. Animals on intervention farms were significantly less likely than those on control farms to be seropositive for BVDV in years 2 and 3 and for L. hardjo in year 3 of the study. Variations by study year in animal-level odds of seropositivity to BHV1 or MAP were not associated with farm intervention status. All farms had significantly reduced odds of BHV1 seropositivity in year 2 than at the outset. Variations in farm-level MAP seropositivity were not associated with intervention status. There were increased odds of M. bovis on intervention farms compared with control farms at the end of the study. Results suggest a structured annual risk assessment process, conducted as a collaboration between veterinarian and farmer, is valuable in encouraging improved biosecurity practices. There were some indications, but not conclusive evidence, that tailored biosecurity advice packages have potential to reduce pathogen presence. These findings will inform development of a collaborative approach to biosecurity between veterinarians and farmers, including adoption of cost-effective strategies effective across pathogens

One Health contributions towards more effective and equitable approaches to health in low- and middle-income countries

This research was supported by the UK Biotechnology and Biological Sciences Research Council (BB/J010367/1) and the UK Zoonoses and Emerging Livestock Systems Initiative (BB/L017679/1, BB/L018926/1 and BB/L018845/1) (S.C., J.E.B.H., J.S., J.B., A.D., J.A.C., W.A.d.G., R.R.K., T.K., D.T.H., B.T.M., E.S.S., L.W.). The Wellcome Trust provided supported for K.H. and A.L. (095787/Z/11/Z) and K.J.A. (096400/Z/11/Z). The US National Institutes of Health provided support for J.A.C. (R01AI121378) and M.P.R. (R01AI121378, K23AI116869).Emerging zoonoses with pandemic potential are a stated priority for the global health security agenda, but endemic zoonoses also have a major societal impact in low-resource settings. Although many endemic zoonoses can be treated, timely diagnosis and appropriate clinical management of human cases is often challenging. Preventive ‘One Health’ interventions, e.g. interventions in animal populations that generate human health benefits, may provide a useful approach to overcoming some of these challenges. Effective strategies, such as animal vaccination, already exist for the prevention, control and elimination of many endemic zoonoses, including rabies, and several livestock zoonoses (e.g. brucellosis, leptospirosis, Q fever) that are important causes of human febrile illness and livestock productivity losses in low- and middle-income countries. We make the case that, for these diseases, One Health interventions have the potential to be more effective and generate more equitable benefits for human health and livelihoods, particularly in rural areas, than approaches that rely exclusively on treatment of human cases. We hypothesize that applying One Health interventions to tackle these health challenges will help to build trust, community engagement and cross-sectoral collaboration, which will in turn strengthen the capacity of fragile health systems to respond to the threat of emerging zoonoses and other future health challenges. One Health interventions thus have the potential to align the ongoing needs of disadvantaged communities with the concerns of the broader global community, providing a pragmatic and equitable approach to meeting the global goals for sustainable development and supporting the global health security agenda.Publisher PDFPeer reviewe

How can we realise the full potential of animal health systems for delivering development and health outcomes?

Animal health services play an essential role in supporting livestock production, with the potential to address the challenges of hunger, poverty, health, social justice and environmental health as part of the path towards the Sustainable Development Goal (SDG) defined in the United Nations, 2030 Agenda. However, the provision of animal health services remains chronically underfunded. Although the aspiration that ‘no one will be left behind’ is core to the SDG agenda, animal health service provision still fails to meet the basic needs of many of the poorest livestock owners. This review draws largely on experience from Tanzania and highlights the obstacles to equitable provision of animal health services, as well as identifying opportunities for improvement. Delivery models that rely on owners paying for services, whether through the private sector or public−private partnerships, can be effective for diseases that are of clear economic importance to animal keepers, particularly in more market-orientated production systems, but are currently constrained by issues of access, affordability, availability and quality. Substantial challenges remain when attempting to control diseases that exert a major burden on animal or human health but are less well recognised, as well as in the delivery of veterinary public health or other public good interventions. Here, the authors propose solutions that focus on: improving awareness of the potential for animal health services to address the SDGs, particularly those concerning public and environmental health; linking this more explicitly with advocacy for increased investment; ensuring that the voices of stakeholders are heard, particularly those of the rural poor; and embracing a cross-cutting and expanded vision for animal health services to support more adaptive development of livestock system

The value of livestock abortion surveillance in Tanzania: identifying disease priorities and informing interventions

Background: Lack of reliable data on the aetiology of livestock diseases, especially in Africa, is a major factor constraining the design of effective livestock health interventions to improve livelihoods, food security and public health. Rationale: Livestock abortion is an important disease syndrome that affects productivity and livestock economies, and poses risks to public health. Worldwide, several pathogens are associated with livestock abortions but across Africa livestock disease surveillance data rarely include information from abortion events, little is known about the aetiology and impacts of livestock abortions, and data are not available to inform prioritisation of disease interventions. Methods: This paper describes outcomes from a surveillance platform that was set up in 15 wards in northern Tanzania spanning pastoral, agropastoral and smallholder agro-ecological systems to investigate the causes and impacts of livestock abortion. Abortion cases were reported by farmers to Ministry of Livestock and Fisheries livestock field officers and on to investigation teams. The abortion was eligible for inclusion if the research field team or livestock field officer could attend within 72 hours of the event occurring. If so, a field investigation was carried out to collect diagnostic samples from aborted materials and aborting dams and questionnaire data on herd/flock management. Laboratory diagnostic tests were carried out for a range of abortigenic pathogens, and laboratory and questionnaire data analysed to investigate a) determinants of attribution; b) patterns of investigated events, including species and breed affected, previous abortion history and recent stressful events, and the seasonality of cases; c) determinants of reporting, investigation and attribution; (d) cases in which zoonotic pathogens were detected. Results: Over a two-year period (2017-2019), 215 abortion events in cattle (n=71), sheep (n=44) and goats (n=100) were investigated from 13 of the 15 wards. The number of investigated cases varied widely across wards, with three of the 15 field officers (20%) reporting 70% of investigated cases. Aetiological attribution, achieved for 19.5% of cases through PCR-based diagnostics, was significantly affected by delays in obtaining samples from field investigation. Histopathology proved less useful than PCR diagnostics due to rapid deterioration of field samples. Vaginal swabs from aborting dams provided a practical and sensitive source of diagnostic material for pathogen detection. Discussion / Conclusion: Livestock abortion surveillance, even at a small scale and when capturing only a small proportion of events, can generate valuable information on causes of zoonotic disease outbreaks, livestock reproductive losses and can identify important pathogens that are not easily captured through other forms of livestock disease surveillance. This study demonstrated the feasibility of establishing an effective reporting and investigation system that could be implemented across a range of settings, including remote rural areas. This has been achieved through effective engagement of community-based field officers, establishment of practical sample collection protocols and application of molecular diagnostic platforms