Epidemiological connectivity between humans and animals across an urban landscape.

Urbanization is predicted to be a key driver of disease emergence through human exposure to novel, animal-borne pathogens. However, while we suspect that urban landscapes are primed to expose people to novel animal-borne diseases, evidence for the mechanisms by which this occurs is lacking. To address this, we studied how bacterial genes are shared between wild animals, livestock, and humans (n = 1,428) across Nairobi, Kenya-one of the world's most rapidly developing cities. Applying a multilayer network framework, we show that low biodiversity (of both natural habitat and vertebrate wildlife communities), coupled with livestock management practices and more densely populated urban environments, promotes sharing of Escherichia coli-borne bacterial mobile genetic elements between animals and humans. These results provide empirical support for hypotheses linking resource provision, the biological simplification of urban landscapes, and human and livestock demography to urban dynamics of cross-species pathogen transmission at a landscape scale. Urban areas where high densities of people and livestock live in close association with synanthropes (species such as rodents that are more competent reservoirs for zoonotic pathogens) should be prioritized for disease surveillance and control.

Antimicrobial Resistance in Slaughterhouses, Kenya.

Slaughterhouses are hotspots for the transmission of antimicrobial-resistant pathogens. We conducted stakeholder discussions on antimicrobial-resistant pathogens within the slaughterhouse setting. Butchers were described as powerful stakeholders; challenges included limited funding and staff, inadequate infrastructure, and limited laboratory capacity. Slaughterhouse workers understood that their work increased their risk for exposure.

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.

Molecular screening reveals non-uniform malaria transmission in western Kenya and absence of Rickettsia africae and selected arboviruses in hospital patients.

BACKGROUND: In sub-Saharan Africa, malaria is the common diagnosis for febrile illness and related clinical features, resulting in the under-diagnosis of other aetiologies, such as arboviruses and Rickettsia. While these may not be significant causes of mortality in malaria-endemic areas, they affect the daily life and performance of affected individuals. It is, therefore, important to have a clear picture of these other aetiologies to institute correct diagnoses at hospitals and improve patient outcomes. METHODS: Blood samples were collected from patients with fever and other clinical features associated with febrile illness at selected hospitals in the malaria-endemic counties of Busia, Bungoma, and Kakamega, and screened for Crimean-Congo haemorrhagic fever, Sindbis, dengue and chikungunya viruses, Rickettsia africae, and Plasmodium spp. using high-throughput real-time PCR techniques. A logistic regression was performed on the results to explore the effect of demographic and socio-economic independent variables on malaria infection. RESULTS: A total of 336 blood samples collected from hospital patients between January 2018 and February 2019 were screened, of which 17.6% (59/336) were positive for Plasmodium falciparum and 1.5% (5/336) for Plasmodium malariae. Two patients had dual P. falciparum/P. malariae infections. The most common clinical features reported by the patients who tested positive for malaria were fever and headache. None of the patients were positive for the arboviruses of interest or R. africae. Patients living in Busia (OR 5.2; 95% CI 2.46-11.79; p < 0.001) and Bungoma counties (OR 2.7; 95% CI 1.27-6.16; p = 0.013) had higher odds of being infected with malaria, compared to those living in Kakamega County. CONCLUSIONS: The reported malaria prevalence is in line with previous studies. The absence of arboviral and R. africae cases in this study may have been due to the limited number of samples screened, low-level circulation of arboviruses during inter-epidemic periods, and/or the use of PCR alone as a detection method. Other sero-surveys confirming their circulation in the area indicate that further investigations are warranted.

Socio-ecological drivers of vertebrate biodiversity and human-animal interfaces across an urban landscape.

Urbanization can have profound impacts on the distributional ecology of wildlife and livestock, with implications for biodiversity conservation, ecosystem services and human health. A wealth of studies have assessed biotic responses to urbanization in North America and Europe, but there is little empirical evidence that directly links human activities to urban biodiversity in the tropics. Results from a large-scale field study conducted in Nairobi, Kenya, are used to explore the impact of human activities on the biodiversity of wildlife and livestock with which humans co-exist across the city. The structure of sympatric wildlife, livestock and human populations are characterized using unsupervised machine learning, and statistical modelling is used to relate compositional variation in these communities to socio-ecological drivers occurring across the city. By characterizing landscape-scale drivers acting on these interfaces, we demonstrate that socioeconomics, elevation and subsequent changes in habitat have measurable impacts upon the diversity, density and species assemblage of wildlife, livestock and humans. Restructuring of wildlife and livestock assemblages (both in terms of species diversity and composition) has important implications for the emergence of novel diseases at urban interfaces, and we therefore use our results to generate a set of testable hypotheses that explore the influence of urban change on microbial communities. These results provide novel insight into the impact of urbanization on biodiversity in the tropics. An understanding of associations between urban processes and the structure of human and animal populations is required to link urban development to conservation efforts and risks posed by disease emergence to human health, ultimately informing sustainable urban development policy.

Molecular prevalence and risk factors associated with tick-borne pathogens in cattle in western Kenya.

BACKGROUND: Tick-borne pathogens (TBPs) are of global importance, especially in sub-Saharan Africa where they represent a major constraint to livestock production. Their association with human disease is also increasingly recognized, signalling their zoonotic importance. It is therefore crucial to investigate TBPs prevalence in livestock populations and the factors associated with their presence. We set out to identify TBPs present in cattle and to determine associated risk factors in western Kenya, where smallholder livestock production is important for subsistence and market-driven income. RESULTS: Tick-borne pathogen infections in blood samples collected from cattle at livestock markets and slaughterhouses between May 2017 and January 2019 were identified by high-resolution melting analysis and sequencing of PCR products of genus-specific primers. Of the 422 cattle sampled, 30.1% (127/422) were infected with at least one TBP, while 8.8% (37/422) had dual infections. Anaplasma spp. (19.7%) were the most prevalent, followed by Theileria (12.3%), Ehrlichia (6.6%), and Babesia (0.2%) spp. Sequence analysis of the TBPs revealed them to be Anaplasma platys-like organisms (13.5%), Theileria velifera (7.4%), Anaplasma marginale (4.9%), Theileria mutans (3.1%), Theileria parva (1.6%), and Babesia bigemina (0.2%). Ehrlichia ruminantium, Rickettsia spp., and arboviruses were not detected. Exotic breeds of cattle were more likely to be infected with A. marginale compared to local breeds (OR: 7.99, 95% CI: 3.04-22.02, p <  0.001). Presence of ticks was a significant predictor for Anaplasma spp. (OR: 2.18, 95% CI: 1.32-3.69, p = 0.003) and Ehrlichia spp. (OR: 2.79, 95% CI: 1.22-7.23, p = 0.022) infection. Cattle sampled at slaughterhouses were more likely to be positive for Anaplasma spp. (OR: 1.64, 95% CI: 1.01-2.70, p = 0.048) and A. marginale (OR: 3.84, 95% CI: 1.43-12.21, p = 0.012), compared to those sampled at livestock markets. CONCLUSION: This study reports TBP prevalence and associated risk factors in western Kenya, factors which are key to informing surveillance and control measures.

Serological and molecular evidence of Brucella species in the rapidly growing pig sector in Kenya.

BACKGROUND: Brucellosis is an emerging yet neglected zoonosis that has been reported in Kenya. Epidemiological data on brucellosis in ruminants is readily accessible; however, reports on brucellosis in pigs remain limited. This study sought to detect Brucella infection in pig serum by both serological and molecular techniques. Serum from 700 pigs randomly collected at a centralized abattoir in Nairobi region, Kenya were screened in parallel, using both Rose Bengal Test (RBT) and competitive Enzyme-Linked Immuno-sorbent Assay (cELISA) for antibodies against Brucella spp. All sera positive by RBT and 16 randomly selected negative samples were further tested using conventional PCR targeting bcsp31 gene and real-time PCR (RT-PCR) assays targeting IS711 and bcsp31 genes. RESULTS: A prevalence of 0.57% (n = 4/700) was estimated using RBT; none of these samples was positive on cELISA. All RBT positive sera were also positive by both PCRs, while two sero-negative samples also tested positive on RT-PCR (n = 6/20). Brucella abortus was detected in four out of the six PCR positive samples through a real-time multiplex PCR. CONCLUSION: The detection of antibodies against Brucella spp. and DNA in serum from slaughterhouse pigs confirm the presence of Brucella in pigs. Therefore, investigation of the epidemiology and role of pigs in the transmission of brucellosis in Kenya is needed. Further targeted studies would be useful to systematically quantify and identify the spp. of Brucella in pigs.

Seroprevalence and associated risk factors of leptospirosis in slaughter pigs; a neglected public health risk, western Kenya.

BACKGROUND: Leptospirosis is a neglected zoonosis of public health importance transmitted through contact with contaminated soil, water or urine of infected animals. In pigs the disease is characterized by abortion, still births and weak piglets. A cross-sectional study was conducted in May to July 2018 to estimate the sero-prevalence of leptospirosis and factors associated with seropositivity in slaughter pigs. A questionnaire was used to collect information on animal demographics. Serum was tested for anti-leptospiral antibodies using microscopic agglutination test (MAT) with a panel of 8 serovars. Sera were considered positive for sero-reactivity at a MAT titre ≥1:40 against at least one serovar. Chi-square tests were used to measure the strength of association between the MAT test result and exploratory variables. RESULTS: A total of 252 pig serum samples from seven slaughterhouses were tested for Leptospira antibodies by MAT. Of the 252 pigs sampled, 88.8% (244/252) were indigenous breeds; 55.6% (140/252) were female and 88.7% (220/252) were reared in extensive production systems. Eighty-three (32.9%; 83/252) sera samples tested positive on MAT against at least one serovar. Of the 8 serovars, the highest prevalence was recorded for serovar Lora 21.4% followed by Kenya 5.2%, Sokoine 3.6% and Grippotyphosa at 3.2%. Risk factors for leptospirosis seropositivity in pigs were: originating from farms with other types of livestock (OR 2.3; 95% CI 1.0-4.5) and mature pigs (OR 1.9; 95% CI 1.1-3.3). CONCLUSION: This study demonstrates that there is a high prevalence of leptospirosis positive pigs at slaughter in a small-holder livestock keeping region of the Lake Victoria basin. The potential for cross species transmission of pathogenic serovars is highlighted as well as the potential for occupational exposure to slaughterhouse personnel. Improvements in husbandry practices (confinement and rodent control) and public health education among slaughterhouse workers and other high-risk groups is recommended.

Does urbanization make emergence of zoonosis more likely? Evidence, myths and gaps.

Rapid urbanization in the global South is adding epidemiological and nutritional challenges and increasing disease and health burdens for citizens. Greater movement of people, animals, food and trade often provides favourable grounds for the emergence of infectious diseases, including zoonoses. We conduct a rapid evidence scan to explore what is known and hypothesized about the links between urbanization and zoonosis emergence. This points to rapid demographic growth, migration and density, increased movement of people and animals, and changes in land uses as the main processes linked to the prevalence of zoonosis in the urban global South. We argue that this emerging global health challenge is also deeply connected with the urbanization of poverty and inequalities within cities. Tackling the micro-level causal relationships between urbanization and zoonosis requires urgent attention to living conditions, as well as the wider socioenvironmental transitions and structural drivers that produce and reproduce risk accumulation in urban settings.

Are Food Animals Responsible for Transfer of Antimicrobial-Resistant Escherichia coli or Their Resistance Determinants to Human Populations? A Systematic Review.

The role of farm animals in the emergence and dissemination of both AMR bacteria and their resistance determinants to humans is poorly understood and controversial. Here, we systematically reviewed the current evidence that food animals are responsible for transfer of AMR to humans. We searched PubMed, Web of Science, and EMBASE for literature published between 1940 and 2016. Our results show that eight studies (18%) suggested evidence of transmission of AMR from food animals to humans, 25 studies (56%) suggested transmission between animals and humans with no direction specified and 12 studies (26%) did not support transmission. Quality of evidence was variable among the included studies; one study (2%) used high resolution typing tools, 36 (80%) used intermediate resolution typing tools, six (13%) relied on low resolution typing tools, and two (5%) based conclusions on co-occurrence of resistance. While some studies suggested to provide evidence that transmission of AMR from food animals to humans may occur, robust conclusions on the directionality of transmission cannot be drawn due to limitations in study methodologies. Our findings highlight the need to combine high resolution genomic data analysis with systematically collected epidemiological evidence to reconstruct patterns of AMR transmission between food animals and humans.

Mapping Nairobi's dairy food system: An essential analysis for policy, industry and research.

Demand for dairy products in sub-Saharan Africa, is expected to triple by 2050, while limited increase in supply is predicted. This poses significant food security risk to low income households. Understanding how the dairy food system operates is essential to identify mitigation measures to food insecurity impact. This study aims to determine the structure and functionality of Nairobi's dairy system using a value chain mapping approach. Primary data were gathered through focus group discussions and key informant interviews with dairy value chain stakeholders in Nairobi to obtain qualitative information on people and products in the chains while describing their interactions and flows. Qualitative thematic analysis combined with flowcharts created by participants enabled identification of key food system segments and the development of chain profiles (or flow-diagrams) which together form Nairobi's dairy system. Seven chain profiles forming Nairobi's dairy value chain were identified. These were found to be dominated by small-scale individuals who operate largely independently. Our profiles for the urban and peri-urban farming systems were structurally similar in their downstream networks, obtaining inputs from similar sources. Upstream, the urban systems were shorter, supplying mostly to immediate neighbours or based on own consumption, while the peri urban systems supplied to a wider network and showed some affiliations to producers' associations. Two distinct profiles characterize the milk flow from traders belonging either to a Dairy Traders Association (DTA) or those not belonging to this association (non-DTA). DTA traders sell mainly to fixed retailers and non-DTA traders to mobile retailers (hawkers or roadside vendors). Profiles associated with medium and large cooperatives were driven by networks of collection centres, but with medium-sized cooperatives selling half of their production to large processing companies, and large cooperatives only to fixed retailers. Large processing companies' profiles indicated distribution of high volumes and value addition processing. They reported strategic milk collection arrangements with suppliers on long, medium - or short - term contracts and with well-established product distribution channels. We have identified numerous inter-linkages across dairy chain profiles in Nairobi's complex system, demonstrating significant interdependency among the stakeholders. Therefore, enhancing the system's efficiency requires a holistic, system-wide approach and any policy interventions should consider every segment of the value chain. This study provides a methodological approach for organizations and policy makers to understand and address structural and functional vulnerabilities within food systems more broadly. The insights from this study are relevant to other rapidly growing cities in the region.

Identification of production challenges and benefits using value chain mapping of egg food systems in Nairobi, Kenya.

Commercial layer and indigenous chicken farming in Nairobi and associated activities in the egg value chains are a source of livelihood for urban families. A value chain mapping framework was used to describe types of inputs and outputs from chicken farms, challenges faced by producers and their disease control strategies. Commercial layer farms were defined as farms keeping exotic breeds of chicken, whereas indigenous chicken farms kept different cross breeds of indigenous chicken. Four focus group discussions were held with producers of these chickens in peri-urban area: Dagoretti, and one informal settlement: Kibera. Qualitative data were collected on interactions between farmers, sources of farm inputs and buyers of poultry products, simple ranking of production challenges, farmers' perception on diseases affecting chicken and strategies for management of sick chicken and waste products. Value chain profiles were drawn showing sources of inputs and channels for distribution of chicken products. Production challenges and chicken disease management strategies were presented as qualitative summaries. Commercial layer farms in Dagoretti kept an average of 250 chickens (range 50-500); while flock sizes in Kibera were 12 chickens (range 5-20). Farms keeping indigenous chicken had an average of 23 chickens (range 8-40) in Dagoretti, and 10 chickens (range 5-16) in Kibera. Commercial layer farms in Dagoretti obtained chicks from distributors of commercial hatcheries, but farms in Kibera obtained chicks from hawkers who in turn sourced them from distributors of commercial hatcheries. Indigenous chicken farms from Dagoretti relied on natural hatching of fertilised eggs, but indigenous chicken farms in Kibera obtained chicks from their social connection with communities living in rural areas. Outlets for eggs from commercial layer farms included local shops, brokers, restaurants and hawkers, while eggs from indigenous chicken farms were sold to neighbours and restaurants. Sieved chicken manure from Dagoretti area was fed to dairy cattle; whereas non-sieved manure was used as fertilizer on crops. Production challenges included poor feed quality, lack of space for expansion, insecurity, occurrence of diseases and lack of sources of information on chicken management. In Kibera, sick and dead chickens were slaughtered and consumed by households; this practice was not reported in Dagoretti. The chicken layer systems contribute to food security of urban households, yet they have vulnerabilities and deficiencies with regard to disease management and food safety that need to be addressed with support on research and extension.

Serologic Evidence for Influenza C and D Virus among Ruminants and Camelids, Africa, 1991-2015.

Influenza D virus has been identified in America, Europe, and Asia. We detected influenza D virus antibodies in cattle and small ruminants from North (Morocco) and West (Togo and Benin) Africa. Dromedary camels in Kenya harbored influenza C or D virus antibodies, indicating a potential new host for these viruses.

An integrated study of human and animal infectious disease in the Lake Victoria crescent small-holder crop-livestock production system, Kenya.

BACKGROUND: The neglected zoonotic diseases (NZD) are an understudied group that are a major cause of illness throughout the developing world. In general, little is known about the prevalence and burden of NZDs in affected communities, particularly in relation to other infectious diseases with which they are often co-endemic. We describe the design and descriptive epidemiological outputs from an integrated study of human and animal zoonotic and non-zoonotic disease in a rural farming community in western Kenya. METHODS: This cross-sectional survey involved 2113 people, their cattle (n = 983) and pigs (n = 91). People and animals were tested for infection or exposure to a wide range of zoonotic and non-zoonotic pathogens. Prevalence estimates, with adjustment for the complex study design, were derived. Evidence for spatial clustering in exposure or infection was identified using the spatial scan statistic. RESULTS: There was a high prevalence of human parasitism in the community, particularly with hookworm (Ancylostoma duodenale or Necator americanus) (36.3% (95% CI 32.8-39.9)), Entamoeba histolytica/dispar (30.1% (95% CI 27.5-32.8)), and Plasmodium falciparum (29.4% (95% CI 26.8-32.0)). Human infection with Taenia spp. was also prevalent (19.7% (95% CI 16.7-22.7)), while exposure to other zoonotic pathogens was comparatively rarer (Brucella spp., 0.6% (95% CI 0.2-0.9); Coxiella burnetii, 2.2% (95% CI 1.5-2.9); Rift Valley fever, 0.5% (95% CI 0.2-0.8)). A low prevalence of exposure to Brucella spp. was observed in cattle (0.26% (95% CI 0-0.56). This was higher for Rift Valley fever virus (1.4% (95% CI 0.5-2.22)) and C. burnetii (10.0% (95% CI 7.7-12.2)). The prevalence of Taenia spp. cysticercosis was 53.5% (95% CI 48.7-58.3) in cattle and 17.2% (95% CI 9.1-25.3) in pigs. Mycobacterium bovis infection was found in 2.2% of cattle (95% CI 1.3-3.2), while the prevalence of infection with Mycobacterium spp. was 8.2% (95% CI 6.8-9.6) in people. CONCLUSION: Zoonotic infections in people and animals occur in the context of a wide range of co-endemic pathogens in a rural community in western Kenya. The wide diversity of pathogens under study provides a unique opportunity to explore the distribution and determinants of infection in a multi-pathogen, multi-host system.

Mapping of beef, sheep and goat food systems in Nairobi - A framework for policy making and the identification of structural vulnerabilities and deficiencies.

Nairobi is a large rapidly-growing city whose demand for beef, mutton and goat products is expected to double by 2030. The study aimed to map the Nairobi beef, sheep and goat systems structure and flows to identify deficiencies and vulnerabilities to shocks. Cross-sectional data were collected through focus group discussions and interviews with people operating in Nairobi ruminant livestock and meat markets and in the large processing companies. Qualitative and quantitative data were obtained about the type of people, animals, products and value adding activities in the chains, and their structural, spatial and temporal interactions. Mapping analysis was done in three different dimensions: people and product profiling (interactions of people and products), geographical (routes of animals and products) and temporal mapping (seasonal fluctuations). The results obtained were used to identify structural deficiencies and vulnerability factors in the system. Results for the beef food system showed that 44-55% of the city's beef supply flows through the 'local terminal markets', but that 54-64% of total supply is controlled by one 'meat market'. Numerous informal chains were identified, with independent livestock and meat traders playing a pivotal role in the functionality of these systems, and where most activities are conducted with inefficient quality control and under scarce and inadequate infrastructure and organisation, generating wastage and potential food safety risks in low quality meat products. Geographical and temporal analysis showed the critical areas influencing the different markets, with larger markets increasing their market share in the low season. Large processing companies, partly integrated, operate with high quality infrastructures, but with up to 60% of their beef supply depending on similar routes as the informal markets. Only these companies were involved in value addition activities, reaching high-end markets, but also dominating the distribution of popular products, such as beef sausages, to middle and low-end market. For the small ruminant food system, 73% of the low season supply flows through a single large informal market, Kiamaiko, located in an urban informal settlement. No grading is done for these animals or the meat produced. Large companies were reported to export up to 90% of their products. Lack of traceability and control of animal production was a common feature in all chains. The mapping presented provides a framework for policy makers and institutions to understand and design improvement plans for the Nairobi ruminant food system. The structural deficiencies and vulnerabilities identified here indicate the areas of intervention needed.

Lingual palpation for porcine cysticercosis: a rapid epidemiological tool for estimating prevalence and community risk in Africa.

OBJECTIVE: To assess the association between the prevalence of tongue cyst-positive and antigen-positive pigs across different settings in Africa, to evaluate whether examining pigs for cysts could be used as a rapid surveillance tool for identifying geographical areas with a higher probability of high transmission of cysticercosis. METHODS: Published data were collated from 26 study sites across Africa that reported the prevalence of porcine cysticercosis by both lingual and serological examinations. The study sites were located in 10 countries across Africa. RESULTS: Seroprevalence rates ranged from 4% to 41%. Despite the varied study sites, the relationship between the two variables was highly consistent and suggests identification of tongue cysts may be useful for cysticercosis surveillance. We found that all areas with more than 10% of pigs having cysts in their tongues had at least 30% seroprevalence (PPV of 100%), although this cut-off is less reliable at predicting that an area is of low transmission (NPV of 84%). CONCLUSION: Assessing the prevalence of tongue cyst-positive pigs is a potential rapid epidemiological tool for identifying areas at high risk of cysticercosis, although further refinement and validation is required using standardised data sets.

Evidence for the presence of African swine fever virus in an endemic region of Western Kenya in the absence of any reported outbreak.

BACKGROUND: African swine fever (ASF), caused by African swine fever virus (ASFV), is a severe haemorrhagic disease of pigs, outbreaks of which can have a devastating impact upon commercial and small-holder pig production. Pig production in western Kenya is characterised by low-input, free-range systems practised by poor farmers keeping between two and ten pigs. These farmers are particularly vulnerable to the catastrophic loss of livestock assets experienced in an ASF outbreak. This study wished to expand our understanding of ASFV epidemiology during a period when no outbreaks were reported. RESULTS: Two hundred and seventy six whole blood samples were analysed using two independent conventional and real time PCR assays to detect ASFV. Despite no recorded outbreak of clinical ASF during this time, virus was detected in 90/277 samples analysed by conventional PCR and 142/209 samples analysed by qPCR. Genotyping of a sub-set of these samples indicated that the viruses associated with the positive samples were classified within genotype IX and that these strains were therefore genetically similar to the virus associated with the 2006/2007 ASF outbreaks in Kenya. CONCLUSION: The detection of ASFV viral DNA in a relatively high number of pigs delivered for slaughter during a period with no reported outbreaks provides support for two hypotheses, which are not mutually exclusive: (1) that virus prevalence may be over-estimated by slaughter-slab sampling, relative to that prevailing in the wider pig population; (2) that sub-clinical, chronically infected or recovered pigs may be responsible for persistence of the virus in endemic areas.

World Health Organization Estimates of the Global and Regional Disease Burden of 11 Foodborne Parasitic Diseases, 2010: A Data Synthesis.

BACKGROUND: Foodborne diseases are globally important, resulting in considerable morbidity and mortality. Parasitic diseases often result in high burdens of disease in low and middle income countries and are frequently transmitted to humans via contaminated food. This study presents the first estimates of the global and regional human disease burden of 10 helminth diseases and toxoplasmosis that may be attributed to contaminated food. METHODS AND FINDINGS: Data were abstracted from 16 systematic reviews or similar studies published between 2010 and 2015; from 5 disease data bases accessed in 2015; and from 79 reports, 73 of which have been published since 2000, 4 published between 1995 and 2000 and 2 published in 1986 and 1981. These included reports from national surveillance systems, journal articles, and national estimates of foodborne diseases. These data were used to estimate the number of infections, sequelae, deaths, and Disability Adjusted Life Years (DALYs), by age and region for 2010. These parasitic diseases, resulted in 48.4 million cases (95% Uncertainty intervals [UI] of 43.4-79.0 million) and 59,724 (95% UI 48,017-83,616) deaths annually resulting in 8.78 million (95% UI 7.62-12.51 million) DALYs. We estimated that 48% (95% UI 38%-56%) of cases of these parasitic diseases were foodborne, resulting in 76% (95% UI 65%-81%) of the DALYs attributable to these diseases. Overall, foodborne parasitic disease, excluding enteric protozoa, caused an estimated 23.2 million (95% UI 18.2-38.1 million) cases and 45,927 (95% UI 34,763-59,933) deaths annually resulting in an estimated 6.64 million (95% UI 5.61-8.41 million) DALYs. Foodborne Ascaris infection (12.3 million cases, 95% UI 8.29-22.0 million) and foodborne toxoplasmosis (10.3 million cases, 95% UI 7.40-14.9 million) were the most common foodborne parasitic diseases. Human cysticercosis with 2.78 million DALYs (95% UI 2.14-3.61 million), foodborne trematodosis with 2.02 million DALYs (95% UI 1.65-2.48 million) and foodborne toxoplasmosis with 825,000 DALYs (95% UI 561,000-1.26 million) resulted in the highest burdens in terms of DALYs, mainly due to years lived with disability. Foodborne enteric protozoa, reported elsewhere, resulted in an additional 67.2 million illnesses or 492,000 DALYs. Major limitations of our study include often substantial data gaps that had to be filled by imputation and suffer from the uncertainties that surround such models. Due to resource limitations it was also not possible to consider all potentially foodborne parasites (for example Trypanosoma cruzi). CONCLUSIONS: Parasites are frequently transmitted to humans through contaminated food. These estimates represent an important step forward in understanding the impact of foodborne diseases globally and regionally. The disease burden due to most foodborne parasites is highly focal and results in significant morbidity and mortality among vulnerable populations.

Prevalence of porcine cysticercosis in the Lake Kyoga Basin, Uganda.

BACKGROUND: Taenia solium is a zoonotic helminth with the potential to cause life threatening epilepsy in people through the aberrant larval infection of the brain called Neurocysticercosis (NCC). The pig is the intermediate host for T. solium where the larval form, cysticercus cellulosae, normally develops after the pig eats eggs of the parasite. Humans are the definitive host where the adult tapeworm develops and are infected through the consumption of poorly cooked, infected meat. T. solium has been acknowledged by the World Health Organization (WHO), Food and Agriculture Organization (FAO) and UK Department for International Development (DFID) as being a neglected zoonotic disease, and was recently included in the WHO roadmap for control of neglected tropical diseases. This neglect encompasses a lack of epidemiological data and a lack of validated, effective control strategies being adopted. Understanding the epidemiology of this parasite in the intermediate host is the first step towards designing suitable intervention strategies for the improvement of public health. This study was undertaken to provide an accurate and up-to-date estimate for the prevalence of porcine cysticercosis in the Lake Kyoga basin. RESULTS: Sera from 378 pigs were analysed with the HP10 Antigen Enzyme Linked Immunosorbant Assay (ELISA) and the prevalence was found to be 25.7% (95% confidence interval 21.0% to 30.0%). Previous sero- surveillance in this region, using the B158/B60 Ag Elisa had indicated a prevalence of 8.6% in 2005 indicating a dramatic increase in prevalence (J. Parasitol Res, Article ID 375493, 2009) within a 6 year period. CONCLUSION: This increasing prevalence in the disease indicates to us that there is currently no effective control of this parasite and that in this region of Uganda at least; cysticercosis remains a neglected zoonotic disease.

Measuring underreporting and under-ascertainment in infectious disease datasets: a comparison of methods.

BACKGROUND: Efficient and reliable surveillance and notification systems are vital for monitoring public health and disease outbreaks. However, most surveillance and notification systems are affected by a degree of underestimation (UE) and therefore uncertainty surrounds the 'true' incidence of disease affecting morbidity and mortality rates. Surveillance systems fail to capture cases at two distinct levels of the surveillance pyramid: from the community since not all cases seek healthcare (under-ascertainment), and at the healthcare-level, representing a failure to adequately report symptomatic cases that have sought medical advice (underreporting). There are several methods to estimate the extent of under-ascertainment and underreporting. METHODS: Within the context of the ECDC-funded Burden of Communicable Diseases in Europe (BCoDE)-project, an extensive literature review was conducted to identify studies that estimate ascertainment or reporting rates for salmonellosis and campylobacteriosis in European Union Member States (MS) plus European Free Trade Area (EFTA) countries Iceland, Norway and Switzerland and four other OECD countries (USA, Canada, Australia and Japan). Multiplication factors (MFs), a measure of the magnitude of underestimation, were taken directly from the literature or derived (where the proportion of underestimated, under-ascertained, or underreported cases was known) and compared for the two pathogens. RESULTS: MFs varied between and within diseases and countries, representing a need to carefully select the most appropriate MFs and methods for calculating them. The most appropriate MFs are often disease-, country-, age-, and sex-specific. CONCLUSIONS: When routine data are used to make decisions on resource allocation or to estimate epidemiological parameters in populations, it becomes important to understand when, where and to what extent these data represent the true picture of disease, and in some instances (such as priority setting) it is necessary to adjust for underestimation. MFs can be used to adjust notification and surveillance data to provide more realistic estimates of incidence.