An open-source digital contact tracing system tailored to haulage.

Digital contact tracing presents numerous advantages compared to manual contact tracing methods, especially in terms of enhanced speed and automation. Nevertheless, a lack of comprehensive evaluation regarding functionality, efficiency, benefits, and acceptance within communities remains. Here we primarily focus on the functionality of THEA-GS, an open-source digital contact tracing tool developed through consultation with stakeholders. Additionally, we provide insights from its implementation on a limited sample of haulage drivers in Uganda, serving as a representative case for a low- and middle-income country. THEA-GS comprises two primary components: (a) a smartphone application, and (b) a suite of server-programs responsible for data processing and analysis, including databases and a web-based interface featuring dashboards. In essence, the mobile application records the timestamped location of haulage drivers within the road network and identifies possible transmission hotspots by analyzing factors such as the duration of stops and the communities associated with them. The tool can be integrated with national infrastructure to compare drivers' diagnostic results and contact structure, thereby generating individual and community risk assessments relative to the road network. During the Omicron-variant wave of the COVID-19 pandemic, a total of 3,270 haulage drivers were enrolled between October 2021 and October 2022. Around 75% of these drivers utilized THEA-GS for approximately two months. Based on an analysis of 3,800 test results, which included 48 positive cases, 125 contacts, and 40 million time-stamped GPS points, THEA-GS shows a significant speed improvement, being approximately 90 times faster than MCT. For instance, the average time from sample collection to notifying a case and their contacts was approximately 70 and 80 min, respectively. The adoption of this tool encountered challenges, mainly due to drivers' awareness of its purpose and benefits for public health. THEA-GS is a place-based digital contact tracing tool specifically designed to assist National Public Health Institutions in managing infectious disease outbreaks involving the haulage industry as a high-risk group. While its utility, acceptance, and accuracy have not been fully evaluated, our preliminary tests conducted in Uganda indicate the tool's functionality is robust, but social acceptance and adoption are heavily reliant on establishing trust among users.

A scoping review of foot-and-mouth disease risk, based on spatial and spatio-temporal analysis of outbreaks in endemic settings.

Foot-and-mouth disease (FMD) is one of the most important transboundary animal diseases affecting livestock and wildlife species worldwide. Sustained viral circulation, as evidenced by serological surveys and the recurrence of outbreaks, suggests endemic transmission cycles in some parts of Africa, Asia and the Middle East. This is the result of a complex process in which multiple serotypes, multi-host interactions and numerous socio-epidemiological factors converge to facilitate disease introduction, survival and spread. Spatial and spatio-temporal analyses have been increasingly used to explore the burden of the disease by identifying high-risk areas, analysing temporal trends and exploring the factors that contribute to the outbreaks. We systematically retrieved spatial and spatial-temporal studies on FMD outbreaks to summarize variations on their methodological approaches and identify the epidemiological factors associated with the outbreaks in endemic contexts. Fifty-one studies were included in the final review. A high proportion of papers described and visualized the outbreaks (72.5%) and 49.0% used one or more approaches to study their spatial, temporal and spatio-temporal aggregation. The epidemiological aspects commonly linked to FMD risk are broadly categorizable into themes such as (a) animal demographics and interactions, (b) spatial accessibility, (c) trade, (d) socio-economic and (e) environmental factors. The consistency of these themes across studies underlines the different pathways in which the virus is sustained in endemic areas, with the potential to exploit them to design tailored evidence based-control programmes for the local needs. There was limited data linking the socio-economics of communities and modelled FMD outbreaks, leaving a gap in the current knowledge. A thorough analysis of FMD outbreaks requires a systemic view as multiple epidemiological factors contribute to viral circulation and may improve the accuracy of disease mapping. Future studies should explore the links between socio-economic and epidemiological factors as a foundation for translating the identified opportunities into interventions to improve the outcomes of FMD surveillance and control initiatives in endemic contexts.

Bovine Tuberculosis Epidemiology in Cameroon, Central Africa, Based on the Interferon-Gamma Assay.

Despite sub-Saharan Africa (SSA) accounting for ~20% of the global cattle population, prevalence estimates and related risk factors of bovine tuberculosis (bTB) are still poorly described. The increased sensitivity of the IFN-γ assay and its practical benefits suggest the test could be useful to investigate bTB epidemiology in SSA. This study used a population-based sample to estimate bTB prevalence, identify risk factors and estimate the effective reproductive rate in Cameroonian cattle populations. A cross-sectional study was conducted in the North West Region (NWR) and the Vina Division (VIN) of Cameroon in 2013. A regional stratified sampling frame of pastoral cattle herds produced a sample of 1,448 cattle from 100 herds. In addition, a smaller cross-sectional study sampled 60 dairy cattle from 46 small-holder co-operative dairy farmers in the NWR. Collected blood samples were stimulated with bovine and avian purified protein derivatives, with extracted plasma screened using the IFN-γ enzyme-linked immunosorbent assay (Prionics Bovigam®). Design-adjusted population prevalences were estimated, and multivariable mixed-effects logistic regression models using Bayesian inference techniques identified the risk factors for IFN-γ positivity. Using the IFN-γ assay, the prevalence of bTB in the dairy cattle was 21.7% (95% CI: 11.2-32.2). The design-adjusted prevalence of bTB in cattle kept by pastoralists was 11.4% (95% CI: 7.6-17.0) in the NWR and 8.0% (95% CI: 4.7-13.0) in the VIN. A within-herd prevalence estimate for pastoralist cattle also supported that the NWR had higher prevalence herds than the VIN. Additionally, the estimates of the effective reproductive rate R t were 1.12 for the NWR and 1.06 for the VIN, suggesting different transmission rates within regional cattle populations in Cameroon. For pastoral cattle, an increased risk of IFN-γ assay positivity was associated with being male (OR = 1.89; 95% CI:1.15-3.09), increasing herd size (OR = 1.02; 95% CI:1.01-1.03), exposure to the bovine leucosis virus (OR = 2.45; 95% CI: 1.19-4.84) and paratuberculosis (OR = 9.01; 95% CI: 4.17-20.08). Decreased odds were associated with contacts at grazing, buffalo (OR = 0.20; 95% CI: 0.03-0.97) and increased contact with other herds [1-5 herds: OR = 0.16 (95% CI: 0.04-0.55); 6+ herds: OR = 0.18 (95% CI: 0.05-0.64)]. Few studies have used the IFN-γ assay to describe bTB epidemiology in SSA. This study highlights the endemic situation of bTB in Cameroon and potential public health risks from dairy herds. Further work is needed to understand the IFN-γ assay performance, particularly in the presence of co-infections, and how this information can be used to develop control strategies in the SSA contexts.

The Epidemiology of Bovine Viral Diarrhea Virus in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis.

Introduction: Bovine viral diarrhea virus (BVDV) causes reproductive inefficiencies and negatively impacts the economy of low- and middle-income countries (LMICs). It is characterized by a combination of syndromes that result in poor production performance and calf morbidity and mortality. BVDV control is possible by introduction of biosecurity measures, test-and-cull, and vaccination programs as accomplished in high-income countries. Knowledge of BVDV epidemiology is limited in many LMICs, which hinders implementation of effective control programs. We carried out a systematic review and meta-analysis to estimate the burden of BVDV, identify risk factors related to its occurrence, and health and economic impacts on production systems. Materials and Methods: Relevant BVD articles were collated from library databases; 690 abstracts and full texts were found in an initial search followed by filtering of 59 manuscripts. We accounted for quality and risk of bias in the meta-analysis. Prevalence, exposure, and current infection at regional, production, and farming system levels were estimated using logistic random-effects meta-regression models. Finally, we calculated the proportion of studies that addressed risk factors and health and economic impacts across different production systems to inform future preventative strategies in LMICs. Results: Seroprevalence was high and varied between regions. Mean weighted prevalence was 39.5% (95% CI 25-56.1), 45.2% (95% CI 35.9-54.8), 49.9% (95% CI 25.5-74.3), and 21.6% (95% CI 0.5-56) for sub-Saharan Africa, South America, Middle East, and Asia, respectively. Seroprevalence varied across farming systems, with smallholder farming showing the highest values. Herdsize was the most frequently reported risk factor, and the percentage of articles that reported herdsize as a risk factor were 20.6%, 33.3%, and 38.4% for dairy, beef and mixed systems respectively. Abortion (13.7% of articles) was the main reported health impact in dairy systems. Some articles reported milk drop (4.6% of articles), but no article investigated the economic cost of BVDV in farming systems. Conclusion: Animal-level seroprevalence varied across all regions. Most of the studies focused on BVDV seroprevalence. There were some articles that investigated risk factors and health impacts, and there were even less that investigated economic impacts. Future studies should focus on identifying risk factors and quantifying health and economic impacts across systems. Understanding these aspects is crucial to develop management strategies to apply across diverse production systems in LMICs.

Bovine Tuberculosis Antemortem Diagnostic Test Agreement and Disagreement in a Naturally Infected African Cattle Population.

The interferon-gamma (IFN-γ) assay and single comparative cervical skin test (SCITT) are used to estimate bovine tuberculosis (bTB) prevalence globally. Prevalence estimates of bTB, caused by Mycobacterium bovis, are poorly quantified in many Sub-Saharan African (SSA) cattle populations. Furthermore, antemortem diagnostic performance can vary at different stages of bTB pathogenesis and in different cattle populations. In this study, we aim to explore the level of agreement and disagreement between the IFN-γ assay and SCITT test, along with the drivers for disagreement, in a naturally infected African cattle population. In, 2013, a pastoral cattle population was sampled using a stratified clustered cross-sectional study in Cameroon. A total of 100 pastoral cattle herds in the North West Region (NWR) and the Vina Division (VIN) were sampled totalling 1,448 cattle. Individual animal data and herd-level data were collected, and animals were screened using both the IFN-γ assay and SCITT. Serological ELISAs were used to detect exposure to immunosuppressing co-infections. Agreement analyses were used to compare the performance between the two bTB diagnostic tests, and multivariable mixed-effects logistic regression models (MLR) were developed to investigate the two forms of IFN-γ assay and SCITT binary disagreement. Best agreement using the Cohen's κ statistic, between the SCITT (>2 mm) and the IFN-γ assay implied a 'fair-moderate' agreement for the NWR [κ = 0.42 (95%CI: 0.31-0.53)] and 'poor-moderate' for the VIN [κ = 0.33 (95% CI: 0.18-0.47)]. The main test disagreement was the animals testing positive on the IFN-γ assay and negative by the SCITT. From MLR modeling, adults (adults OR: 7.57; older adults OR = 7.21), females (OR = 0.50), bovine leucosis (OR = 2.30), and paratuberculosis positivity (OR = 6.54) were associated with IFN-γ-positive/SCITT-negative disagreement. Subsets to investigate diagnostic test disagreement for being SCITT-positive and IFN-γ-negative also identified that adults (adults OR = 15.74; older adults OR = 9.18) were associated with IFN-γ-negative/SCITT-positive disagreement. We demonstrate that individual or combined use of the IFN-γ assay and SCITT can lead to a large variation in bTB prevalence estimates. Considering that animal level factors were associated with disagreement between the IFN-γ assay and SCITT in this study, future work should further investigate their impact on diagnostic test performance to develop the approaches to improve SSA prevalence estimates.

Ranging patterns and factors associated with movement in free-roaming domestic dogs in urban Malawi.

Rabies is a neglected zoonotic disease that causes around 59,000 deaths per year globally. In Africa, rabies virus is mostly maintained in populations of free-roaming domestic dogs (FRDD) that are predominantly owned. Characterizing the roaming behavior of FRDD can provide relevant information to understand disease spread and inform prevention and control interventions. To estimate the home range (HR) of FRDD and identify predictors of HR size, we studied 168 dogs in seven different areas of Blantyre city, Malawi, tracking them with GPS collars for 1-4 days. The median core HR (HR50) of FRDD in Blantyre city was 0.2 ha (range: 0.08-3.95), while the median extended HR (HR95) was 2.14 ha (range: 0.52-23.19). Multivariable linear regression models were built to identify predictors of HR size. Males presented larger HR95 than females. Dogs living in houses with a higher number of adults had smaller HR95, while those living in houses with higher number of children had larger HR95. Animals that received products of animal origin in their diets had larger HR95, and only in the case of females, animals living in low-income areas had larger HR50 and HR95. In contrast, whether male dogs were castrated or not was not found to be associated with HR size. The results of this study may help inform rabies control and prevention interventions in Blantyre city, such as designing risk-based surveillance activities or rabies vaccination campaigns targeting certain FRDD subpopulations. Our findings can also be used in rabies awareness campaigns, particularly to illustrate the close relationship between children and their dogs.

Developing digital contact tracing tailored to haulage in East Africa to support COVID-19 surveillance: a protocol.

INTRODUCTION: At the peak of Uganda's first wave of SARS-CoV-2 in May 2020, one in three COVID-19 cases was linked to the haulage sector. This triggered a mandatory requirement for a negative PCR test result at all ports of entry and exit, resulting in significant delays as haulage drivers had to wait for 24-48 hours for results, which severely crippled the regional supply chain.To support public health and economic recovery, we aim to develop and test a mobile phone-based digital contact tracing (DCT) tool that both augments conventional contact tracing and also increases its speed and efficiency. METHODS AND ANALYSIS: To test the DCT tool, we will use a stratified sample of haulage driver journeys, stratified by route type (regional and local journeys).We will include at least 65% of the haulage driver journeys ~83 200 on the network through Uganda. This allows us to capture variations in user demographics and socioeconomic characteristics that could influence the use and adoption of the DCT tool. The developed DCT tool will include a mobile application and web interface to collate and intelligently process data, whose output will support decision-making, resource allocation and feed mathematical models that predict epidemic waves.The main expected result will be an open source-tested DCT tool tailored to haulage use in developing countries.This study will inform the safe deployment of DCT technologies needed for combatting pandemics in low-income countries. ETHICS AND DISSEMINATION: This work has received ethics approval from the School of Public Health Higher Degrees, Research and Ethics Committee at Makerere University and The Uganda National Council for Science and Technology. This work will be disseminated through peer-reviewed publications, our websites https://project-thea.org/ and Github for the open source code https://github.com/project-thea/.

Latent class evaluation of the performance of serological tests for exposure to Brucella spp. in cattle, sheep, and goats in Tanzania.

BACKGROUND: Brucellosis is a neglected zoonosis endemic in many countries, including regions of sub-Saharan Africa. Evaluated diagnostic tools for the detection of exposure to Brucella spp. are important for disease surveillance and guiding prevention and control activities. METHODS AND FINDINGS: Bayesian latent class analysis was used to evaluate performance of the Rose Bengal plate test (RBT) and a competitive ELISA (cELISA) in detecting Brucella spp. exposure at the individual animal-level for cattle, sheep, and goats in Tanzania. Median posterior estimates of RBT sensitivity were: 0.779 (95% Bayesian credibility interval (BCI): 0.570-0.894), 0.893 (0.636-0.989), and 0.807 (0.575-0.966), and for cELISA were: 0.623 (0.443-0.790), 0.409 (0.241-0.644), and 0.561 (0.376-0.713), for cattle, sheep, and goats, respectively. Sensitivity BCIs were wide, with the widest for cELISA in sheep. RBT and cELISA median posterior estimates of specificity were high across species models: RBT ranged between 0.989 (0.980-0.998) and 0.995 (0.985-0.999), and cELISA between 0.984 (0.974-0.995) and 0.996 (0.988-1). Each species model generated seroprevalence estimates for two livestock subpopulations, pastoralist and non-pastoralist. Pastoralist seroprevalence estimates were: 0.063 (0.045-0.090), 0.033 (0.018-0.049), and 0.051 (0.034-0.076), for cattle, sheep, and goats, respectively. Non-pastoralist seroprevalence estimates were below 0.01 for all species models. Series and parallel diagnostic approaches were evaluated. Parallel outperformed a series approach. Median posterior estimates for parallel testing were ≥0.920 (0.760-0.986) for sensitivity and ≥0.973 (0.955-0.992) for specificity, for all species models. CONCLUSIONS: Our findings indicate that Brucella spp. surveillance in Tanzania using RBT and cELISA in parallel at the animal-level would give high test performance. There is a need to evaluate strategies for implementing parallel testing at the herd- and flock-level. Our findings can assist in generating robust Brucella spp. exposure estimates for livestock in Tanzania and wider sub-Saharan Africa. The adoption of locally evaluated robust diagnostic tests in setting-specific surveillance is an important step towards brucellosis prevention and control.

The epidemiology of bacterial zoonoses in pastoral and dairy cattle in Cameroon, Central Africa.

Previous work identified that bacterial zoonoses (Brucella species, Coxiella burnetii and Leptospira hardjo) were present in Cameroonian pastoral cattle. To assess the characteristics of this zoonotic risk, we analyse seroprevalence of each pathogen and the associated management, herd and environmental factors in Cameroonian pastoral and dairy cattle. Cross-sectional samples included pastoralist herds in the Northwest Region (NWR n = 750) and Vina Division (VD n = 748) and small holder dairy herds in the NWR (n = 60). Exposure to Brucella spp., C. burnetii and L. hardjo were screened for using commercial ELISAs and population adjusted estimates made. In addition, individual, herd and ecological metadata were collected and used to identify risk factors associated with animal-level seropositivity. In the pastoral cattle, seroprevalence to Brucella spp. was relatively low but was higher in the NWR (4.2%, CI: 2.5%-7.0%) than the VD (1.1%: CI 0.5%-2.4%), while L. hardjo seroprevalence was much higher though similar in the NWR (30.7%, CI 26.3%-35.5%) and VD (35.9%, CI 31.3%-40.7%). No differences were noted in C. burnetii seroprevalence between the two study sites (NWR: 14.6%, CI 11.8%-18.0%. VD: 12.4%, 9.6%-15.9%). Compared to pastoral, dairy cattle had lower seroprevalences for L. hardjo (1.7%, CI: 0.0%-4.9%), C. burnetii (0.0%, CI 0.0%-6.0%) but similar for Brucella spp. (5.0%, CI 0.0%-10.6%). Increased odds of Brucella spp. seropositivity were associated with owning sheep or rearing sheep and fencing cattle in at night. Adult cattle had increased odds of being seropositive for both C. burnetii and L. hardjo. Additionally, exposure to C. burnetii was associated with local ecological conditions and L. hardjo was negatively associated with cattle undertaking transhumance. This work highlights that exposure to these 3 important production diseases and occupational zoonoses are widespread in Cameroonian cattle. Further work is required to understand transmission dynamics between humans and livestock to inform implementation of effective control measures.

Surveillance of a vomiting outbreak in dogs in the UK using owner-derived and internet search data.

BACKGROUND: In early 2020, the Small Animal Veterinary Surveillance Network reported evidence of an outbreak of acute prolific vomiting in dogs in the UK. The aims of this study were to investigate whether there was evidence for a vomiting outbreak in Dogslife and Google Trends data and to describe its characteristics. METHODS: Incidence of Dogslife vomiting reports and the Google search index for 'dog vomiting' and 'puppy vomiting' between December 2019 and March 2020 was compared to the respective data from the same months in previous years. Risks for dogs vomiting and factors influencing veterinary attendance in Dogslife were identified using multivariable logistic regression. RESULTS: This study confirmed a vomiting outbreak was evident in UK dogs between December 2019 and March 2020 using data from Dogslife and Google Trends. The odds of a vomiting incident being reported to Dogslife was 1.51 (95% CI: 1.24-1.84) in comparison to previous years. Dogslife data identified differences in owner-decision making when seeking veterinary attention and identified factors associated with dogs at higher odds of experiencing a vomiting episode. CONCLUSION: Owner-derived data including questionnaires and internet search queries should be considered a valid, valuable source of information for veterinary population health surveillance.

Using data-driven approaches to improve delivery of animal health care interventions for public health.

Rabies kills ∼60,000 people per year. Annual vaccination of at least 70% of dogs has been shown to eliminate rabies in both human and canine populations. However, delivery of large-scale mass dog vaccination campaigns remains a challenge in many rabies-endemic countries. In sub-Saharan Africa, where the vast majority of dogs are owned, mass vaccination campaigns have typically depended on a combination of static point (SP) and door-to-door (D2D) approaches since SP-only campaigns often fail to achieve 70% vaccination coverage. However, D2D approaches are expensive, labor-intensive, and logistically challenging, raising the need to develop approaches that increase attendance at SPs. Here, we report a real-time, data-driven approach to improve efficiency of an urban dog vaccination campaign. Historically, we vaccinated ∼35,000 dogs in Blantyre city, Malawi, every year over a 20-d period each year using combined fixed SP (FSP) and D2D approaches. To enhance cost effectiveness, we used our historical vaccination dataset to define the barriers to FSP attendance. Guided by these insights, we redesigned our vaccination campaign by increasing the number of FSPs and eliminating the expensive and labor-intensive D2D component. Combined with roaming SPs, whose locations were defined through the real-time analysis of vaccination coverage data, this approach resulted in the vaccination of near-identical numbers of dogs in only 11 d. This approach has the potential to act as a template for successful and sustainable future urban SP-only dog vaccination campaigns.

Determinants of vitamin D status in Kenyan calves.

Vitamin D plays a critical role in calcium homeostasis and in the maintenance and development of skeletal health. Vitamin D status has increasingly been linked to non-skeletal health outcomes such as all-cause mortality, infectious diseases and reproductive outcomes in both humans and veterinary species. We have previously demonstrated a relationship between vitamin D status, assessed by the measurement of serum concentrations of the major vitamin D metabolite 25 hydroxyvitamin D (25(OH)D), and a wide range of non-skeletal health outcomes in companion and wild animals. The aims of this study were to define the host and environmental factors associated with vitamin D status in a cohort of 527 calves from Western Kenya which were part of the Infectious Disease of East African Livestock (IDEAL) cohort. A secondary aim was to explore the relationship between serum 25(OH)D concentrations measured in 7-day old calves and subsequent health outcomes over the following 12 months. A genome wide association study demonstrated that both dietary and endogenously produced vitamin D metabolites were under polygenic control in African calves. In addition, we found that neonatal vitamin D status was not predictive of the subsequent development of an infectious disease event or mortality over the 12 month follow up period.

Factors associated with mobile phone ownership and potential use for rabies vaccination campaigns in southern Malawi.

BACKGROUND: Rabies is a fatal but preventable viral disease, which causes an estimated 59 000 human deaths globally every year. The vast majority of human rabies cases are attributable to bites from infected domestic dogs and consequently control of rabies in the dog population through mass vaccination campaigns is considered the most effective method of eliminating the disease. Achieving the WHO target of 70% vaccination coverage has proven challenging in low-resource settings such as Sub Saharan Africa, and lack of public awareness about rabies vaccination campaigns is a major barrier to their success. In this study we surveyed communities in three districts in Southern Malawi to assess the extent of and socio-economic factors associated with mobile phone ownership and explore the attitudes of communities towards the use of short message service (SMS) to inform them of upcoming rabies vaccination clinics. METHODS: This study was carried out between 1 October-3 December 2018 during the post-vaccination assessment of the annual dog rabies campaign in Blantyre, Zomba and Chiradzulu districts, Malawi. 1882 questionnaires were administered to households in 90 vaccination zones. The surveys gathered data on mobile phone ownership and use, and barriers to mobile phone access. A multivariable regression model was used to understand factors related to mobile phone ownership. RESULTS: Most survey respondents owned or had use of a mobile phone, however there was evidence of an inequality of access, with higher education level, living in Blantyre district and being male positively associated with mobile phone ownership. The principal barrier to mobile phone ownership was the cost of the phone itself. Basic feature phones were most common and few owned smartphones. SMS was commonly used and the main reason for not using SMS was illiteracy. Attitudes to receiving SMS reminders about future rabies vaccination campaigns were positive. CONCLUSIONS: The study showed a majority of those surveyed have the use of a mobile phone and most mobile phone owners indicated they would like to receive SMS messages about future rabies vaccination campaigns. This study provides insight into the feasibility of distributing information about rabies vaccination campaigns using mobile phones in Malawi.

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage.

Group antimicrobial administration is used to control disease in livestock, but we have little insight into how this impacts antimicrobial resistance (AMR) gene dynamics. Here, a longitudinal study was carried out during a single production cycle on a commercial pig unit with high historic and current antimicrobial usage. Quantitative PCR, 16S rRNA gene metabarcoding and shotgun metagenomic sequencing were used to track faecal AMR gene abundance and diversity and microbiome alpha diversity. Shotgun metagenomic sequencing identified 144 AMR genes in total, with higher AMR gene diversity present in young pigs compared to dry sows. Irrespective of in-feed antibiotic treatment or changes in microbiome diversity, mean AMR gene copy number was consistently high, with some AMR genes present at copy numbers comparable to the bacterial 16S rRNA gene. In conclusion, AMR gene prevalence and abundance were not influenced by antibiotic use, either during the production cycle or following whole-herd medication. The high levels of certain genes indicate they are widely disseminated throughout the microbial population, potentially aiding stability. Despite the high and relatively stable levels of resistance genes against the main antimicrobials used, these compounds continue to control production limiting diseases on this unit.

Implementation of a mass canine rabies vaccination campaign in both rural and urban regions in southern Malawi.

Rabies is a devastating zoonotic disease causing nearly 60,000 deaths globally each year. The disease causes Malawi an economic loss of 13 million USD and kills almost 500 people annually. Domestic dogs are the main reservoir for rabies and vaccinating over 70% of the dog population is the most efficient method to reduce its incidence in both humans and canines. However, achieving such coverages is often difficult and depend on many geospatial factors. Rural and pastoral regions are considered difficult to vaccinate efficiently due to low dog densities, and reports of campaigns spanning large areas containing vastly different communities are lacking. This study describes a mass canine vaccination campaign covering rural and urban regions in southern Malawi. The campaign achieved an average vaccination coverage of 83.4% across 3 districts, and vaccinated over 89,000 dogs through a combined static point and door-to-door effort. A dog population of 107,574 dogs was estimated (dog:human ratio of 1:23). The canine population was found to be almost completely owned (99.2%) and mostly kept for security purposes (82.7%). The dogs were mainly adults, males, and not neutered. Regression analysis identified education level and proportion of young dogs as the only factors influencing (positively and negatively, respectively) whether vaccination coverage over 70% was achieved in a region, independently of variables such as population density or poverty. A second regression analysis was performed predicting absolute vaccination coverage. While education level and the proportion of confined dogs were associated with positive vaccination coverage, higher proportions of young animals and female dogs were associated with a decrease in coverage. This study confirms the feasibility of homogeneously vaccinating over 70% of the dogs in a large area including rural and urban communities. These findings can inform the logistics of future campaigns and might be used as a template to facilitate high-number, high-coverage vaccination campaigns to other regions in sub-Saharan Africa.

Multilayer network analysis unravels haulage vehicles as a hidden threat to the British swine industry.

When assessing the role of live animal trade networks in the spread of infectious diseases in livestock, attention has focused mainly on direct movements of animals between premises, whereas the role of haulage vehicles used during transport, an indirect route for disease transmission, has largely been ignored. Here, we have assessed the impact of sharing haulage vehicles from livestock transport service providers on the connectivity between farms as well as on the spread of swine infectious diseases in Great Britain (GB). Using all pig movement records between April 2012 and March 2014 in GB, we built a series of directed and weighted static multiplex networks consisting of two layers of identical nodes, where nodes (farms) are linked either by (a) the direct movement of pigs and (b) the shared use of haulage vehicles. The haulage contact definition integrates the date of the move and the duration Δ s that lorries are left contaminated by pathogens, hence accounting for the temporal aspect of contact events. For increasing Δ s , descriptive network analyses were performed to assess the role of haulage on network connectivity. We then explored how viruses may spread throughout the GB pig sector by computing the reproduction number R . Our results showed that sharing haulage vehicles increases the number of contacts between farms by >50% and represents an important driver of disease transmission. In particular, sharing haulage vehicles, even if Δ s  < 1 day, will limit the benefit of the standstill regulation, increase the number of premises that could be infected in an outbreak, and more easily raise R above 1. This work confirms that sharing haulage vehicles has significant potential for spreading infectious diseases within the pig sector. The cleansing and disinfection process of haulage vehicles is therefore a critical control point for disease transmission risk mitigation.

Development of a high number, high coverage dog rabies vaccination programme in Sri Lanka.

BACKGROUND: Rabies is estimated to cause 59,000 deaths and economic losses of US$8.6 billion every year. Despite several years of rabies surveillance and awareness programmes, increased availability of post-exposure prophylaxis vaccinations and dog population control, the disease still remains prevalent in Sri Lanka. This study reports the roll-out of a high number, high coverage canine rabies vaccination campaign in Sri Lanka, providing estimates for the vaccination coverage achieved, analysing the local dog demographics, and identifying barriers of attendance to static vaccination clinics. METHODS: A mass dog vaccination campaign was undertaken in Negombo, Sri Lanka. The campaign was composed of static point and door-to-door vaccination stages, with a final survey of vaccination coverage. A large volume of data on the distribution, health, and signalment of vaccinated dogs was collected through a mobile phone application. A logistic regression model was developed to investigate which socio-spatial and dog-related factors influenced attendance of owners to static vaccination points. RESULTS: The campaign vaccinated over 7800 dogs achieving a vaccination coverage of 75.8%. A dog:human ratio of 1:17 was estimated. Most dogs were owned, and the dog population was mostly male, adult, and non-sterilized. Unawareness, unavailability and handling problems were the most common reasons given by owners to explain failure to attend a static vaccination point. The regression analysis showed that increasing distance to a static point, in addition to young age and poor health of the dog, were associated with a decrease in the likelihood of attendance to a static vaccination points. CONCLUSION: This study demonstrates the feasibility of high number, high coverage vaccination campaigns in Sri Lanka. The information on dog ecology and barriers of attendance to static point vaccination clinics will facilitate development of future vaccination campaigns.

Comparison of Two Rift Valley Fever Serological Tests in Cameroonian Cattle Populations Using a Bayesian Latent Class Approach.

Rift Valley Fever is an important zoonotic viral disease of livestock occurring across much of Africa causing acute febrile illness, abortion, and neonatal death in livestock particularly sheep and cattle and a range of disease in humans from mild flu-like symptoms to more severe haemorrhagic fever and death. Understanding the epidemiology requires well-evaluated tools including antibody detection ELISAs. It is well-recognized that tests developed in one population do not necessarily perform as well when used in different populations and it is therefore important to assess tests in the populations in which they are to be used. Here we describe the performance of a commercial RVF ELISA (ID.Vet) and an in-house plaque reduction neutralization test (PRNT80). A Bayesian no gold standard latent class model for two tests and ≥2 populations based on the Hui-Walter model was used to estimate the test parameters using a range of populations based on geographical separation and age to assess consistency of performance across different sub-populations. The ID.Vet ELISA had an estimated diagnostic sensitivity (Se) of 0.854 (0.655-0.991 95%BCI) and specificity (Sp) of 0.986 (0.971-0.998 95%BCI) using all the data and splitting the population by geographical region compared to 0.844 (0.660-0.973 95%BCI) and 0.981 (0.965-0.996 95%BCI) for the PRNT80. There was slight variation in the mean Se and Sp in different sub-populations mainly in Se estimates due to small numbers of positives in the sub-populations but the 95% BCI generally overlapped suggesting a very consistent performance across the different geographical areas and ages of animals. This is one of few reports of serological evidence of RVF in Central Africa and strongly suggests the virus is actively circulating in this cattle population. This has important public health implications and RVF should be considered as a differential in both livestock disease cases as well as human febrile cases in West and Central Africa not just East Africa. We also demonstrate that the performance of the commercial ELISA is comparable to the PRNT80 but has the advantages of speed, lower cost and no containment needs making it a much more useful test for low and middle income settings (LMICs).

Randomised trial of perioperative tramadol for canine sterilisation pain management.

Surgical sterilisation to manage free-roaming dog populations is widely used in many countries. However, few studies have examined optimal postoperative pain management regimens at low-resource, high-throughput veterinary clinics. The aim of this study was to examine the efficacy of two intravenous analgesic regimens, preoperative administration of meloxicam and tramadol, or meloxicam alone, in free-roaming dogs undergoing sterilisation. A total of 125 dogs were included, with 64 dogs in the meloxicam-tramadol arm and 61 dogs in the meloxicam-only arm in a non-inferiority study design. Pain levels in sterilisation surgery patients were assessed at four time points after surgery using the Colorado State University Canine Acute Pain Scale, a Visual Analogue Scale and a modified version of the Glasgow Composite Measure Pain Scale - Short Form. Non-inferiority was supported for each of the main scoring outcomes using non-inferiority margins of 0.5, 5 and 0.8, respectively. One dog from the meloxicam-tramadol group and four dogs in the meloxicam-only arm required rescue analgesia, with no difference between groups (P=0.21).The study demonstrated that meloxicam was effective in controlling postoperative pain in a high proportion of dogs. The addition of tramadol alongside meloxicam treatment was not found to be of clinical benefit.

Whole Genome Sequence Analysis Reveals Lower Diversity and Frequency of Acquired Antimicrobial Resistance (AMR) Genes in E. coli From Dairy Herds Compared With Human Isolates From the Same Region of Central Zambia.

Antibiotic treatment of sick dairy cattle is critical for the sustainability of this production system which is vital for food security and societal prosperity in many low and middle-income countries. Given the increasingly high levels of antibiotic resistance worldwide and the challenge this presents for the treatment of bacterial infections, the rational use of antibiotics in humans and animals has been emphatically recommended in the spirit of a "One Health" approach. The aim of this study was to characterize antimicrobial resistance (AMR) genes and their frequencies from whole genome sequences of Escherichia coli isolated from both dairy cattle and human patients in central Zambia. Whole genome sequences of E. coli isolates from dairy cattle (n = 224) and from patients at a local hospital (n = 73) were compared for the presence of acquired AMR genes. In addition we analyzed the publicly available genomes of 317 human E. coli isolates from over the wider African continent. Both acquired antibiotic resistance genes and phylogroups were identified from de novo assemblies and SNP based phylogenetic analyses were used to visualize the distribution of resistance genes in E. coli isolates from the two hosts. Greater acquired AMR gene diversity was detected in human compared to bovine E. coli isolates across multiple classes of antibiotics with particular resistance genes for extended-spectrum beta lactamases (ESBL), quinolones, macrolides and fosfomycin only detected in E. coli genomes of human origin. The striking difference was that the Zambian or wider African human isolates were significantly more likely to possess multiple acquired AMR genes compared to the Zambian dairy cattle isolates. The median number of resistance genes in the Zambian cattle cohort was 0 (0-1 interquartile range), while in the Zambian human and wider African cohorts the medians and interquartile ranges were 6 (4-9) and 6 (0-8), respectively. The lower frequency and reduced diversity of acquired AMR genes in the dairy cattle isolates is concordant with relatively limited antibiotic use that we have documented in this region, especially among smallholder farmers. The relatively distinct resistant profiles in the two host populations also indicates limited sharing of strains or genes.