What’s ZooLink?

The Zoonoses in Livestock in Kenya project abbreviated as “ZooLink”, seeks to develop an integrated surveillance system for fifteen (15) pathogens transmissible between humans and animals (zoonoses) piloted in three counties (Busia, Bungoma and Kakamega) geographically positioned in Western Kenya. In subsequent components, the project will: (1) validate, deploy and develop high-throughput laboratory assays for the targeted zoonotic diseases; (2) model their risk; (3) determine their socio-economic implications and (4) forecast how demographics, husbandry and genetics of livestock will change over time. An in-depth description of the project work packages is available on the project website avaulable at: http://www.zoonotic-diseases.org/project/zoolink-project/). My name is Dr Kelvin Momanyi and I work as a Research Assistant under this exciting project and in subsequent paragraphs, I will share with you “what a day working in “ZooLink” feels like in the context of our field activities from the animal team.

The tri-team structure

The ZooLink multi and trans-disciplinary operational field activities are implemented by three functionally interlinked teams: (1) the animal team (Fig.1) that collects, stores, delivers samples and electronically relays data related to livestock and their owners from the livestock markets and slaughterhouses; (2) the human team that collects stores, delivers samples and electronically relays data related to the human patients visiting county, sub-county and mission hospitals and; (3) the laboratory team that receives, processes and stores (long-term) the samples as recieved from both the animal and human teams.

Fig-1: A section of the field team examining, sampling and capturing metadata of a cow at the Koyonzo slaughterhouse

The sampling sites

A day in the ZooLink animal team normally starts at 5 am when visiting field sites far away i.e. Webuye, Chwele, Kimilili, Lubao, Webuye, Shinyalu, Malaba, and Angurai or at 5:30 am when visiting close-by sites i.e. Myanga, Butula, Funyula, and Koyonzo. There are 3 sampling days per week, where each selected livestock market, slaughterhouse and hospital is visited once every month.

The animal team is disaggregated into two intradisciplinary teams (the livestock market team and the slaughterhouse team). A day prior to the field activity the consumables for the two teams are prepared in two separate field carriers, one with a pink lid designated for the slaughterhouse as well as packing their coveralls in a red disposable bag and consumables for the livestock market team are packed in a yellow-lidded carrier with coveralls in a black disposal bag (Fig.2). The separation aims in seemless identification.

Fig-2: Field car fully packed and ready for dispatch to the field

Whom we work with 

The goal is to arrive at the field site at or before 7 am when abattoirs are designated to open. At the field site, the first stage is to gown-up with Personal Protective Equipment (coveralls and gloves) followed by role allocation which would fall into two categories i.e. data entry and animal sampling). At the livestock animal market, the first step is to inform the livestock market chairperson and/or the livestock market master of our presence and activities for the day (the chairperson is contacted a day prior to the visit). The livestock market chairperson/master would then help in identifying a local person to aid in animal restraint (a crucial step to ensure and assure the safety of the staff, the handler, the animal and other market participants). At the slaughterhouse, the meat inspector and slaughterhouse workers are informed of the day’s activities (the meat inspector is also contacted a day prior to the visit). Animal restraint, at the slaughterhouse, is normally undertaken by the field staff and with the occasional recruitment of an animal restrainer. Working in both the livestock markets and slaughterhouses is facilitated by closely working together with the County and sub-county Directors of Veterinary Services of the study sites.

In-training mentorship programme of the AHITI interns

Our multidisciplinary teams (human, animal and laboratory) also offer hands-on practical mentorship and training (Fig.3) to recent graduates from the AHITI (an animal health training institute in Kenya) who are attached to the project through a memorandum of understanding between the project and the training institute.

Fig-3: One of the AHITI intern under cohort 5 being trained on how to collect blood from a cow

Animal identification and consent

At both the livestock market and slaughterhouse the goal is to sample 10 animals (6 cattle, 2 sheep and 2 goats) as may be possible. At the livestock market, the animals are recruited randomly from each corner of the livestock market ring. Although in some markets there is no clear-cut demarcation of the market, hence a “virtual ring” is maintained. After the animal is recruited the owner is identified. The project is described to the owner using one of the two national languages (either English or Kiswahili) conversant to the respondent. The owner is informed of how the animal was recruited, the purpose of the project (Fig.3), the procedures to be undertaken, confidentiality of the information and on how feedback will be provided as pooled results at a later stage. If the animal owner accepts to participate in the study, animal sampling and data collection commences and if he/she declines he/she is thanked and the next animal is identified and recruited.

Animal sampling and human metadata collection

During animal sampling, two staff members examine and collect samples from the animal while the other takes notes, labels the samples and collects further metadata from the animal owner, (Fig.3) detailing the source of the animal, reasons for buying/selling, and the destination of the animal among others. When the owner is a farmer further information regarding other animals kept, history of treatment, vaccination and episodes of sudden death are recorded. If the animal is from a different county then a movement permit is requested and photo-captured.

Fig-3: Obtaining consent, explaining the project to a participant and sampling of a goat in one of the livestock market

Animal sampling involves the collection of baseline information about the animal, examining the animal for possible pointers (signs) to illness and collection of samples. Baseline information includes the breed, age, and gender of the animal; the pointers to illness (signs) include visually determining the demeanour, body condition score (prominence of the ribs and hip bones), haircoat, weight (extrapolated from measuring the heart girth), nature of the ocular mucous membranes (whether pale/anaemic, congested, jaundice, or cyanotic), presence of vesicles, sores or lesions in the mouth or feet; collection of samples: (1) Blood from the jugular vein (Fig.5) into a red-topped vacutainer for serum to investigate exposure to pathogens such as Brucella, Rift Valley Fever, purple-topped vacutainer for whole blood to investigate extracellular parasites such as Trypanosomes and intracellular parasites such as Coxiella burnetti, Anthrax and a green-topped vacutainer for heparinised blood to investigate the zoonotic Mycobaterium bovis;

Figure 5: Blood collection from the jugular vein of a pig at the Shinyalu pig slaughter slab

(2) Nasal swab (Fig.6) to investigate the methicillin-resistant Staphylococcus aureus;

Fig-6: Collection of a nasal swab at the Myanga livestock market

(3) Per-rectal fecal sample collection to investigate pathogens causing gastrointestinal infections such as Salmonella, E. coli, and Campylobacter; at the slaughterhouse level further samples collected include; (4) parasites such as the Fasciola spp from an infested liver; (5) tissue sample collection of affected organs such as a cyst from the liver/lung to investigate Echinococcus spp and other hydatid-causing pathogens or tongue to investigate Cysticercosis; (6) ear tissue sample collection (Fig.7) for genetic and breed-purity investigation (subsequent blog entries will describe in detail the pathogens and their role human disease burden, so stay tuned);

Fig-7: Ear tissue collection from a cow at the Amukura livestock market

(7) Tick samples (Fig-8) from infested animals are collected to further detect disease-causing pathogens.

Fig-8: Tick samples are collected and stored for further investigation

Data entry and relay

The first stage of the data entry process, at the field, is to barcode all the samples (blood, faecal, nasal swabs, tissues). The barcodes help to uniquely identify the samples and help in sample tracking. The data is entered with the aid of the Gather® application installed in the project’s mobile devices (Fig-9).

Fig-9: Data entry using a mobile device installed with the Gather® application

The first stage is to scan a barcode that serves as an animal ID, followed by the entry of the metadata i.e. baseline information, pointers to illness, owner responses and scanning in all the sample-barcodes belonging to each individual animal. All the information entered is transmitted in real-time to a secure project server managed by the Kestrel Technologies Group.

Afterwards a field feedback form is filed detailing on the number of project staff involved in the sampling process, the number of local staff involved, number of animals sampled and if few than 10 animals were sampled reasons for not attaining the maximum number, number of declines to consent and reasons, number of animals with incomplete data and lastly rating the difficulty in sampling from that site.

Sample storage and transport to the laboratory

Sampling normally ends at around mid-day. All the samples are always kept in cool boxes (after collection, when barcoding and during transport back to the lab). The consumables that were used are disinfected as well as the gumboots and car contact points (Fig-10).

Fig-10: Disinfection of the car

On our way to the office, a WhatsApp message is sent to the laboratory team informing them of the number of animals sampled and tentative time of arrival. On arrival at the laboratory, the cool boxes with samples are received by the laboratory team and processing of the samples initiated. Afterwards, both the livestock market and slaughterhouse consumable boxes are checked and refilled as appropriate, the coveralls are replaced with clean ones and the gumboots are further thoroughly washed and sanitized with Virkon in preparation for the subsequent field visits.

Feedback and significance of the study

The fifteen diseases being investigated by ZooLink affect both humans and animals. The study seeks to determine if indeed such diseases are circulating in the human and animal population. If these diseases are detected, feedback is provided at the hospital, livestock market (Fig-11) and slaughterhouse level. So far the feedback has been provided to medical officers, public health officers, nursing officers, clinical officers and laboratory staff at Bumula sub-county hospital in Busia County (28/02/2018) Mukumu mission hospital in Kakamega county (07/02/2018) and Lukolis health centre in Bungoma County (14/12/2017). Public engagement with livestock traders, butchers, meat inspectors and animal health officers at Myanga slaughterhouse and livestock market in Bungoma County (28/02/2018) and in Shinyalu slaughterhouse and livestock market in Kakamega County (07/02/2018).

Fig-11: A public engagement session in one of the livestock market to provide feedback

The objective of the public engagements at the health facilities, livestock markets and slaughterhouses are to share preliminary research sampling results so far based on study screening tests, to inform every one of the work we do, zoonoses covered by the study and offer recommendations on control and prevention of the zoonoses detected. The public engagements are done through talks and info-booklets highlighting ZooLink’s objectives, study areas, detected zoonoses through info-stories, including their control & prevention options and the project’s next steps.

All the previous study info-booklets are available on the study website available at: http://www.zoonotic-diseases.org/project/zoolink-project/