Letter from the Co-Principal Investigator: Prof Mark Woolhouse

Prof Mark Woolhouse

It is hard to believe that, as I write this, ZooLinK is almost four years old. During those four years, the topic of surveillance has risen even higher up the infectious diseases agenda. There are two main reasons for this. First, there is the recurring threat of emerging viral diseases, such as Ebola and Lassa fever in Africa, where early detection is a key element of a successful public health response. Second, there is a greatly increased global awareness of the public health threat posed by antimicrobial resistance (AMR), leading to the realisation that AMR surveillance is challenging and, often, is not being done particularly well. Despite this, diagnostics and surveillance are not priority topics for many funders; though thankfully some, such as our own BBSRC and others such as B&MGF, do ‘get it’. So projects such as ZooLinK have an opportunity (and perhaps a responsibility) to make the case for surveillance by demonstrating actual or potential public health benefits. I believe that we are doing that although, in these late stages of the project, it is important that we put our arguments out there in the form of conference talks and publications.

I frequently use the Busia lab as an example of what can be done when I am speaking on infectious disease surveillance at conferences and meetings. That small facility has a great deal going for it. First and foremost, it’s in a very appropriate location, a densely populated largely rural area where the infectious disease burden is high and local resources are inevitably overstretched. Second, it’s appropriately set up and equipped so that we can do what needs to be done even when working in less than ideal conditions, just as you would find in so many other locations in Africa and elsewhere. Third, we have a small but very skilled team, without whom nothing could be done at all but with whom so much is possible. Many thanks to Laura and everyone else in the Busia team for all their hard work.

I’m particularly excited by the fact that we can use the Busia lab to generate genome sequences. Stefan Rooke’s work with the Minion portable sequencing system has proved the principle. It wasn’t so long ago that genome sequencing was a multi-million dollar activity requiring considerable investment in equipment, infrastructure and technical support. Now we can do it in Busia!

Stefan is working on bacteria, especially plasmids carrying antimicrobial resistance genes, but the technology will work for any kind of genome we might be interested in. That said, turning proof of principle into routine practice is not going to be easy. There are many challenges in making genome sequencing directly relevant to patients and local communities in a setting like Busia – cost and ease of use come to mind immediately. But we have to start somewhere, and I believe that ZooLinK taking the first steps down a path that will one day make a real difference to infectious disease surveillance right across Africa.

Letter from the Co-Principal Investigator: Prof Mark Woolhouse

Kenya’s urban poor federation Muungano wa Wanavijiji is working with food vendors in informal settlements to reveal their challenges and explore how to promote food security. Muungano is a member of Slum Dwellers International (SDI), a network that aims to improve shelter, services, and government responsiveness to the urban poor. The ongoing project is complement-ing other Urban Zoo activities, as well as building upon Muungano’s past experience with grassroots data-collection and advo-cacy. Working alongside Muungano are community residents, pro-poor financial analysts at Akiba Mashinani Trust (Muungano’s financial wing), and researchers at University College London and UC Berkeley.

This action-research project is utilizing participatory methods to understand vendors in Nairobi’s informal settlements of Korogocho and Viwandani. Vendors sell a variety of items in these settlements such as fresh produce; meat, fish, and eggs; cooked and uncooked foods; beverages; and snacks. A mobile phone application is capturing vendors’ demographic and business profile, while base-maps and balloon-mapping (low-cost aerial photography with balloons and a simple camera) are generating detailed spatial data on their locations. Finally, focus group discussions (FGDs) are delving into traders’ constraints, coping strategies, and priorities for change.  

These vendors are poorly organised and frequently overlooked or stigmatised by policy-makers, yet vending is a vital source of affordable, accessible foods and a key income-generating activity. Customers may appreciate the convenience and their personal relations with traders; food vending is also a widespread livelihood strategy, particularly for female traders seek-ing to combine work with childcare. As a female vendor explained in a Viwandani FGD, “I’ll be doing my work and also doing the house chores and also look after my kids…But if you are outside [the settlement], sometimes you have to look for someone to take care of your kids and sometimes you don’t have that money.” 

However, vendors often face multiple challenges in their settlements like overflowing drains, minimal water and sanitation, uncollected rubbish, and elevated insecurity. In turn, widespread hazards and poor infrastructure or services can threaten food security by jeopardising vendors’ livelihoods and customers’ access to food. But the project’s maps and FGDs are uncovering these concerns and, moreover, a Food Vendors’ Association (FVA) has been established to increase their collective strength, amplify their voices, and advocate for much-needed interventions in the future.

This action-research project is utilizing participatory methods to understand vendors in Nairobi’s informal settlements of Korogocho and Viwandani, with support from APHRC and ILRI team members from the Urban Zoonoses project.

This article has been written by the Muungano team

Surveillance of zoonoses in livestock and humans: experiences from AHITI interns cohort 5

Surveillance of zoonoses in livestock and humans: experiences from AHITI interns cohort 5

Our participation in the ZooLinK suite of projects will remain memorable. We have acquired sufficient knowledge and experience through the exposure given to us by ZooLinK staff and our participation in the target areas of the project. Since we joined the project on May 2018, we have rotated among the three functional units of the project, namely: (1) veterinary team who visit the livestock markets and slaughterhouses; (2) laboratory team and (3) clinicians team who visit the health centres. The following report will focus on the veterinary team. It describes the activities carried out therein and their relevance to the project.

Two of the interns working in the laboratory (foreground)

A normal ZooLinK day begins with packing the field car with the required consumables a day before the field. Such consumables include; red and purple topped vacutainers, nasal swabs, digital thermometer, heart girth measuring tape, ziplock bags, barcodes, consent forms, faecal pots, gloves, disinfectant, water, coveralls and gumboots etc.

“…our internship has equipped us with adequate disease surveillance skills in the animal field that will help us to extend the knowledge of disease control to farmers…”

In the field, the veterinary team splits into two groups; one group works at the livestock markets and the other at the slaughterhouse. Upon arrival, at the livestock market, the animal is randomly selected and the owner identified to seek consent for sampling the animal and to answer a few questions. If he/she agrees, he/she signs two consent forms one of which goes with the animal owner while the other one remains for ZooLinK records. Before sampling, the animal is humanely restrained to ensure the safety of the animal, handler and person collecting the samples. Physical examination begins before the actual sample collection. Which entails checking for any abnormal discharges from the mouth, eyes, genitals and nose. On the skin swellings and injuries are recorded when present. Nature of the ocular mucous membranes is assessed and recorded, the mouth is checked for any lesions and sores as well the ageing is done from the dentition. The pre-scapula lymph nodes are palpated on both sides to ascertain any enlargement. Lifting of the loose skin of the neck is done to test for skin elasticity. The body condition of the animal is cored in a scale of 1-5. The fleece condition is recorded as either rough or normal and a tape measure used to measure the heart-girth to estimate the weight of the animal. The temperature is taken per-rectal. After the physical examination, the actual collection of the samples begins. Blood is collected from the jugular vein into a red top vacutainer (plain blood) for serology and an EDTA-purple top vacutainer (uncoagulated blood) for parasitology and hematology.

One of the AHITI interns sampling blood from a sheep

Nasal swabs are used to collect swabs from the nose. Nasal swabs are later cultured in the lab and used to test for the presence of Staphylococcus aureus. Fresh faeces are collected per-rectal and placed into a faecal pot. The faecal sample is cultured in the lab to determine the presence of E. coli, Salmonella and Campylobacter. External parasites like ticks, lice etc. are also collected if encountered. The same procedure takes place in the slaughterhouses but in addition, post-motem lesions like cysts, flukes, are recorded and collected inclusive of mesenteric lymph nodes from the pigs.

We are glad to declare that our internship has equipped us with adequate disease surveillance skills in the animal field that will help us to extend the knowledge of disease control to farmers and other stakeholders back at home.

This article was authored by the cohort 5 interns from the Animal Health and Industry Training Institute (AHITI): Sarah Nyambura, John Parkasio and Silas Muriithi.

Establishing a serum bank of samples from confirmed cysticercosis positive and negative pigs

Establishing a serum bank of samples from confirmed cysticercosis positive and negative pigs

This serum bank will serve as a platform for future development and validation of diagnostic tools that will allow for a quicker and more accurate diagnosis of porcine cysticercosis. The disease is zoonotic, meaning that it can be transmitted between humans and animals (pigs). The tapeworm, Taenia solium, causes taeniasis in people and can cause abdominal pain, diarrhoea, nausea and indigestion. The larval stage of the worm can infect both pigs and people. In people, the larval stage can become encysted in the brain and/or spinal cord, causing neuro-cysticercosis. This is an important cause of acquired epilepsy – a debilitating disease. The signs of the disease in humans include seizures, chronic headaches, dementia, and may result in death.

“The project aims to establish a bank of serum samples from confirmed cysticercosis positive and negative pigs.”

Fig.1. Making 3mm thick slices

We have organized to visit and buy pigs from 13 slaughter slabs spread across Busia and Kakamega Counties. The process involves contacting a trader/farmer at the slaughterhouse to deliver a pig on site. On the day of slaughter, intricate bargaining with the trader/farmer to ensure value for money ensues. This is a complex process given that the pricing is usually fluid, with no clear parameters to determine the price. The prices are usually based on the physical appearance of the pig which requires a lot of experience. Once the prices have been settled, photos of the pig are taken, and demographic information, such as age, heart-girth measurement and back length, are recorded. The blood is collected at ante-mortem and lingual palpation is performed. The pig is slaughtered and weighted perimortem, and then skinned. This is a source of amusement among the butchers who have christened this ‘naked pig carcass’ as Mbuzi ulaya loosely translating to a ‘European goat.’ The carcass, together with the head, lungs, liver and diaphragm, are chilled overnight and sliced (Fig.1.) in the morning.

The slices ought to be at least 3mm thick to ensure any cyst present can be exposed. This is a laborious process that usually takes 3-4 hours to complete. The most recent studies carried out in the same region recorded a prevalence of 37.6% using a serological method, and 34.4% by lingual palpation. It is such findings, combined with an increase in pig keeping and consumption, that call for such a study. Currently, there exist several serological tests which detect circulating T. solium cyst antigens in humans and animals. Yet most of these tests have poor specificity, leading to a large number of false positives and hence, limiting their diagnostic capacity. We look forward to sharing more insights from this project in subsequent newsletters.

This article was authored by Dr Maurice Karani who is ZooLinK Research Assistant and Field Coordinator.

Surveillance of Zoonoses in livestock and humans: a note from the post-doc

Surveillance of Zoonoses in livestock and humans: a note from the post-doc

After many months of careful planning and preparation, the main ZooLinK surveillance project has set sail! We have been sampling in the twelve selected live-stock markets, four each in the counties of Busia, Bungoma and Kakamega. At each market, we are collecting data on, and biological samples from, up to ten randomly selected cattle and small ruminants. Sampling in livestock markets can be challenging as traders are busy people who want to sell their animals. Moreover, some shared with us the perception that having their animal sampled may send the wrong message to future buyers. We are reminded once again of the importance of engaging local stakeholders at an early stage to help explain the study purpose and facilitate study participation.

Public engagement session in one of our sampling sites

We then expanded our sampling by including cattle, small ruminants and pigs that are taken for slaughter at selected slaughterhouses and slaughter slabs in the surroundings of the included livestock markets. Concurrently, we are also sampling outpatients at the three County referral hospitals and other selected health centres in the study area. All collected biological samples are processed and tested for fifteen selected zoonotic diseases at our field lab in Busia. Some of the animal samples shall also be used for genetic studies to identify changes in breeds as farming systems intensify over time.

We are all looking forward to working and learning together during our ZooLinK journey!

This article was authored by Dr Laura Falzon who is the Post-doctoral scientist (surveillance component) in the ZooLinK suite of projects.

Research Assistant II : Opportunity to work with a multidisciplinary ZooLink project in Kenya

Research Assistant II : Opportunity to work with a multidisciplinary ZooLink project in Kenya

Click here to apply

The International Livestock Research Institute (ILRI) seeks to recruit a Research Assistant to support surveillance programme for zoonoses across the animal health sectors and targeted zoonotic pathogens. S/he will work within the ZooLinK suite of projects based in Busia, Western Kenya.

ILRI works to improve food and nutritional security and reduce poverty in developing countries through research for efficient, safe and sustainable use of livestock. It is the only one of 15 CGIAR research centres dedicated entirely to animal agriculture research for the developing world. Co-hosted by Kenya and Ethiopia, it has regional or country offices and projects in East, South and Southeast Asia as well as Central, East, Southern and West Africa. www.ilri.org

Key Responsibilities

  • Responsible for questionnaire administration aimed at zoonotic disease surveillance.
  • Conduct interviews and focus group discussions with the different stakeholders in western Kenya
  • Collect biological samples in the slaughter houses and livestock markets, under the guidance of senior project staff
  • Collect and organize statistical data, geospatial data, and other information (e.g. livestock demographics) as directed;
  • Manage biological sampling from peri-domestic species in the study area, including managing regulatory requirements for such work, under the guidance of senior project staff
  • Responsible for electronic data entry and data entry tool development, including interactions with a commercial partner firm which developed the data capture technology
  • Maintain relationships with different multi-disciplinary teams within the ZooLinK project in order to link the analysis with the other on-going studies.
  • Assist in organizing stakeholder meetings and seminars, and (when applicable) participate in scientific workshops and conferences
  • Take primary responsibility in managing the project’s public facing communications, including management of social media related to zoonoses and one health research activity


  • BSc. Animal Health, Veterinary or related fields and an understanding of livestock zoonotic disease surveillance and One Health
  • At least 3 years of relevant experience
  • Demonstrable education and experience of working in Veterinary or/and ‘One Health’ related research activities
  • Experience in data entry in electronic databases and working with a geospatial software (e.g. ArcGIS); conducting interviews and focus groups; managing communications tools for scientific communication; handling electronic data (entry and management); the livestock productions chains in Kenya
  • Ability to communicate with the different study participants
  • Ability to work in a multi-disciplinary environment
  • Veterinary or/and One Health educational background

Terms of Appointment

These are Nationally Recruited Staff (NRS) position; based at Busia, Kenya and open to Kenyan nationals only. The position is on a 2-year contract, renewable subject to satisfactory performance and availability of funding.

Job Level

This position is job level 2B, ILRI offers a competitive salary and benefits package which includes; pension, medical and other insurances for ILRI’s Nationally Recruited Staff.

How to apply: Applicants should send a cover letter and CV expressing their interest in the position, what they can bring to the job and the names and addresses (including telephone and email) of three referees who are knowledgeable about the candidate’s professional qualifications and work experience to the Director, People and Organizational Development by clicking on the “Apply Now” tab above before 23 May 2018. The position title and reference number REF: RA/05/18 should be clearly marked on the subject line of the cover letter.

ILRI does not charge a fee at any stage of the recruitment process (application, interview meeting, processing or training). ILRI also does not concern itself with information on applicants’ bank accounts.

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