Herd-level prevalence of selected endemic infectious diseases of dairy cows in Great Britain

To implement appropriate and effective disease control programs at national level, up-to-date and unbiased information on disease frequency is needed. The aim of this study was to estimate the prevalence of selected endemic infectious diseases in the population of dairy herds in Great Britain. Bulk milk tank (BMT) samples from 225 randomly selected dairy farms stratified by region and herd size were tested for antibodies against bovine viral diarrhoea virus (BVDV), bovine herpesvirus type 1 (BHV-1), Mycobacterium avium subspecies paratuberculosis (MAP), Leptospira hardjo , Salmonella spp., Coxiella burnetii , Fasciola hepatica , Neospora caninum , and Ostertagia ostertagi . Furthermore, the presence of BVDV, C. burnetii and Chlamydia-like organisms was determined by polymerase chain reaction (PCR). The apparent herd prevalence was estimated as a weighted proportion of positive herds. The true prevalence was calculated when a test was used with known test characteristics for the cut-off value used. Amongst unvaccinated herds, the true prevalence ofBMT antibodies against BVDV was estimated at 66% (95% Confidence 47 Interval, CI: 56-77%), MAP 68% (95% CI: 59-77%), BHV-1 62% (95% CI: 52-73%), L. hardjo 47% (95% CI: 34-60%) and Salmonella spp. 48% (95% CI: 39-56%). The apparent prevalence of BMT antibodies against C. burnetii was 80% (95% CI: 75-85%), F. hepatica 55% (95% CI: 48- 62%), N. caninum 46% (95% CI: 38-54%), and O. ostertagi 95% (95% CI: 91-98%). BVDV, C. burnetii and Chlamydia-like antigens were detected in 5% (95% CI: 2-9%), 29% (95% CI: 21-36%) and 31% (95% CI: 24-38%) of herds, respectively. Our results show that dairy cows across GB are frequently exposed to the studied pathogens, which are endemic at high levels with some geographical variations. These prevalence estimates provide a much needed basis to assess whether nationwide control programs for the studied pathogens are justified by their potential economic, environmental and public health implications. Should surveillance and control programs be initiated, the estimates presented here are a baseline against which progress can be assessed

Microbiological risk ranking of foodborne pathogens and food products in scarce-data settings

In the absence of epidemiological, microbiological or outbreak data, systematic identification of the hazards and food products posing the higher risk to the consumers is challenging. It is usually in Low- and Middle-Income Countries (LMICs), where the burden of foodborne disease is highest that data tend to be particularly scarce. In this study, we propose qualitative risk-ranking methods for pathogens and food products that can be used in settings where scarcity of data on the frequency/concentration of pathogens in foodstuff is a barrier towards the use of classical risk assessment frameworks. The approach integrates the existing knowledge on foodborne pathogens, manufacturing processes and intrinsic/extrinsic properties of food products with key context-specific information regarding the supply chain(s), characteristics of the Food Business Operators (FBOs) and cultural habits to identify: (i) the pathogens that should be considered as a “High” food safety priority and (ii) the food products posing the higher risk of consumer exposure to microbiological hazards via the oral (ingestion) route. When applied to the dairy sector of Andhra Pradesh (India) as a case study, Shiga toxin-producing E. coli, Salmonella spp., S. aureus and L. monocytogenes were identified as a “High” food safety priority across all FBOs. C. sakazakii was identified as a “High” priority for the FBOs producing infant formula/milk powder whilst Shigella spp., and Cryptosporidium spp. a “High” priority when considering the FBOs operating in the unregulated sector. Given the diversity of dairy products considered in the assessment, cluster analysis was used to identify products that shared similar intrinsic/extrinsic features known to drive the microbiological risk. The risk ranking was then done integrating the results of the cluster analysis with context-specific information. Products manufactured/retailed by FBOs in the informal market were considered as posing a “High” risk for the consumers due to a widespread lack of compliance to sanitary regulations. For dairy products produced by FBOs operating in the middle and formal end of the formal-informal spectrum, the risk of consumers exposure to microbiological hazards ranged from “Moderate” to “Extremely low” depending on the FBO and the intrinsic/extrinsic properties of the products. While providing risk estimates of lower precision if compared to data-driven risk assessments, the proposed method maximises the value of the information that can be easily gathered in LMICs and provide informative outputs to support food safety decision-making in contexts where resources to be allocated for prevention of foodborne diseases are limited and the food system is complex

Risk-based inspection as a cost-effective strategy to reduce human exposure to cysticerci of Taenia saginata in low-prevalence settings

Taenia saginata cysticercus is the larval stage of the zoonotic parasite Taenia saginata, with a life-cycle involving both cattle and humans. The public health impact is considered low. The current surveillance system, based on post-mortem inspection of carcasses has low sensitivity and leads to considerable economic burden. Therefore, in the interests of public health and food production efficiency, this study aims to explore the potential of risk-based and cost-effective meat inspection activities for the detection and control of T. saginata cysticercus in low prevalence settings

Eimeria species occurrence varies between geographic regions and poultry production systems and may influence parasite genetic diversity

Coccidiosis is one of the biggest challenges faced by the global poultry industry. Recent studies have highlighted the ubiquitous distribution of all Eimeria species which can cause this disease in chickens, but intriguingly revealed a regional divide in genetic diversity and population structure for at least one species, Eimeria tenella. The drivers associated with such distinct geographic variation are unclear, but may impact on the occurrence and extent of resistance to anticoccidial drugs and future subunit vaccines. India is one of the largest poultry producers in the world and includes a transition between E. tenella populations defined by high and low genetic diversity. The aim of this study was to identify risk factors associated with the prevalence of Eimeria species defined by high and low pathogenicity in northern and southern states of India, and seek to understand factors which vary between the regions as possible drivers for differential genetic variation. Faecal samples and data relating to farm characteristics and management were collected from 107 farms from northern India and 133 farms from southern India. Faecal samples were analysed using microscopy and PCR to identify Eimeria occurrence. Multiple correspondence analysis was applied to transform correlated putative risk factors into a smaller number of synthetic uncorrelated factors. Hierarchical cluster analysis was used to identify poultry farm typologies, revealing three distinct clusters in the studied regions. The association between clusters and presence of Eimeria species was assessed by logistic regression. The study found that large-scale broiler farms in the north were at greatest risk of harbouring any Eimeria species and a larger proportion of such farms were positive for E. necatrix, the most pathogenic species. Comparison revealed a more even distribution for E. tenella across production systems in south India, but with a lower overall occurrence. Such a polarised region- and system-specific distribution may contribute to the different levels of genetic diversity observed previously in India and may influence parasite population structure across much of Asia and Africa. The findings of the study can be used to prioritise target farms to launch and optimise appropriate anticoccidial strategies for long-term control

Investigating market-based opportunities for the provision of nutritious and safe diets to prevent childhood stunting: a UKRI-GCRF action against stunting hub protocol paper

Background Inadequate access to affordable, safe, desirable and convenient nutrient-dense food is one of the underlying causes of child stunting. While targeted nutrition-sensitive interventions (e.g., backyard ‘nutri-gardens’) may increase dietary diversity within farming households, such interventions have limited scalability across the wider food system where markets remain underdeveloped. This research aims to develop and assess market-based interventions for key nutrient-dense foods to help improve the diets of women and children in the first 1000 days of life. Methods Data collection uses four parallel approaches in each of the three study countries (India, Indonesia and Senegal). (1) A novel food environment tool will be developed to characterise the accessibility and affordability of nutrient-dense foods in the study countries. The tool will be validated through pretesting using cognitive interviewing and piloting in purposively sampled households, 10 (cognitive interviewing) and 30 (piloting) households in each country; (2) stakeholder interviews (e.g., with producers, intermediaries and retailers) will be conducted to map out nutrition-sensitive entry points of key value chains (e.g., animal-sourced foods), before hotspots of potential food safety hazards will be identified from food samples collected along the chains; (3) the Optifood and Agrifood tools will be used to identify foods that can address food system nutrient gaps and engage key stakeholders to prioritise market interventions to improve nutrition outcomes. Optifood and Agrifood parameters will be informed by publicly available data, plus interviews and focus groups with value chain stakeholders; (4) informed by the previous three approaches and a campaign of participatory ‘group model building’, a novel system dynamics model will evaluate the impact of alternative market-based solutions on the availability and affordability of nutrient-dense foods over time. Ethics and dissemination The study has received ethical approval in the United Kingdom, Senegal, Indonesia and India. Dissemination comprises peer-reviewed journals, international disciplinary conferences and multistakeholder dissemination workshops

Brucellosis in dairy herds: a public health concern in the milk supply chains of West and Central Africa

Ten herd-level cross-sectional studies were conducted in peri-urban dairy production areas of seven West and Central African countries (Burkina Faso, Burundi, Cameroon, Mali, Niger, Senegal and Togo). The objectives were to estimate herd level Brucella spp. seroprevalence and identify risk factors for seropositivity. In each of the ten study areas, herds (between 52 and 142 per area, total = 965) were selected probabilistically and a structured questionnaire was administered to gather information on their structure and management. A bulk milk sample from each herd was tested by indirect ELISA for Brucella spp. For each area, herd seroprevalence estimates were obtained after adjusting for the assumed performance of the diagnostic test. Herd level risk factors for Brucella spp. seropositivity were identified by means of stratified logistic regression, with each peri-urban zone as a stratum. Area-specific models were also explored. Estimated herd seroprevalences were: Lomé (Togo) 62.0% (95% CI:55.0-69.0), Bamako (Mali) 32.5% (95% CI:28.0-37.0), Bujumbura (Burundi) 14.7% (95%CI:9.4-20.8), Bamenda (Cameroon) 12.6% (95% CI:7.6-21.9), Ouagadougou (Burkina Faso) 3.0% (95% CI:1.0-9.1), Ngaoundere (Cameroon) 2.3% (95% CI:1.0-7.0), Thies (Senegal) 1.3% (95% CI:0.1, 5.3), Niamey (Niger) 1.2% (95% CI:0.08-5.3), Dakar (Senegal) 0.2% (95% CI:0.01-1.7) and Niakhar (Senegal) <0.04%. Logistic regression modelling revealed transhumant herds to be at lower risk of infection (adjusted OR: 0.25, 95% CI: 0.13 - 0.5) and in one of the areas (Bamenda), regular purchase of new animals was found to be strongly associated with Brucella spp. seropositivity (adjusted OR = 5.3, 95% CI: 1.4-25.9). Our findings confirm that Brucella spp. circulates among dairy cattle supplying milk to urban consumers in West and Central Africa, posing a serious public health concern. Control programs are urgently needed in areas such as Lomé or Bamako, where more than 30% of the herds show evidence of infection

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing

Different alpha diversity indices for each sample of university farm data estimated using QIIME for primer pair P2 data. OTUs were clustered at > 97% similarity. (XLSX 12 kb

"Everything in this world has been given to us from cows", a qualitative study on farmers' perceptions of keeping dairy cattle in Senegal and implications for disease control and healthcare delivery.

The dairy industry in Senegal is growing and evolving against a backdrop of rapid urbanisation and increasing consumer demand for dairy products. Consideration of appropriate cattle healthcare delivery and disease control in these evolving farming systems is of paramount importance given the risks posed by zoonotic pathogens and the economic consequences of disease for livestock keepers. Planning and implementation of disease control and healthcare delivery generally follows a top down approach. Often this does not take into account the views and perceptions of the farmers it impacts and who must behave in the expected way for successful outcomes to materialise. In this study, we asked 76 farmers to discuss their experience and opinions of farming milk producing cattle in 11 focus group discussions conducted in two peri-urban areas of Senegal. The objectives were to investigate farmers' perceptions of the current conditions in farming, to understand how these might impact the future direction of this particular system and how this might affect the feasibility and appropriate methods of cattle healthcare delivery and disease control. The data collected were subjected to thematic analysis and four themes were identified; 1. Revered cattle, 2. The changing face of livestock keeping, 3. Powerlessness, 4. Optimism for the future. Farmers in our study had a deep affinity with their cattle, they respected the traditions surrounding cattle keeping at the same time as striving for advances within the system and their animal's productivity. Within strong social groupings and hierarchical structures they recognised the inherent challenges they face but were hopeful and optimistic about growth and opportunity in the future of milk production. A holistic approach to embedding healthcare delivery and disease control within the broader context in which farmers operate may prove successful. This could involve consideration of funding channels for farmers, access to appropriate inputs and utilising the strong community spirit and social norms of farmers to initiate and facilitate change