{"doc_desc":{"title":"Urban Zoonosis final 09 July 2015","idno":"APHRC-URBZ-2015-1.0","producers":[{"name":"African Population and Health Research Center","abbreviation":"APHRC","affiliation":"APHRC","role":"Meta data producer"}],"prod_date":"2015-07-09","version_statement":{"version":"Version 1.0"}},"study_desc":{"title_statement":{"idno":"APHRC-URBZ-2015-1.0","title":"Epidemiology Ecology and Socio-Economics of disease Emergence in Nairobi- Urban Zoonosis Project","alt_title":"URBAN ZOONOSIS"},"authoring_entity":[{"name":"African Population and Health Research Center","affiliation":"APHRC"}],"production_statement":{"producers":[{"name":"Dr Catherine Kyobutungi","affiliation":"Research Organization","role":"Principal Investigator"},{"name":"Dr Eric Fever","affiliation":" Institute of Infection and Global Health, University of Liverpool","role":"Co - Principal Investigator"}],"copyright":"\u00a9 APHRC, 2015","funding_agencies":[{"name":"Medical Research Council","abbreviation":"MRC","role":"Funder"}],"grant_no":"G1100783\/1"},"distribution_statement":{"distributors":[{"name":"Djesika Amenda","abbreviation":"Dr.","affiliation":"African Population and Health Research Center- APHRC","uri":"Project Manager"},{"name":"Nicholas Ngomi","abbreviation":"Mr.","affiliation":"African Population and Health Research Center- APHRC","uri":"Research Offficer"},{"name":"Peter Muriuki","abbreviation":"Mr.","affiliation":"African Population and Health Research Center- APHRC","uri":"Research Assistant"},{"name":"Martin Kavao","abbreviation":"Mr.","affiliation":"African Population and Health Research Center- APHRC","uri":"Data analyst"}]},"series_statement":{"series_name":"Other Household Survey [hh\/oth]"},"version_statement":{"version_date":"2013-09-05","version_notes":"Version 1.0 (July 2015): Datasets edited and anonymised."},"holdings":[{"text":"","location":"","callno":"","uri":"doi:11239\/176-2015-033-1.0"}],"study_info":{"keywords":[{"keyword":"NUHDSS","vocab":"Nairobi Urban Health Demographic Surveillance Survey","uri":""},{"keyword":"KEMRI CMR","vocab":"Kenya Medica Research-Center for Microbiology Research","uri":""},{"keyword":"MCH","vocab":"Maternal and Child Health","uri":""},{"keyword":"IVP","vocab":"Indepth Vaccination Project","uri":""},{"keyword":"CCDC","vocab":"Case Control for Diarhoea among Children","uri":""}],"abstract":"Background: It is often claimed that urbanization makes pathogen emergence more likely, but the underlying mechanisms are poorly understood. What characteristics of urban environments might predispose to an emergence event, and what is the contribution of livestock keeping to this process? \n\nWe focused on livestock as sources of these pathogens: emerging diseases are likely to be zoonotic in origin, and livestock pathogens, through the close interactions between livestock, their products and people, are at high of risk crossing the species barrier. We studied Escherichia coli (E. coli), an exemplar of many potential emerging pathogens, which exists in a diversity of hosts, in the environment, on food, in waste. \n\nObjective: The overall objective of the project was to understand the mechanisms leading to the introduction of pathogens into urban populations, and their subsequent spread. More specifically, this study focused on the association between diarrhoea among children under the age of 5 years and E. coli in the faeces, E. coli flora in the immediate environment and in the food chain.\n\nApproach: We conducted a case-control study in two Nairobi informal settlements, namely Korogocho and Viwandani, where the Nairobi Urban Health and Demographic Surveillance Survey (NUHDSS) is run. We selected children reporting diarrhoea within the last 3 days and matched them with similar controls who did not have diarrhoea. For both group, we collected data on socio-demographic characteristics of the household, livestock keeping and contact, residential history and a sample of stools. We also randomly sampled the environment; the usual garbage dumping site of the study participants' households, livestock if any, among others -- and from important sources of food like butcheries, milk shops etc in the vicinity.\n\nOutput and significance: Our approach, which builds on state-of-the-art methodologies across a range of disciplines, creates a benchmark for future studies, and is applicable to a wide range of situations where animals, people and the environment interact. The findings inform development of policy on urban livestock keeping by improving knowledge of the public health risks and by putting those risks in a wider socio-economic context, including the risks associated with alternative sources of livestock products.","coll_dates":[{"start":"2013-09-05","end":"2014-04-25","cycle":""}],"nation":[{"name":"KENYA","abbreviation":"KEN"}],"geog_coverage":"Nairobi Informal settlement- Korogocho and Viwandani","analysis_unit":"Individuals","universe":"This study was a population-based case-control design based on children in the Maternal and Child Health (MCH) study. Children =5yrs from the MCH sampling frame reporting diarrhoea within the last 3 days (case group) were matched with respect to sex and age with others (control group) who had not had diarrhoea in this period. For every \u201ccase\u201d, two controls were drawn from the MCH, or from the wider NUHDSS if controls from the MCH were not available.","notes":"The study seeks to explore in a population-based matched case-control study the urban risk factors including contact with livestock\/livestock products for diarrheagenic E.coli and diarrhoea among children under 5 years residing in two informal settlements (Korogocho and Viwandani) in Nairobi and who are enrolled in either Maternal Child Health (MCH) study or In-depth Vaccination Project (IVP) both of whom are nested within a continuous Nairobi Urban Health and Demographic Surveillance Survey (NUHDSS). The NUHDSS covers the two informal settlements, and each child born within the NUDHDSS are recruited into the MCH study at 6 months or below. Diagnosis of E.coli was done using bacterial culture of faecal samples from cases and controls. For each study case, two controls, matched for age, sex and locality, were selected from the MCH\/NUDHSS database. Parents or close caregivers of each case and control were interviewed to obtain information on social, economic, demographic, environmental and other possible risk factors for diarrhea caused by pathogenic E.coli. Molecular typing, specifically DNA fingerprinting was used to determine the sources\/origin of pathogenic E.coli isolates from children with diarrhea. Samples from livestock, environment, and livestock products served as source material for E.coli isolates from the sick children. The DNA fingerprinting methods was used to assess the genomic similarity or dissimilarity between E.coli isolates from the sick children and those from livestock samples, livestock product samples, and other environmental samples.","study_scope":"The study seeks to explore in a population-based matched case-control study the urban risk factors including contact with livestock\/livestock products for diarrheagenic E.coli and diarrhoea among children under 5 years residing in two informal settlements (Korogocho and Viwandani) in Nairobi and who are enrolled in either Maternal Child Health (MCH) study or In-depth Vaccination Project (IVP) both of whom are nested within a continuous Nairobi Urban Health and Demographic Surveillance Survey (NUHDSS). The NUHDSS covers the two informal settlements, and each child born within the NUDHDSS are recruited into the MCH study at 6 months or below. Diagnosis of E.coli was done using bacterial culture of faecal samples from cases and controls. For each study case, two controls, matched for age, sex and locality, were selected from the MCH\/NUDHSS database. Parents or close caregivers of each case and control were interviewed to obtain information on social, economic, demographic, environmental and other possible risk factors for diarrhea caused by pathogenic E.coli. Molecular typing, specifically DNA fingerprinting was used to determine the sources\/origin of pathogenic E.coli isolates from children with diarrhea. Samples from livestock, environment, and livestock products served as source material for E.coli isolates from the sick children. The DNA fingerprinting methods was used to assess the genomic similarity or dissimilarity between E.coli isolates from the sick children and those from livestock samples, livestock product samples, and other environmental samples."},"method":{"data_collection":{"time_method":"January 2013- July 2014","sampling_procedure":"The study was based on the MCH sampling frame. This sampling included all children born within the NUHDSS between 2006 and 2010, and who had been previously recruited in the MCH study between the ages of 1 to 6 months. Those children had been followed up quarterly since their recruitment. Some of those children were ineligible for this study as they were older than 5, but those who met the age criteria were offered an opportunity to participate.\n\nQuestionnaires about the maternal and child health (ERB approval N0 KEMRI\/RES\/7\/3\/1\/) were administered by fieldworkers to mothers or in case she was absent, to another close caregiver of the child. Diarrhoea which was explained to the respondents as >3 loose stools in 24 hours within the last three days was easily recognized by the mother or the caregiver. A child found to have diarrhoea was offered the opportunity to be included in the study. \n\nFieldworkers were given a list of children in the MCH study stratified by enumeration area, age and sex. Respondents (children =5yrs) from the MCH sampling frame reporting diarrhoea within the last 3 days were offered the opportunity to participate in the study. Each \"case\" was matched with respect to sex, age with two controls who had not had diarrhoea in this period. Those two controls were drawn from the same enumeration area and the MCH sample preferably or the wider NUHDSS if no control from the MCH was available. The nearest match was selected and if (s)he declines to participate then the second nearest matching control was selected and so on.","sampling_deviation":"None","coll_mode":"Face-to-face [f2f]","research_instrument":"This study used the WHO definition of diarrhea as \u201cthe passage of 3 or more loose or liquid stools per day\u201d. Pre-tested structured questionnaires to gather information on household economic data for a wealth ranking exercise, food consumption habits, food sources, livestock keeping (in the city or in rural homes), animal contact, hygiene habits, water sources, water treatment etc. Risk factor data e.g. residential history, food eating habits, livestock or animal contact etc. will be collected. In addition, clinical examination was performed by a clinical officer on the children =5yrs and measurements taken for weight, height, Mid-Upper Arm Circumference, temperature, as well as a recent history of a range of signs and symptoms (e.g. headache, splenomegaly, membrane palour, weight loss, diarrhoea, vomiting, chest pain, tiredness, known disease episodes, etc.).","act_min":"The data collection consisted of four teams of 15 field workers, a supervisor for each team of either gender and a clinical officer for each site. Recruitment was done based on past performance and experiences in surveys, ability to relate to the target group, and ability to speak the survey languages. \n\nThe training of data collectors consisted a detailed, question-by-question explanation of the questionnaires\/interview guides, demonstration of interviewing techniques through role-plays, group discussions, research ethics, procedures for seeking of informed consent, and field logistics. The supervisors received additional training on management of data collection; team dynamics, survey planning and logistics, observing interviews, and spot checking for data quality.","weight":"Previous studies  indicated that the point prevalence of diarrhoea in child cohorts in Kenya is ~18%-30% , or approximately 8 diarrhoea days per child per year , such that 750 to 1600 children with diarrhoea could be reasonably recruited from the MCH. \n\nConservatively assuming 20% decrease in the prevalence of diarrhoea and using a formula to get proportion of cases exposed, The number of cases required was 215. Thus as few as 215 \u201ccases\u201d could give us 90% power to detect significant associations at 5% significance level with odds ratios of at least 1.8 odds ratio"}},"data_access":{"dataset_use":{"contact":[{"name":"African Population and Health Research Center","affiliation":"APHRC","email":"datarequests@aphrc.org","uri":"www.aphrc.org"}],"cit_req":"African Population and Health Research Center, Epidemiology Ecology and Soci-Economics of disease Emergence in Nairobi- Urban Zoonosis, Kenya, July 2015. APHRC, Nairobi - Kenya. doi:11239\/176-2015-033-1.0","deposit_req":"Deposit of Reports\/Papers: The user should submit electronic and paper copies of all publications generated using APHRC data to the Policy Engagement and Communications Department, with copies to the Director of Research.","conditions":"All non-APHRC staff seeking to use data generated at the Center must obtain written approval to use the data from the Director of Research. This form is developed to assess applications for data use and facilitate responsible sharing of data with external partners\/collaborators\/researchers. By entering into this agreement, the undersigned agrees to use these data only for the purpose for which they were obtained and to abide by the conditions outlined below:\n\n1.\tData Ownership: The data remain the property of APHRC; any unauthorized reproduction and sharing of the data is strictly prohibited. The user will, therefore, not release nor permit others to use or release the data to any other person without the written authorization from the Center.\n\n2.\tPurpose: The provided data must be used for the purpose specified in the Data Request Form; any other use not specified in the form must receive additional or separate authorization.\n\n3.\tRespondent Identifiers: The Center is committed to protecting the identity of the respondents who provide information in its research. All analytical data sets (both qualitative and quantitative) released by the Data Unit MUST are stripped of respondent identifiers to protect the identity of the respondents. By accepting to use APHRC data, the user is pledging that he\/she will not, under any circumstance, regenerate the identifiers or permit others to use the data to learn the identity of any individual, household or community included in any data set.\n\n4.\tConfidentiality pledge: The user will not use nor permit others to use the data to report any information in the data sets that could identify, directly or by inference, individuals or households.\n\n5.\tReporting of errors or inconsistencies: The user will promptly notify the Head of the Statistics and Survey Unit any errors discovered in the data as soon as the errors are discovered.\n\n6.\tPublications resulting from APHRC data: The Center requires external collaborators to work with APHRC staff on all publications resulting from its data. In order to facilitate this, lead authors should send a detailed concept note of the paper (including the background, rationale, data, analytical methods, and preliminary findings) to the Principle Investigator (or Theme Leader) for the project (with a copy to the Director of Research), who will circulate the abstract to concerned researchers for possible expression of interest in participating in the publication as co-authors. Any exception to the involvement of APHRC staff should be approved by the Director of Research, APHRC.\n\n7.\tSecurity: The user will take responsibility for the security of the data by ensuring that the data are used and stored in a secure environment where access is password protected. This will ensure that non-authorized people should not have access to the data.\n\n8.\tLoss of privilege to use data: In the event that APHRC determines that the data user is in violation of the conditions for using the data, or if the user wishes to cancel this agreement, the user will destroy the data files provided to him\/her. APHRC retains the right to revoke this agreement or informs publishers to withhold publication of any work based wholly or in part on its data if the conditions for using the data are violated.\n\n9.\tAcknowledgement: Any work\/reports from this data must acknowledge APHRC as the source of these data. For example, the suggested acknowledgement for NUHDSS data is: \n\n\"This research uses livelihoods data collected under the longitudinal Nairobi Urban Health and Demographic Surveillance System (NUHDSS) since 2006. The NUHDSS is carried out by the African Population and Health Research Center in two slums settlements (Korogocho and Viwandani) in Nairobi City.\"\n\nAdditionally all funders, the study communities that provided the data, and staff who collected and analyzed or processed the data should be acknowledged.\n\n10.\tDeposit of Reports\/Papers: The user should submit electronic and paper copies of all publications generated using APHRC data to the Policy Engagement and Communications Department, with copies to the Director of Research.\n\n11.\tChange of contact details: The user will promptly inform the Director of Research of any change in your personal details as contained on this data request form.","disclaimer":"The user of the data acknowledges that APHRC and the relevant funding agency bear no responsibility for use of the data or for interpretations or inferences based upon such uses."}}}}