Issue 3 Volume 3
Page 2-3 : Editorial
Page 4 : New staff and students
Page 5 : Project updates
Page 6-7 : Students section
Zoonoses in Livestock and Humans in Kenya
Several of our ILRI employed staff have been working towards degree qualifications.
Maurice Karani and Patrick Muinde completed their Masters in Veterinary Epidemiology and Public health, by distance learning from the Royal Veterinary College, University of London in 2017. Maurice wrote his dissertation on the Epidemiology of acute Q fever among patients presenting with febrile illness in 2 Hospitals in Busia County. Patrick’s dissertation was on the Spatial Ecology of free roaming owned dogs in western Kenya.
Lorren Alumasa successfully completed her Masters in Public Health (MPH) by distance learning from the University of Liverpool in October 2018. As well as obtaining a MERIT grade, Lorren was also awarded the prize for 'Dissertation of the Year,' for her work on comparing rapid diagnostic tests (RDT), clinical diagnosis and microscopy with Polymerase Chain Reaction (PCR) in diagnosis of malaria infection among asymptomatic individuals in Busia.
Alice Kiyong’a completed her Masters of Public Health from the University of Liverpool by distance learning. Her project was on : the sero prevalence and associated risk factors of Q fever among slaughterhouse workers and herders in Isiolo, Laikipia, and Machakos Counties of Kenya.
Congrats to all!
Students and Staff
P. Büscher, IMT et V. Lejon, IRD. Des formateurs tout terrain et tout sourires.
Letter from the Co-Principal Investigator
Prof. Mark Woolhouse
"I’m particularly excited by the fact that we can use the Busia lab to generate genome sequences."
Dr Tatenda Chuiya: PhD Fellow
Tatenda is an African Regional Postgraduate Programme in Insect Sciences (ARPPIS) - PhD scholar supported by a German Academic Exchange (DAAD) scholarship. He is part of our team jointly with the International Center of Insect Physiology and Ecology (ICIPE). His research is entitled: One Health approach to vector biology and arbovirus epidemiology in smallholder livestock systems in western Kenya. Tatenda’s research interests include pathogen-vector-host interactions affecting the epidemiology of vector-borne zoonotic diseases using molecular tools. Within the ZooLinK project his research is focussing on arthropod-borne viruses (arboviruses) in domestic cattle and mosquito/tick vectors in humans in western Kenya.
Recent Academic Qualifications
Dr. Nicholas Bor: New staff
Nicholas Bor joined the International Livestock Research Institute as a Research Assistant under the the ZooLinK project that is based in Busia, Western Kenya. He holds a Bachelor of Veterinary Medicine (BVM) from the University of Nairobi. Nicholas has experiences in data collection, analysis and public engagement. He has a strong interest in the research sphere and is currently pursuing a Masters degree in One Health from the University of Edinburgh that is funded by the much coveted Commonwealth scholarship. His entry into the team is valuable since he will be able to share his experiences while putting to practice what he has learnt.
A Warm welcome to the Animal Health and Industry Training Institute (AHITI) interns
During this issue we welcome AHITI interns, namely: Elizabeth Kamau, Abdiharam Ibrahim and Paul Karanja who joined ZooLink project in September for a 3 month internship experience. These three are now the 7th Cohort to join the project. So far, ZooLinK Project has hosted 20 interns from AHITI! ZooLinK has been hosting interns from AHITI for the past 2 years now! The interns get to participate in all project activities from job shadowing in field work activities in both livestock markets and slaughter houses in western Kenya. They also get to participate in laboratory activities in our well equipped field lab in Busia.
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.
A Continuing Medical Education session
The processes involved during data collection to investigate the presence of 15 zoonotic diseases in livestock study sites have been detailed in earlier editions of these newsletters. Not much has however been highlighted on the processes and experiences within health facilities, also key study sites in the project. Like livestock, human patients are also assessed for these zoonoses to not only estimate their burden over time but also compare these with the livestock population from the same geographical location, that are potential sources for disease transmission to humans.
I am excited to share with you hospital experiences that provide opportunities to interact with people of different backgrounds and cultures. In hospitals, health care providers appreciate the fact that these ‘neglected’ diseases will finally be accurately identified and hopefully their burden reduced following appropriate interventions. Patients on the other hand are surprised at the possibility of being infected with up to 15 diseases from animals! Though quite relieved to know that these can be prevented.
Two research assistants Lorren Alumasa and Fredrick Amanya, with backgrounds in Clinical Medicine conduct hospital sampling. We work in close collaboration with at least 3 hospital staff during each sampling visit. These include 2 clinical officers at the outpatient departments and a laboratory technologist. Other staff may also be called upon in instances of hospital staff changes and these usually require re-introductions to the project activities. Often times students or visitors within the project also accompany us to hospitals in order to get a hands on experience and we are always happy to have them!
In hospitals, clinical officers are the first point of contact with patients seeking health care services. They then make initial assessments and decisions to either conduct laboratory investigations and manage the case or may decide to refer. The clinical officers help us identify patients meeting the study’s inclusion criteria: Presence of fever, anemia, muscle pains, joint pains, headaches, cough, chest pains, abdominal pains, diarrhea, vomiting, skin lesions and a negative malaria test. To obtain an informed consent from eligible patients, they are briefed about the project, its benefits, possible risks of participation in the study, and an emphasis is made that their participation is optional and they may opt out of the study at any time. Patients’ privacy is also enhanced through administering questionnaires and carrying out physical examination in an enclosed room. A nasal swab is then taken to assess for any resistance to a variety of drugs.
Blood and feacal samples are then collected with the help of hospital laboratory technologists who have been trained on the operating procedures of sample collection. The collected biological samples are then transported in cold chain, to the research laboratory in Busia for diagnosis of zoonoses.
We target to sample up to 10 patients in each hospital visit. This sample size is sometimes not met due to logistical issues such as hospital staff turnover that slows down sampling and, lack of patients who meet the study inclusion criteria. Such challenges have enabled us to appreciate the importance of close collaboration with hospital stakeholders. After the laboratory diagnosis, hospital findings are periodically disseminated through talks in Continuing Medical Education (CME) meetings. During CME meetings, knowledge and skills to improve patient care are shared at the hospitals, Info-booklets detailing these findings and project objectives are also disseminated.
Sharing of results enhances awareness and knowledge of zoonotic diseases present, their burden and appropriate prevention and control measures. Sharing results also ensures that the hospital personnel are aware about the diseases diagnosed within their respective hospitals. Additionally, the Hospitals are able to compare our project findings against their own. These talks further enhance interactions and knowledge sharing with other hospital stakeholders like nurses, medical officers, consultants and medical students who attend the CME sessions.
These experiences at the hospital study sites have enabled me to appreciate the gaps within the current surveillance of zoonotic diseases in western Kenya, additionally, I have gotten to appreciated the economic benefits patients stand to gain when they have accurate disease diagnosis. During the course of our hospital sites sampling, we have created a great rapport between the project and the health care system in western Kenya!
"..appreciate how the project informs decision making during patient diagnosis, having broadened their mindset to think beyond common conditions such as malaria .."
Blood sample collection from a human patient
ZooLinK project: human component
A peek at experiences in ZooLinK Hospital sampling
One of the interns sampling blood from a cow
The experience we have acquired under ZooLinK will forever remain in our minds and heart. This is with excellent collaboration with the ZooLinK staff and us as the AHITI interns in the required fields of study as set by ZooLinK.
Since we joined the project in September, 2018 we’ve been involved in animal sampling at the livestock markets and the slaughterhouses and human sampling at the sub-county, missionary and county referral hospitals. Samples collected are blood, faecal and nasal swabs. The samples are delivered under a strict cold chain to the ZooLinK lab and screened for 15 zoonotic diseases such as salmonellosis, campylobacteriosis, staphylococcosis among others.
Our participation in public engagement sessions at the slaughterhouses and livestock markets helped us learn on best ways and methods on how to approach farmers during extension services.
The most interesting part of our internship was how to collect blood from the pigs which sometimes became tricky but we managed with time.
We got to interact with the traders, farmers, butchers and workers in the livestock markets and slaughterhouses and learnt some of the challenges they experience in their day-to-day work. We participated in educating them on disease control and prevention options available such as regular deworming and vaccination of their animals such that as their animals are healthier they also become wealthier by accruing better prices in the market. We advised the slaughterhouse workers to always have their protective gear to avoid different risky exposures to zoonotic diseases.
We also worked in the lab where we got experience on different kinds of lab activities such as media preparation, handling of samples, sterilization of specimen and different techniques of streaking for culturing bacteria. We also learnt on how to culture and isolate different species of bacteria such as Salmonella, Campylobacter, Staphylococcus and Escherichia coli.
We got to learn different kinds of lab materials which include vacutainers (the red top, purple top and the green top) and the purpose of each vacutainer where the red top vacutainer used to extract serum while the purple top vacutainer (contains EDTA) used to collect whole/uncoagulated blood. Blood is used for different serological tests as well as parasitology. Nasal swabs collected are later cultured in the lab and used to test for presence of methicillin resistant Staphylococcus aureus.
We got to learn how to handle samples before and after they have arrived in the lab. We were also involved in the process of data entry both manual and electronic.
We would like to extend our sincere gratitude to the entire ZooLinK team for making our internship process a success and hope for the continual progress of the entire project.
"The effort by the project was highly appreciated by the stakeholders, and most of them were keen to learn."
The AHITI interns, cohort-7
My name is Christian Onyando. I recently qualified as a veterinarian with a Bachelor’s degree in Veterinary Medicine (BVM) from the University of Nairobi, 2017. I joined the ZooLinK project in March 2018 for a 52 week on-the job training. This training is an opportunity to consolidate my knowledge, skills and attitude to achieve competence in veterinary practice in order to enhance the delivery of veterinary services. This training is also a requirement in order to be a registered veterinarian by the Kenya Veterinary Board. During my internship with the ZooLinK project, I have actively participated in scientific research activities in selected slaughterhouses and livestock markets in Western Kenya, spanning three counties of Busia, Bungoma and Kakamega. I have also participated in various laboratory activities from receiving field samples, media preparation, bacterial culturing and identification among others, in the Busia field lab.
This article aims to narrate my experiences, in a feedback system that was adopted, by project researchers with the aim of sharing findings, so far, from samples collected from the selected sampling sites. The feedback system aims to improve animal welfare and meat hygiene in the sampling sites.
Most of the slaughterhouses that we visit are simple structures with basic facilities such as a slaughter slab and hoisting bars. The slaughterhouses are either privately owned or managed by the respective county governments. The number of animals slaughtered per day varies from one slaughterhouse to the other which informs their categorization to either a small, medium or large slaughterhouse. Most of the slaughterhouses in rural areas have the same traders/butchers bringing animals to be slaughtered. These traders/butchers are in constant communication with the meat inspectors. As part of our feedback system to the slaughterhouses, the project conducted public engagement sessions aimed to improve hygiene and welfare in these settings. We developed posters with photos and information about good slaughter and meat hygiene practices. Gumboots were provided by the project to boost slaughter hygiene.
We also took the opportunity to pass information regarding good hygiene practices, such as hand-washing, wearing appropriate protective clothing, and maintenance of slaughter equipment. The effort by the project was highly appreciated by the stakeholders, and most of them were keen to learn. Plans are now underway to purchase more personal protective and slaughter equipment, such as aprons and knives. Also, there will be organized training and workshops to continue improving on the welfare and hygiene practices.
Fig.3. Measuring the heart-girth
Interns from the Animal Health and Industry Training Institute (AHITI), cohort-7: Elizabeth Kamau, Abdiharam Ibrahim , and Paul Karanja
Insights on slaughterhouse dynamics in western Kenya: notes from a veterinary interns’ diary
The infobooklets issued can be accessed here: http://www.zoonotic-diseases.org/project/zoolink-project/
Fig . 4. Formation du personnel de santé à Kinshasa, mai 2017
Issuing of gumboots in one of the slaughterslabs in western Kenya
"The most interesting part of our internship was how to collect blood from the pigs which sometimes became tricky but we managed with time."
Previous issues of ZooLink newsletters can be accessed here: http://www.zoonotic-diseases.org/project/zoolink-project/