Epidemiology, ecology and socio-economics of disease emergence in Nairobi (Urban Zoo)

Permanent URI for this collectionhttps://hdl.handle.net/10568/27660

This research project is focused around the important question of pathogen emergence, and the role of urbanization in the emergence of zoonotic pathogens. The overall objective is to understand the mechanisms leading to the introduction of pathogens into urban populations through livestock commodity value chains, and their subsequent spread.

The focus is on livestock as sources of these pathogens, because 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.

The focus in this project is on Escherichia coli, as an exemplar of many potential emerging pathogens, which exists in a diversity of hosts, in the environment, on food, in waste etc. The geographical focus is the city of Nairobi, Kenya, and its hinterlands. In the microbiology components, the project takes a landscape genetics approach to understanding E. coli distribution and spread, with a view to understanding how this is affected by environmental and socio-economic factors.

The project includes a public health component investigating the etiology of diarrhoea in children in low income settlements, centred on the Korogocho and Viwandani slums, part of the Nairobi Urban Health Demographic Surveillance System.

For more information, visit the project website

Browse

Now showing 1 - 20 of 83

Epidemiological connectivity between humans and animals across an urban landscape
(Journal Article, 2023-07-18) Hassell, James M.; Muloi, Dishon M.; VanderWaal, K.L.; Ward, M.J.; Bettridge, Judy M.; Gitahi, N.; Ouko, T.; Imboma, Titus; Akoko, James M.; Karani, Maurice K.; Muinde, Patrick; Nakamura, Y.; Alumasa, Lorren; Furmaga, E.; Kaitho, T.; Amanya, Fredrick; Ogendo, Allan; Fava, Francesco P.; Wee, B.A.; Phan, H.; Kiiru, J.; Kang'ethe, Erastus K.; Kariuki, S.; Robinson, T.; Begon, M.; Woolhouse, Mark E.J.; Fèvre, Eric M.
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.
Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya
(Journal Article, 2022-12-08) Muloi, Dishon M.; Hassell, James M.; Wee, B.A.; Ward, M.J.; Bettridge, Judy M.; Kivali, Velma; Kiyong'a, Alice; Ndinda, Christine; Gitahi, N.; Ouko, T.T.; Imboma, Titus; Akoko, James M.; Murungi, Maurice K.; Njoroge, Samuel M.; Muinde, Patrick; Alumasa, Lorren; Kaitho, T.; Amanya, Fredrick; Ogendo, Allan; Bunnik, B.A.D. van; Kiiru, J.; Robinson, Timothy P.; Kang'ethe, Erastus K.; Kariuki, S.; Pedersen, A.B.; Fèvre, Eric M.; Woolhouse, Mark E.J.
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.
Draft genome sequence of an enterotoxigenic Escherichia coli strain carrying genes for colonization surface antigen 13 and a heat-labile toxin
(Journal Article, 2022-10-20) Njoroge, Samuel M.; Madé, L.F.; Mentzer, A. von; Kulohoma, B.W.; Kamanu, T.K.; Ouko, T.T.; Kiiru, J.; Ward, M.J.; Thomson, N.R.; Fèvre, Eric M.; Woolhouse, Mark E.J.; Kariuki, S.
Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.
Assessment of milk quality and food safety challenges in the complex Nairobi dairy value chain
(Journal Article, 2022-06-08) Kiambi, S.; Fèvre, Eric M.; Alarcón, P.; Gitahi, N.; Masinde, J.; Kang'ethe, Erastus K.; Aboge, G.; Rushton, J.; Onono, J.O.
Food networks present varying food safety concerns because of the complexity of interactions, production, and handling practices. We investigated total bacteria counts (TBCs) and total coliform counts (TCCs) in various nodes of a Nairobi dairy value chain and identified practices that influence food safety. A value chain analysis framework facilitated qualitative data collection through 23 key informant interviews and 20 focus group discussions. Content thematic analysis identified food safety challenges. Cow milk products (N = 290) were collected from farms (N = 63), collection centers (N = 5), shops/kiosks (N = 37), milk bars (N = 17), roadside vendors (N = 14), restaurants (N = 3), milk vending machines (N = 2), mobile traders (N = 2) and a supermarket (N = 1). Mean values of colony-forming units for TBC and TCC were referenced to East African Standards (EAS). Logistic regression analysis assessed differences in milk acceptability based on EAS. The raw milk from farms and collection centers was relatively within acceptable EAS limits in terms of TBC (3.5 × 105 and 1.4 × 106 respectively) but TCC in the milk from farms was 3 times higher than EAS limits (1.5 × 105). Compared to farms, the odds ratio of milk acceptability based on TBC was lower on milk bars (0.02), restaurants (0.02), roadside vendors (0.03), shops/kiosks (0.07), and supermarkets (0.17). For TCC, the odds that milk samples from collection centers, milk bars, restaurants, roadside vendors, and shops/kiosks were acceptable was less than the odds of samples collected from farms (0.18, 0.03, 0.06, 0.02, and 0.12, respectively). Comparison of raw milk across the nodes showed that the odds of milk samples from restaurants, roadside vendors, and shops/kiosks being acceptable were less than the odds of samples collected the farm for TBC (0.03, 0.04, and 0.04, respectively). For TCC, the odds of raw milk from collection centers, restaurants, roadside vendors, milk bars, and shops/kiosks being acceptable were lower than the odds of acceptability for the farm samples (0.18, 0.12, 0.02, 0.04, and 0.05, respectively). Practices with possible influence on milk bacterial quality included muddy cowsheds, unconventional animal feed sources, re-use of spoilt raw milk, milk adulteration, acceptance of low-quality milk for processing, and lack of cold chain. Therefore, milk contamination occurs at various points, and the designing of interventions should focus on every node.
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape
(Journal Article, 2022-04) Muloi, Dishon M.; Wee, B.A.; McClean, D.M.H.; Ward, M.J.; Pankhurst, L.; Phan, H.; Ivens, A.C.; Kivali, Velma; Kiyong'a, Alice; Ndinda, Christine; Gitahi, N.; Ouko, T.T.; Hassell, James M.; Imboma, Titus; Akoko, James M.; Karani, Maurice K.; Njoroge, Samuel M.; Muinde, Patrick; Nakamura, Y.; Alumasa, Lorren; Furmaga, E.; Kaitho, T.; Öhgren, E.M.; Amanya, Fredrick; Ogendo, Allan; Wilson, D.J.; Bettridge, Judy M.; Kiiru, J.; Kyobutungi, C.; Tacoli, C.; Kang'ethe, Erastus K.; Davila, J.D.; Kariuki, S.; Robinson, Timothy P.; Rushton, J.; Woolhouse, Mark E.J.; Fèvre, Eric M.
Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance.
Understanding the urban soup: Investigating microbiology at the scale of a whole city in the tropics
(Blog Post, 2022-03-14) Fèvre, Eric M.
The importance of a food systems approach to low and middle income countries and emerging economies: A review of theories and its relevance for disease control and malnutrition
(Journal Article, 2021-04-14) Alarcón, P.; Domínguez-Salas, Paula; Fèvre, Eric M.; Rushton, Jonathan
Our review explores the changing food production, distribution and consumption environment in low and middle-income countries and emerging economies as a basis for framing how to study food systems in order to address public health issues of food safety and nutrition. It presents the state of knowledge on existing food systems science and its use in terms of sustainable actions for food safety and public health. The review identifies a knowledge gap in food system mapping and governance, with value chain mapping of key commodities often missing. Despite a number of initiatives, the application of food systems methods is highly variable in scope and quality. Most analyses concentrate on specific commodities, rarely taking into account the need for a whole diet approach when looking at nutrition or the assessment of a range of infectious agents and their interactions when looking at food safety. Of the studies included in the review there is a growing observation of “informal” food systems, a term used inconsistently and one that requires revision. “Informal” food systems link to the formal sector to provide food security, yet with trade-offs between economic efficiencies and food safety. Efforts to improve food safety are hampered by inadequate food safety capacities and a lack of policy coherence leading to: inadequate investment; fragmented food quality control systems; weak or non-existent traceability mechanisms; weak foodborne disease surveillance; obsolete food regulation; and weak regulatory enforcement. In-depth food systems assessments can complement risk analysis to identify risky behaviors and understand institutional settings in order to improve codes of practice and enforcement. Methods for looking at food safety from a food systems perspective are emerging, yet existing nutrition and food systems science are not advancing sufficiently in response to nutritional public health problems. There is an urgency for improved understanding of the structure and drivers of the food systems, for better planning of changes that leads to nutrients access and healthy levels of eating. It is proposed that countries and international institutions provide an atlas of food system maps for the key commodities based on an agreed common methodology and developed by multidisciplinary teams.
Nairobi is rapidly losing its green spaces: This could open the door to more diseases
(Blog Post, 2021-03-24) Fèvre, Eric M.; Hassell, J.
The Nairobi pork value chain: Mapping and assessment of governance, challenges, and food safety issues
(Journal Article, 2021-02-10) Murungi, Maurice K.; Muloi, Dishon M.; Muinde, Patrick; Githigia, S.M.; Akoko, James M.; Fèvre, Eric M.; Rushton, Jonathan; Alarcón, P.
The Nairobi pork food system is a growing livestock sub-sector which serves as a source of food and livelihood to its inhabitants. The study aimed to map Nairobi's pork value chains, assess their governance, operational challenges and their impacts on food safety risks and management practices. Qualitative data were collected in seven focus group discussions and 10 key informants' interviews on animal movements and product flows, stakeholders' interactions, perceptions on system governance and challenges, and on their potential impact on food safety management. Quantitative data were obtained to show the importance of flows, business operations and market share. Thematic analysis was conducted to identify themes that provide understanding on the governance, challenges and food safety practices in each profile. The predominant chains identified were [1] The “large integrated company” profile which accounted for 83.6% of pork marketed through abattoirs, and was based on a well-structured supply system, with owned farms (representing 50% of their supply), contract farms and semi-contract farms and [2] Local independent abattoirs, accounting for 16.4%, are privately owned small-scale production, supplied mainly (70%) by small farmers from the immediate neighboring areas. The main challenges associated with governance themes included; (i) Inadequate/lack of enforcement of existing regulation (ii) Negative effect of devolution system of governance (iii) Pig traders' dominance (iii) Lack of association at all system nodes, and (iv) Male dominance across the pig system. The main challenges reported included; (i) Lack of capital to upscale (ii) Poor infrastructure (iii) Pig shortage (iv) Excessive regulation (v) Lack of training (vi) Diseases (v) Lack of knowledge (vi) Unfair competition. Food safety themes were associated with (i) Inadequate slaughter facilities forcing traders/farmers to undertake home slaughter (ii) Lack of knowledge on disease management (iii) Lack of training on hygienic practices in the slaughterhouse and (iv) Lack/insufficient capital to purchase equipment's to ensure proper hygiene e.g., boilers. The study provides insights into the structure of the pork system supplying Nairobi, the governance issues important to the stakeholders, challenges and food safety issues. The framework obtained can be used by policy makers and researchers to investigate and develop pork industry and for food safety and disease control programmes.
Socio‐ecological drivers of vertebrate biodiversity and human‐animal interfaces across an urban landscape
(Journal Article, 2021-02) Hassell, James M.; Bettridge, Judy M.; Ward, Melissa J.; Ogendo, Allan; Imboma, Titus; Muloi, Dishon M.; Fava, Francesco P.; Robinson, Timothy P.; Begon, Michael; Fèvre, Eric M.
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.
Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics
(Journal Article, 2020-12) Wee, B.A.; Muloi, D.M.; Bunnik, B.A.D. van
Background Livestock have been implicated as a reservoir for antimicrobial resistance (AMR) that can spread to humans. Close proximity and ecological interfaces involving livestock have been posited as risk factors for the transmission of AMR. In spite of this, there are sparse data and limited agreement on the transmission dynamics that occur. Objectives To identify how genome sequencing approaches can be used to quantify the dynamics of AMR transmission at the human–livestock interface, and where current knowledge can be improved to better understand the impact of transmission on the spread of AMR. Sources Key articles investigating various aspects of AMR transmission at the human–livestock interface are discussed, with a focus on Escherichia coli. Content We recapitulate the current understanding of the transmission of AMR between humans and livestock based on current genomic and epidemiological approaches. We discuss how the use of well-designed, high-resolution genome sequencing studies can improve our understanding of the human–livestock interface. Implications A better understanding of the human–livestock interface will aid in the development of evidence-based and effective One Health interventions that can ultimately reduce the burden of AMR in humans.
Volunteer based approach to dog vaccination campaigns to eliminate human rabies: Lessons from Laikipia County, Kenya
(Journal Article, 2020-07-02) Ferguson, A.W.; Muloi, Dishon M.; Ngatia, D.K.; Kiongo, W.; Kimuyu, D.M.; Webala, P.W.; Olum, M.O.; Muturi, M.; Thumbi, Samuel M.; Woodroffe, R.; Murugi, L.; Fèvre, Eric M.; Murray, S.; Martins, D.J.
Background An estimated 59,000 people die from rabies annually, with 99% of those deaths attributable to bites from domestic dogs (Canis lupus familiaris). This preventable Neglected Tropical Disease has a large impact across continental Africa, especially for rural populations living in close contact with livestock and wildlife. Mass vaccinations of domestic dogs are effective at eliminating rabies but require large amounts of resources, planning, and political will to implement. Grassroots campaigns provide an alternative method to successful implementation of rabies control but remain understudied in their effectiveness to eliminate the disease from larger regions. Methodology/Principal Findings We report on the development, implementation, and effectiveness of a grassroots mass dog rabies vaccination campaign in Kenya, the Laikipia Rabies Vaccination Campaign. During 2015–2017, a total of 13,155 domestic dogs were vaccinated against rabies in 17 communities covering approximately 1500 km2. Based on an estimated population size of 34,275 domestic dogs, percent coverages increased across years, from 2% in 2015 to 24% in 2017, with only 3 of 38 community-years of vaccination exceeding the 70% target. The average cost of vaccinating an animal was $3.44 USD with in-kind contributions and $7.44 USD without in-kind contributions. Conclusions/Significance The evolution of the Laikipia Rabies Vaccination Campaign from a localized volunteer-effort to a large-scale program attempting to eliminate rabies at the landscape scale provides a unique opportunity to examine successes, failures, and challenges facing grassroots campaigns. Success, in the form of vaccinating more dogs across the study area, was relatively straightforward to achieve. However, lack of effective post-vaccination monitoring and education programs, limited funding, and working in diverse community types appeared to hinder achievement of 70% coverage levels. These results indicate that grassroots campaigns will inevitably be faced with a philosophical question regarding the value of local impacts versus their contributions to a larger effort to eliminate rabies at the regional, country, or global scale.
Investigation of the governance structure of the Nairobi dairy value chain and its influence on food safety
(Journal Article, 2020-06) Kiambi, Stella; Onono, J.O.; Kang'ethe, Erastus K.; Aboge, G.O.; Murungi, Maurice K.; Muinde, Patrick; Akoko, James M.; Momanyi, Kelvin N.; Rushton, Jonathan; Fèvre, Eric M.; Alarcón, Pablo
The dairy value chain of Nairobi is comprised, in its majority, of small-scale independent enterprises that operate within a complex interlinked system. In this complexity, the coordination and power structures of the system may have major influences on the management of dairy food safety. Therefore, the aim of this study was to investigate the governance structure and challenges faced by stakeholders throughout the Nairobi dairy value chain and assess their potential implications on food safety. Qualitative data were collected through focus group discussions and key informant interviews based on a dairy value chain mapping framework previously developed. Thematic analysis enabled identification of governance themes, key challenges and analysis of their implications on food safety. Themes were organized depending on their association with farmers (informal settlement or peri-urban), dairy cooperatives, dairy traders, processing companies, retailers or government officers. The identified governance themes included: i) weak linkage between government and farmers, ii) inadequate compliance with government regulations by traders and retailers, iii) emphasis on business licenses and permits for revenue rather than for food safety, iv) multiple licensing resulting in high business cost and lack of compliance, v) fragmented regulation, vi) unfair competition and vii) sanctions that do not always result in compliance. The key challenges identified included, among others: i) inadequate farmer support, ii) harassment of traders and retailers and iii) high business costs for traders, retailers, dairy cooperatives and large processors. The implication of governance and challenges of food safety were, among others: i) inadequate extension services, ii) insufficient cold chain, iii) delivery of adulterated and low milk quality to bulking centers, iv) inadequate food safety training and v) lack of policies for management of waste milk. The range of issues highlighted are based on stakeholders’ perceptions and reflects the complexity of the relationships between them. Many of the governance themes demonstrate the linkages that are both beneficial or confrontational between the formal and informal sectors, and between industry and regulatory authorities, with possible direct food safety consequences. Findings obtained provide indications to decision-makers of potential governance areas that could help improve efficiency and food safety along the dairy value chain.
Serological and molecular evidence of Brucella species in the rapidly growing pig sector in Kenya
(Journal Article, 2020-12) Akoko, James M.; Pelle, Roger; Kivali, Velma; Schelling, E.; Shirima, G.; Machuka, Eunice M.; Mathew, C.; Fèvre, Eric M.; Kyallo, Victoria; Falzon, Laura C.; Lukambagire, A.S.; Halliday, J.E.B.; Bonfoh, Bassirou; Kazwala, R.; Ouma, C.
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.
Optimizing livestock farming in urban agriculture
(Book Chapter, 2020-02-18) Grace, Delia; Cook, Elizabeth A.J.; Lindahl, Johanna F.
This chapter summarizes the importance of urbanization and how this increases the consumption of livestock products (LP). This increased demand, alongside infrastructure challenges making transporting and storing LP challenging, encourages urban livestock, close to the final consumer. While data on urban livestock keeping is limited, substantive evidence indicates that large numbers of livestock are kept, and that many processing and retailing activities occur in cities. Key issues for urban livestock keeping are related to human health, nutrition, environment, economy and ethics, and while it has many benefits, it is also implicated in significant problems. The chapter describes these in depth, with reviews of key research. The importance of research in optimizing urban livestock systems is demonstrated by a case study from Nairobi. The chapter concludes with a section on how research can contribute to enhanced, sustainable livestock keeping in cities, followed by a guide to finding additional information and references.
Epidemiology of antimicrobial resistance at the livestock-human interface in an urban environment: a One Health approach
(Thesis, 2019-11-25) Muloi, Dishon M.
Livestock have been implicated as a reservoir for antimicrobial resistant (AMR) bacteria that may spread to humans, with the keeping of livestock widely postulated as a risk factor for AMR in humans. However, quantitative evidence of the role of livestock in the emergence and transmission of AMR bacteria to human populations is lacking. This thesis focuses on the role of livestock keeping as a potentially high-risk interface for AMR transmission between humans and livestock in urban Nairobi. To achieve this, E. coli isolates were systematically collected from sympatric human and livestock populations in 99 households across Nairobi, Kenya. E. coli was characterised both phenotypically (through antimicrobial susceptibility testing) and genetically (through whole genome sequencing). In the first part of this thesis, I conduct a comprehensive systematic review to investigate existing evidence that food animals are responsible for transfer of resistant E. coli and their AMR determinants to humans. I demonstrate that the current evidence regarding transmission of drug resistance between food animals and humans is limited and that similarity of AMR bacteria or AMR determinants in the two populations does not, by itself, provide information on directionality of transfer. I highlight the need to use high resolution genomic analysis on human and livestock bacterial samples collected in time and space to better understand the direction and frequency of AMR transmission between these populations. Next, utilising AMR phenotypes and genotypes, I explored the variation in carriage of AMR E. coli and investigated the role of livestock ownership as a risk factor for AMR carriage in humans. First, I explored the epidemiology of clinically relevant AMR phenotypes and AMR genetic markers. I detected high rates of AMR phenotypes, with 47.6% and 21.1% of isolates displaying resistance to ≥ 3 and ≥5 antimicrobial classes respectively. Whole-genome sequencing revealed 60 acquired genes and 14 point mutations conferring AMR to 9 antimicrobial classes. sul2, strA, strB, tetA, and blaTEM-1B were the most frequently detected AMR genes conferring resistance to sulfonamides, aminoglycosides, tetracyclines, and β-lactams respectively – the most commonly found phenotypes. Highest carriage of AMR genes and phenotypes was observed in humans, pigs and poultry compared to goats, rabbits and bovines. Secondly, I demonstrated that the presence of livestock in the household did not influence phenotypic or genotypic AMR carriage in humans, but the impact of keeping livestock on human AMR carriage was instead influenced by presence of animal manure in the household. Utilising high resolution sequencing data, I proceeded to investigate the patterns of bacterial relatedness and strain sharing as a proxy for transmission potential. I showed that livestock and human isolates are genetically heterogeneous, with minimal evidence of clustering by host group, and that E. coli genomes in humans did not segregate according to livestock ownership. Next, I found evidence of 91 sharing events differing by less than ten base pairs (59 involving livestock isolates only 23 human isolates only, and 9 between humans and livestock), and that most of the sharing events were confined within households with only occasional instances of spread between household. I also demonstrate that high-resolution sequence-based analysis of SNPs is more discriminatory than MLST – a widely used tool in describing transmission of E. coli. Next, I described the patterns of antimicrobial sales in humans and livestock, and the level of awareness and common behaviours related to antimicrobial prescribing amongst human and veterinary pharmacists in urban Nairobi. β- lactams, fluoroquinolones, first and second generation cephalosporins, and metronidazole were the most commonly purchased human antimicrobials while tetracyclines, sulphonamides, penicillins, and macrolides were the most commonly purchased veterinary antimicrobials. This finding was in line with the resistance phenotypes and genotypes described in this thesis. I found that whilst most pharmacists were knowledgeable about antimicrobial use and AMR, inappropriate prescribing practices were common and that over the counter sale of antimicrobials, without a prescription, was a common occurrence in both human and veterinary drug stores. In the final section of the thesis, I investigated the co-occurrence patterns of acquired AMR genes and the role of conjugative plasmids on the epidemiology of AMR spread. I found evidence of co-location of multiple AMR genes in both human and livestock isolates, potentially enabling acquisition and dissemination of multi-drug resistance phenotypes in a single step. I found a diversity of known plasmids and plasmid replicons that were associated with the distribution of acquired AMR genes. To conclude, I discuss the findings of this thesis in the context of the current epidemiology of AMR pathogens at the human-livestock interface and highlight future directions for research on AMR transmission, and discuss implications of my findings for public health. This thesis demonstrates how fine-scale genomic analysis explicitly embedded within an epidemiologically structured sampling framework can be utilized to track bacterial sharing and in the surveillance of AMR prevalence in a low income urban setting. The connectivity of bacteria and their AMR determinants between humans and livestock and the ultimate impacts upon human health lends strong support for a holistic ‘One Health’ perspective for AMR surveillance.
Does urbanization make emergence of zoonosis more likely? Evidence, myths and gaps
(Journal Article, 2019-10) Ahmed, S.; Dávila, J.D.; Allen, A.; Haklay, M.; Tacoli, C.; Fèvre, Eric M.
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.
Epidemiology of antimicrobial-resistant Escherichia coli carriage in sympatric humans and livestock in a rapidly urbanizing city
(Journal Article, 2019-11) Muloi, Dishon M.; Kiiru, J.; Ward, M.J.; Hassell, James M.; Bettridge, Judy M.; Robinson, Timothy P.; Bunnik, B.A.D. van; Chase-Topping, M.; Robertson, G.; Pedersen, A.B.; Fèvre, Eric M.; Woolhouse, Mark E.J.; Kang'ethe, Erastus K.; Kariuki, S.
There are substantial limitations in our understanding of the distribution of antimicrobial resistance (AMR) in humans and livestock in developing countries. Here, we present the results of an epidemiological study examining patterns of AMR in Escherichia coli isolates circulating in sympatric human (n=321) and livestock (n=633) samples from 99 households across Nairobi, Kenya. E. coli isolates were tested for susceptibility to 13 antimicrobial drugs representing 9 antibiotic classes. We detected high rates of AMR, with 47.6% and 21.1% of isolates displaying resistance to ≥ 3 and ≥5 antibiotic classes respectively. Human isolates showed higher levels of resistance to sulfonamides, trimethoprim, aminoglycosides and penicillins compared to livestock (p<0.01), while poultry isolates were more resistant to tetracyclines (p=0.01) compared to humans. The most common co-resistant phenotype observed was to tetracyclines, streptomycin and trimethoprim (30.5%). At the household level, AMR carriage in humans was associated with human density (p<0.01) and the presence of livestock manure (p=0.03), but livestock keeping on its own had no influence on human AMR carriage (p>0.05). Our findings revealed a high prevalence of AMR E. coli circulating in healthy humans and livestock in Nairobi, with no evidence to suggest that keeping livestock, when treated as a single risk factor significantly contributed to the burden of AMR in humans, although the presence of livestock waste was significant. These results provide an understanding of the broader epidemiology of AMR in complex, and interconnected urban environments.
A cross-sectional survey of practices and knowledge among antibiotic retailers in Nairobi, Kenya
(Journal Article, 2019-12) Muloi, Dishon M.; Fèvre, Eric M.; Bettridge, Judy M.; Rono, Robert; Ong’are, Daniel; Hassell, James M.; Karani, Maurice K.; Muinde, Patrick; Bunnik, B. van; Street, A.; Chase-Topping, M.; Pedersen, A.B.; Ward, M.J.; Woolhouse, Mark E.J.
Background Antimicrobial resistance (AMR) driven by antibiotic consumption is a growing global health threat. However, data on antimicrobial consumption patterns in low- and middle-income countries (LMICs) is sparse. Here, we investigate the patterns of antibiotic sales in humans and livestock in urban Nairobi, Kenya, and evaluate the level of awareness and common behaviours related to antibiotic use and AMR amongst human and veterinary pharmacists. Methods A total of 40 human and 19 veterinary drug store pharmacists were interviewed in Nairobi in 2018 using a standard questionnaire. Data recorded included demographic variables, types of antibiotics sold, antibiotic customers, antibiotic prescribing practices and knowledge of antibiotic use and AMR. Results Our study shows that at the retail level, there is a considerable overlap between antibiotic classes (10/15) sold for use in both human and veterinary medicine. Whilst in our study, clinical training significantly influenced knowledge on issues related to antibiotic use and AMR and respondents had a relatively adequate level of knowledge about AMR, several inappropriate prescribing practices were identified. For example, we found that most veterinary and human drug stores (100% and 52% respectively) sold antibiotics without a prescription and noted that customer preference was an important factor when prescribing antibiotics in half of the drug stores. Conclusion Although more research is needed to understand the drivers of antibiotic consumption in both human and animal populations, these findings highlight the need for immediate strategies to improve prescribing practices across the pharmacists in Nairobi and by extension other low- and middle-income country settings.
Participatory mapping and food‐centred justice in informal settlements in Nairobi, Kenya
(Journal Article, 2019-01) Ahmed, S.; Haklay, M.; Tacoli, C.; Githiri, G.; Davila, J.; Allen, A.; Fèvre, Eric M.
Food vendors are pivotal in the local food system of most low‐income informal settlements in Nairobi, Kenya, despite being seen as an obstruction and as agents of disease and filth by city authorities. This paper explores the geography of these foodscapes – defined as public sites of food production and consumption – in selected low‐income settlements in Nairobi, focusing on the interaction of food vendors with their surrounding environment and infrastructure services. The research uses participatory geographic information system tools, including food mapping with mobile apps and high‐resolution community aerial views with balloon mapping, to capture and contextualise local knowledge. The community mappers collected data on 660 vendors from 18 villages in Kibera, Mathare, and Mukuru, and situated them on multi‐layered synoptic geographic overviews for each settlement. The resulting data on hazardous areas in relation to food spaces and infrastructure provision allowed local communities to prioritise areas for regular clean‐up activities and assisted advocacy to improve these places in cooperation with local authorities. These multiple visual representations of foodscapes make local food vendors, and the risks they face, visible for the first time. Reframing their “right to safe food and environment” from a social and environmental justice perspective allows local communities to put their experiences, knowledge, and challenges faced at the forefront of urban development planning, policy, and practice.

Browse

Recent Submissions