Eliciting preferences for attributes of Newcastle disease vaccination programmes for village poultry in Ethiopia

Newcastle disease (NCD) is an important disease of poultry, directly affecting the livelihoods of poor farmers across developing countries. Research has identified promising innovations in NCD vaccine development and field trials among village poultry have been promising. However, NCD vaccination is not currently part of village poultry extension programmes in many developing countries. Understanding the preferences for, and relative importance of, different attributes of potential vaccination programmes to prevent NCD will be crucial in designing acceptable and sustainable prevention programmes. This research employed the discrete choice experiment approach to elicit farmers’ preference for attributes of NCD vaccination programmes for village poultry in rural Ethiopia. The choice experiment survey was conducted on 450 smallholder farmers. The relative importance of attributes of NCD vaccines to farmers was estimated using a random parameter logit regression model. The preferred NCD vaccine programme had greater bird-level protection (i.e. greater capacity to reduce mortality should NCD occur in a flock), was delivered by animal health development agents, and could be administered via drinking water. Results from simulations on changes in attribute levels revealed that bird-level protection capacity and delivery of vaccine by animal heath extension affect farmers’ preferences more than other attributes. These findings suggest that it is important to ensure NCD vaccine programmes offer reasonable capacity to protect against mortality. It also suggests the need to understand farmers’ preferred vaccine delivery mechanisms and route of vaccine administration for a wider acceptance of vaccine

Infection-interactions in Ethiopian village chickens

Chickens raised under village production systems are exposed to a wide variety of pathogens, and current or previous infections may affect their susceptibility to further infections with another parasite, and/or can alter the manifestation of each infection. It is possible that co-infections may be as important as environmental risk factors. However, in cross-sectional studies, where the timing of infection is unknown, apparent associations between infections may be observed due to parasites sharing common risk factors. This study measured antibody titres to 3 viral (Newcastle disease, Marek's disease and infectious bursal disease) and 2 bacterial (Pasteurella multocida and Salmonella) diseases, and the infection prevalence of 3 families of endo- and ecto-parasites (Ascaridida, Eimeria and lice) in 1056 village chickens from two geographically distinct populations in Ethiopia. Samples were collected during 4 cross-sectional surveys, each approximately 6 months apart. Constrained ordination, a technique for analysis of ecological community data, was used to explore this complex dataset and enabled potential relationships to be uncovered and tested despite the different measurements used for the different parasites. It was found that only a small proportion of variation in the data could be explained by the risk factors measured. Very few birds (9/1280) were found to be seropositive to Newcastle disease. Positive relationships were identified between Pasteurella and Salmonella titres; and between Marek's disease and parasitic infections, and these two groups of diseases were correlated with females and males, respectively. This may suggest differences in the way that the immune systems of male and female chickens interact with these parasites. In conclusion, we find that a number of infectious pathogens and their interactions are likely to impact village chicken health and production. Control of these infections is likely to be of importance in future development planning

Clinically relevant antimicrobial resistance at the wildlife–livestock–human interface in Nairobi: An epidemiological study

Background Antimicrobial resistance is one of the great challenges facing global health security in the modern era. Wildlife, particularly those that use urban environments, are an important but understudied component of epidemiology of antimicrobial resistance. We investigated antimicrobial resistance overlap between sympatric wildlife, humans, livestock, and their shared environment across the developing city of Nairobi, Kenya. We use these data to examine the role of urban wildlife in the spread of clinically relevant antimicrobial resistance. Methods 99 households across Nairobi were randomly selected on the basis of socioeconomic stratification. A detailed survey was administered to household occupants, and samples (n=2102) were collected from the faeces of 75 wildlife species inhabiting household compounds (ie, the household and its perimeter; n=849), 13 livestock species (n=656), and humans (n=333), and from the external environment (n=288). Escherichia coli, our sentinel organism, was cultured and a single isolate from each sample tested for sensitivity to 13 antibiotics. Diversity of antimicrobial resistant phenotypes was compared between urban wildlife, humans, livestock, and the environment, to investigate whether wildlife are a net source for antimicrobial resistance in Nairobi. Generalised linear mixed models were used to determine whether the prevalence of antimicrobial resistant phenotypes and multidrug-resistant E coli carriage in urban wildlife is linked to variation in ecological traits, such as foraging behaviour, and to determine household-level risk factors for sharing of antimicrobial resistance between humans, wildlife, and livestock. Findings E coli were isolated from 485 samples collected from wildlife between Sept 6,2015, and Sept 28, 2016. Wildlife carried a low prevalence of E coli isolates susceptible to all antibiotics tested (45 [9%] of 485 samples) and a high prevalence of clinically relevant multidrug resistance (252 [52%] of 485 samples), which varied between taxa and by foraging traits. Multiple isolates were resistant to one agent from at least seven antimicrobial classes tested for, and a single isolate was resistant to all antibiotics tested for in the study. The phenotypic diversity of antimicrobial-resistant E coli in wildlife was lower than in livestock, humans, and the environment. Within household compounds, statistical models identified two interfaces for exchange of antimicrobial resistance: between both rodents, humans and their rubbish, and seed-eating birds, humans and their rubbish; and between seed-eating birds, cattle, and bovine manure. Interpretation Urban wildlife carry a high burden of clinically relevant antimicrobial-resistant E coli in Nairobi, exhibiting resistance to drugs considered crucial for human medicine by WHO. Identifiable traits of the wildlife contribute to this exposure; however, compared with humans, livestock, and the environment, low phenotypic diversity in wildlife is consistent with the hypothesis that wildlife are a net sink rather than source of clinically relevant resistance. Wildlife that interact closely with humans, livestock, and both human and livestock waste within households, are exposed to more antimicrobial resistant phenotypes, and could therefore act as conduits for the dissemination of clinically relevant antimicrobial resistance to the wider environment. These results provide novel insight into the broader epidemiology of antimicrobial resistance in complex urban environments, characteristic of lower-middle-income countries

Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

Background Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism. Methods We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock. Results We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households. Conclusions Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control