URBAN ZOO PROJECT: The interesting mix of the 99 household study an interesting and exciting diversity!

URBAN ZOO PROJECT: The interesting mix of the 99 household study an interesting and exciting diversity!

NL10-99HH poultry sampling

99 Household; Poultry sampling

Studying zoonoses of livestock and wildlife in an urban setting presents us with a very interesting study site. We collect samples from the slums (the very low income area), middle income areas and the very high income areas of Nairobi, with varied levels of environmental contamination, ranging from areas that are littered with garbage and permeated with open sewerage systems, (often complemented with the infamous ‘flying toilets’) to the very clean areas with high levels of infrastructure and garbage collection systems. We are eagerly anticipating what these radically different, yet often closely neighbouring environments will yield in terms of microbial diversity!

Another exciting variation is on the human, livestock and wildlife interface; there are sub-locations where livestock keeping is illegal, limiting the human-livestock interaction; whereas free ranging animals like goats and pigs are common in other areas, scavenging on rubbish, or grazing public spaces such as playing fields and road verges. Yet other sub-locations are endowed with lots of wild animals as they are neighbouring forests, or generally consist of large, well-established plots with many mature trees and well-tended vegetable gardens.

NL10-99HH low income area

99 Household; Low income area in Nairobi

In any of the randomly selected households, the project team collect a variety of sample types, including human stools, environmental samples, and  animal-source foods, such as meat, eggs or milk; as well as faeces from birds, rodents, and livestock. E. coli can be found in all of these places, but how are the different strains distributed between each of these different ecological niches that are in such close physical proximity? How much sharing of genetic material goes on between these bacterial communities, especially of those genes that give us cause for concern; ones that confer antibiotic resistance or ability to cause serious disease. In every sub-location, we sample one non-livestock keeping household and two households keeping livestock of diverse types. How these different combinations of people and animals in a similar urban environment influence the diversity of pathogens within a household- is another fascinating aspect of bacterial ecology that we hope this project will uncover.

NL10-99HH high income area

99 Household: High income area in Nairobi

The crowded and dusty streets in the low income areas in Nairobi are always full of food vendors selling both raw and cooked foodstuffs, unlike the high-income areas where majority of the residents buy food from supermarkets and high class butcheries. A difference in the food safety risk is anticipated between different types of suppliers of animal source foods, but the degree of this variation and the pathogens involved is something that remains largely unexplored. The 99 Households component of the Urban Zoo project is contributing to this, by starting to map E.coli and Campylobacter at the level of the consumer. We are beginning the next stage; to survey and collect samples along the length of the value chains that deliver meat to the tables of Nairobi citizens. Maud Carron, a PhD student, has this week begun sampling the chicken meat value chains in two contrasting areas of Nairobi, focusing mainly on Campylobacter; one of the leading causes of food-borne diarrhoeal illness in countries with a modern, intensive chicken production system. In the next few months, sampling will be expanded to the ruminant and pig meat value chains – watch this space for news of the next exciting phase of Urban Zoo!

James AkokoAuthored by James Akoko

Urban Zoo Annual Meeting

Urban Zoo Annual Meeting

NL10-Urban Zoo Annual meeting 2

Post meeting group photo

The multidisciplinary Epidemiology, ecology and socio-economics of disease emergence in Nairobi Project (Urban Zoo project) held its third annual meeting in London on January 19th and 20th, 2016. The meeting was attended by representatives from ILRI, APHRC, KEMRI, University of Nairobi, RVC, University of Liverpool, SOAS and the University of Edinburgh, UCL, IIED.   PIs, PhD students, post docs and other researchers involved in the project, as well as members of the External Panel, our group of ‘friendly critics’ who keep the project on track,  gathered to discuss this year’s progress.

The Urban Zoo project investigates the role of urbanization in the emergence of zoonotic pathogens. It fosters numerous PhD and MSc projects, thus achieving its capacity-building objectives. Jointly, these studies, which cover diversified fields such as peri-urban wildlife, livestock value chains and the social and spatial components of livestock rearing, will allow for a detailed understanding of Nairobi’s human-livestock-wildlife interfaces.

The “99 Households” (99HH) component of the project uses a landscape genetics approach to understanding E. coli distribution across Nairobi. Major progress in this component was reported. Not only have the sampling plan and laboratory protocols been finalised since the last meeting, but sampling across Nairobi is well underway. Thirty households have already been sampled in 10 sub-locations before December 2015. As planned, samples from humans, livestock, the environment and wildlife are being collected in each household. Quality assurance processes such as duplicate sampling and testing between both University of Nairobi and KEMRI laboratories have been put in place.

NL10-Urban Zoo Annual meeting

Meeting participants taking a break

The pipeline for full genome sequencing of the selected 99HH samples has been finalised and tested on a first batch of samples at the University of Edinburgh. A high level of diversity and MLST was noted.

The group discussed next steps in terms of addressing the value chain component of the Urban Zoo project. It was agreed that sampling of the beef and pork value chains will start in a near future, the poultry value chain sampling being already covered by one of the PhD projects.

A proposal was made to initiate a demand survey in order to determine animal source foods consumption in Nairobi. Ongoing discussions about the scope and feasibility of this study are still ongoing. The PIs reported multiple initiatives in terms of public health trainings and promotions materials and the study team received very positive comments from the external panel. The next and final Urban Zoo meeting is planned to take place in Kenya next year.

Maud CarronAuthored by Dr. Maud Carron

Letter from the PI: Emergence of pathogens in the human and animal population

Letter from the PI: Emergence of pathogens in the human and animal population

It’s a real pleasure to have the opportunity to write for the UrbanZoo newsletter in this first quarter of 2016.  This is a job of the co-PIs on this large project do in turn, and as I wrote for the first newsletter, this must make this issue the 10th so far.

The Urban Zoo project is certainly an exciting and challenging ‘beast.’  Funded by the UK Research Council Environmental and Social Ecology of Human Infectious Diseases (ESEI) initiative, we’ve certainly been deeply engaged in building an evidence base that is allowing us to understand the human, natural, wildlife and social environment of the complex and fascinating city of Nairobi.  Our teams, each led by specific expertise in different leading academic institutions in Kenya and the UK, have lifted the lid on the complex worlds of livestock production, food supply, human nutrition, diarrhoeal disease, wildlife-human-livestock interfaces, microbial genetics, low income settlement patterns and urban planning.  The efforts and energy of the field teams and lab teams in delivering the samples and the data on this project are quite astounding.

The last 18 months have been pivotal for this project.  We’ve been working extremely hard on the “99 household study,” which is described in this newsletter and in other newsletters in this series, and which focuses on mapping bacterial genetic relationships in isolates in a diversity of ecological niches at the household level.  The sample frame is stratified both by type of livestock kept and by socio-economic status.  Material gets selected in the field, at the point of collection, for forwarding for whole genome sequencing (WGS) with our partners in the UK.  It won’t be long now before we have our first WGS-derived phylogenetic tree of E. coli isolated from this part of the project, a major milestone.

The productivity in data gathering in the early years of the project is starting to pay off.  At the last count, there are 15 manuscripts in preparation, with a long string of others awaiting data to come back from collaborators so we can get down to analysis and paper writing.  We’re in negotiations with journals to have special issues bringing some of our key papers together, and have our eye on some very high impact journals to report our key results.  We have been, and continue to be, grateful not only to the ESEI programme for funding this far reaching work, but also to the other funders who have contributed to specific elements, including the CGIAR Research Programme on Agriculture, Nutrition and Health, the Leverhulme Centre for Integrative Research on Agriculture and Health and the funders of several of our PhD students.

With now just over a year to go on this project, we are working hard to understand the mechanisms that may lead to the introduction of pathogens into urban environments, and the emergence of those pathogens in the human population.

Eric Fèvre is a Professor of Veterinary Infectious Diseases, Institute of Infection and Global Health, University of Liverpool with expertise in epidemiology of zoonoses at the livestock human interface. View his profile

It is time to rethink the way we handle pets and wildlife

It is time to rethink the way we handle pets and wildlife

In Summary

  • During the Kenya Medical Research Institute’s fifth scientific conference, which also took place in February, scientists raised the alarm over the transmission of diseases from animal to humans.
  • The World Health Organisation says that 60 per cent of the pathogens that cause infectious diseases in human beings come from animals.
  • According to the US’s Centre for Disease Control and prevention, zoonoses include a wide range of diseases, ranging from mass killers such as anthrax, Ebola, swine flu, West Nile Virus, bird flu, Crimean-Congo haemorrhagic fever and the Hendra Virus to subtle and slow killers like rabies, Rift Valley Fever and Brucellosis

During the funeral of a 39-year old woman who died of Aids in Homa Bay in February this year, a clinical officer who had attended to her engaged DN2 in a discussion about the Zika Virus in South America, and how it had triggered yet another debate on how man’s unguided relationship with nature is hurting him.

Sadly, neither the potential victims, nor the government, are adequately conversant of this to take the necessary precautions.

It is worth noting that at the time the Homa Bay funeral was taking place, across the Atlantic Ocean in Boston, US, the annual Conference on Retroviruses and Opportunistic Infections (CROI) was also taking place. The discussion focused on yet another deadly infection that came to human beings from animals: Ebola.

In Kenya, the Ministry of Health allayed fears of possible disease outbreaks from the Ebola and Zika viruses.

Only a few scientists, like Lancet Laboratory’s executive officer, Dr Ahmed Kalebi, took note of the public health issues raised at CROI.

Meanwhile, during the Kenya Medical Research Institute’s (KEMRI) fifth scientific conference, which also took place in February, scientists raised the alarm over the transmission of diseases from animal to humans. They expressed concern about humans’ continued intrusion into wildlife territory.

Whether it is the burgeoning population or the desire to live in quiet, exclusive environments, human intrusion into animal habitats has grown considerably in the country in recent times.

The area around the Lewa Conservancy which straddles Meru and Laikipia counties, is a case in point. Apart from the herds of elephants and buffalos that roam the plains, one can also spot residential houses tucked away in between the trees.

A great deal has been documented about the booming real estate business in Laikipia County, which for decades was dominated by large territorial mammals such as rhinos, elephants and buffaloes.

Not surprisingly, this intrusion has seen elephants destroy crops in the areas neighbouring their habitat.

Now, experts are warning of a threat greater than the destruction of crops of trampling to death of humans: zoonoses.
Zoonoses are diseases transmitted from animals to humans.

The World Health Organisation, (WHO) says that 60 per cent of the pathogens that cause infectious diseases in human beings come from animals.

And researchers warn that the close interaction between humans and animals, whether wild or domesticated, is increasingly making Kenyans ill.

According to the US’s Centre for Disease Control and prevention, zoonoses include a wide range of diseases, ranging from mass killers such as anthrax, Ebola, swine flu, West Nile Virus, bird flu, Crimean-Congo haemorrhagic fever and the Hendra Virus to subtle and slow killers like rabies, Rift Valley Fever and Brucellosis.

Although these diseases are a global health problem, their impact is felt more in Africa than in other parts of the world because they tend to be neglected. African governments dedicate few or no resources to detect and respond to them at the local or national levels. Only 0.7 per cent of these diseases affect people in developed countries as poor nations bear the brunt.

It was only after the Ebola outbreak in West Africa in 2013, which wreaked havoc in West Africa, that people started paying attention to the usually muted voice of researchers on the link between diseases, animals and the environment.

PUTTING UP SKYCRAPPERS

Given the rate at which construction is going on in the country, it is time we sat up and took notice.

Not too long ago, the ambience in Nairobi’s upmarket Kilimani allowed residents and colobus monkeys to live in harmony. Today, the gibbering of monkeys has been replaced by the roar of construction machines putting up skyscrapers.

The same trend can be observed in other parts of the country such as Lower and Upper Kabete, Gathiga, slightly past Kitisuru in Nairobi, Mang’u (Kiambu County), Kabarak and Sobea (Nakuru County) Nyahera (Kisumu County and Kapchorua in Nandi Hills (Nandi County).

Unknown to many, as this trend continues, disease-causing pathogens are mutating, becoming more lethal and embedding themselves in the complex yet delicate human food chain and way of life.

A study in 2012 titled “Zoonoses: A potential Obstacle to the Growing Wildlife Industry of Namibia published in the journal, Infection Ecology and Epidemiology, drew a chilling pattern in Kenya, similar to Namibia’s cases of zoonoses: the serum of buffaloes in Ijara, Nakuru, Laikipia, Nairobi and parts of the North Rift tested positive for antibodies of Rift Valley Fever.

Dr Eric Osoro, a medical epidemiologist at the Zoonotic Diseases Unit (ZDU) in the Ministry of Health, says that at least 2,000 Kenyans die of rabies every year, which is unfortunate, given that it costs less than Sh100 to vaccinate a dog, compared with the thousands of shillings required to treat the viral disease.

“The number of rabies deaths reported is a gross underestimation of the actual number of deaths that occur in Kenya annually from this terrifying fatal disease,” he says.

Many more Kenyans could be dying of rabies, which can be caused even by a scratch by an unvaccinated dog, because the incubation period for the virus is estimated to be about two months.

“Sometimes the wound might have even healed, so none one would suspect it is rabies,” Dr Osoro says.

While rabies can be prevented by vaccinating dogs, WHO says it is 100 per cent fatal once the clinical signs appear.

Apart from rabies, Dr Osoro also cautioned about Brucellosis — a disease one gets from taking milk that has not been boiled properly — and anthrax.

“Anthrax kills cattle in less than 12 hours, but many will consume the flesh because the animal looked healthy,” he says.

Prof Thumbi Mwangi, a clinical assistant professor at Washington State University in the US and a researcher on zoonoses at the Kenya Medical Research Institute (KEMRI), told DN2 that while the interaction between humans and animals is not necessarily a bad thing, failure to keep healthy animals increases the chances of ill health for humans.

PATHOGENS FIND NEW HOSTS

In March last year, Prof Mwangi carried out a study in which he tracked 1,500 households and their livestock in 10 villages in Western Kenya. He and his team obtained data on 6,400 adults and children, 8,000 cattle, 2,400 goats, 1,300 sheep and 18,000 chicken.

The results, published in the open journal, Plos One, revealed that for every 10 cases of animal illnesses or deaths that occurred, the probability of human sickness in the same household increased by about 31 per cent.

Prof Eric Fèvre, a professor of veterinary infectious diseases at the Institute of Infection and Global Health at the University of Liverpool and the International Livestock Research Institute (ILRI), wrote a blog post, “Zoonoses in Africa” on the websitemicrobiologysociety.org, in which he said that urbanisation is presenting opportunities for pathogens to find new hosts to survive.

The post, published on November 11, 2015 read: “The intensification of farming, for example, leads to closer relationships between individuals and animals, generating opportunities for more rapid mutations as organisms move from host to host, while also providing a structured way for those pathogens to enter highly ordered food chains that branch out and reach very large numbers of people”.

Other studies paint an increasingly disturbing pattern of diseases either emerging, or the incidence of existing ones increasing.

A study in Dagoretti, Nairobi, by the International Livestock Research Institute (ILRI), found that women were more exposed to cryptosporidiosis, a diarrhoeal disease transmitted from cattle to humans, because of their involvement in milking, feeding and watering the animals.

And a study by the Kenya Medical and Research Foundation (KEMRI) Kisumu and the US’ CDC linked a strain of tuberculosis to an area in Western Kenya where homes had a higher cattle:human ratio.

In wildlife settings, the situation is more complex. A 2014 study found cases of suspected rabies in Laikipia County where humans had encroached on animal habitat.

When landscapes and bio diversities are altered by activities relating to construction such as roads and farms, diseases are “created”: as trees are felled, the species that protect humans from the ones that act as disease-reservoirs are destroyed.

The harmful pathogens are usually multi-host, meaning they can live in many different animals, which gives them a competitive edge to survive as the protective trees are wiped out by human activity.

In 2012, ILRI reported that 2 million people are killed by zoonoses every year, thanks to the disruption of the ecosystem.

Malaria is a good example: as people in tropical countries like Kenya encroached on the habitat, the incidence of the disease quadrupled.

ECOLOGICAL BALANCE

When DN2 asked nine developers from Nakuru, Nairobi and Kisumu whether they consider the ecological balance of a location important when they are building, six responded with the question, “What is that?” After it was explained to them, all except one said they were “satisfied with the National Environmental Management Authority (NEMA) clearance”.

It is notable that NEMA officials and environmental inspectors have said at scientific forua that many of the constructions approved by the counties do not heed their counsel.

Only 1 per cent solution to wildlife viruses are known, according to WHO, and the ecology of diseases and wildlife immunology is in its infancy in Kenya.

Meanwhile, Kenya’s Zoonotic Disease Unit, has been lauded at various fora for its holistic approach, with its national rabies control strategy highly regarded.

It has conducted a large-scale study on the epidemiology of brucellosis, responded to many zoonotic disease outbreaks, and developed preparedness strategies for epidemic zoonoses such as Rift Valley fever.

But for now, one can only hope that ecological safety will be factored in amid the real estate industry boom.

SOURCE

This article originally appeared in the Kenya Daily Nation website on 9th March, 2016 authored by Verah Okeyo, available athttp://www.nation.co.ke/lifestyle/DN2/Take-care-how-you-interact-with-animals/-/957860/3108294/-/15fadaoz/-/index.html

View the Newspaper pages

Informal food vendors training

The food vendors training was held at Mlango Kubwa on 25th February, 2016 involving 30 plus food vendors carefully selected from thirteen villages in Mathare Valley in Kenya. The food vendors ranged from the ones who sell: meat products, vegetables, fruits, eggs, fish and the ones selling ready made food products.

The aim of the training was to enlighten and empower the participants with practical skills and knowledge on proper food, premise and attire hygiene, sanitation and safety issues.

Muungano wa Wanavijiji food security programme coordinators mobilized the participants while ILRI and APHRC facilitated the training. The activity was in response to vendors’ own requests for capacity-building and offered a crucial opportunity to support livelihoods and bolster community health across eight villages in Mathare.

The training was organised into five sessions:

  • Session 1: Introduced the participants to the Urban Zoo projects which seeks to understand how disease emerge in urban and peri-urban areas of Nairobi 
  • Session 2: Highlighted the relationship between germs and food safety. Participants were introduced to the adverse effects of germs to health, their portals of entry and that proper hand washing, food preparation and hygiene can prevent most food-borne diseases. This session concluded by demystifying the various myths and truths about food.
  • Session 3: Participants were introduced to common food-borne symptoms and how proper PPE, hygiene and sanitation of food, body, containers, clothes and towels prevents most of the food-borne infections. A practical session on how germs spread was also demonstrated using drinking chocolate powder and proper hand washing demonstrated using the Glo-germ.
  • Session 4: This session equipped participants with skills on proper premise hygiene, water treatment, storage of perishable food to avoid spoilage. Various modes of contamination and precautions to take when handling meat, eggs, vegetables, and fruits were also illustrated.
  • Session 5: The last session equipped and empowered participants on: ways and why they need to improve their product quality; why and how they need to deal with customers and suppliers; advised on promotional activities that they can engage in to improve their product sells; participants were also advised on the importance of innovation, diversification, standardization of recipes and processes.
  • Practical sessions: The training came to an end with further practical demonstrations on how to wash equipment, sukuma wiki (kales), and meat.
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Training action photos [Click photo to enlarged image]

Hand hygiene demo

Meat hygiene demo

Hygiene of equipment demo

Hand hygiene demo using Glow-germ

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