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.

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.

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.

Phase two of this study (detailed in the previous ZooLink newsletter) began in November. Over the last two months, we revisited 27 households that we collected GPS data from in phase one in order to track the movements of the same people and livestock as we did in July and August of this year. Briefly, this involves visiting randomly selected households in Busia County and asking the participant to wear a small GPS tracker on a lanyard around their neck or alternatively, to keep it in a pocket on their person for one week. During the same visits, we also attach an identical GPS unit on a collar to one of the livestock belonging to the household. After the week is over we return to the household to collect the trackers and to ask a few questions about the experience.

Cattle with trackers around their necks

Although most people have been keen to participate in the study for a second time, we often hear of challenges they encountered while wearing the trackers. These are nearly always due to other people’s perceptions of the purpose of the trackers and the research. For example, many participants reported that they were questioned by people from other households, which led to participants having to convince other people of the purpose and worth of the study. In the worst cases, participants reported that other people were convinced that the tracker was listening to their conversations, was a bomb or was doing “the work of the devil”. However, it was heartening to hear that in all cases the participant attempted to explain the study to other people, with varying results. Interestingly, the intensity of the questioning by outsiders seemed to be related to the participant’s age and gender: We tended to find that young women wearing the trackers were more likely to be subjected to questioning and (attempted) persuasion to discontinue their participation in the study than others. Nonetheless, participants invariably reported that while others might be doubtful, they themselves remained convinced of the purpose of the study and continued to wear the trackers.

Cattle outside a “boma” with trackers around their necks

Sometimes it was difficult to find our participants and collect the trackers when the week was up – we would drive to a sub-location up to two hours away from Busia town, only to find that the people we wanted to visit were out and we would have to track them down, mainly by asking the villagers where our participants might be. On the bright side, this also meant that our trackers were out collecting interesting data, and has led to us stumbling upon various events within the villages, including a funeral, a circumcision ceremony and a fishing trip.

Overall, this second phase of fieldwork has been largely successful!

This blog article was authored by Jessica Floyd, PhD student, University of Southampton and also appears in our Zoolink Newsletter Volume1 Issue 2

One of the primary objectives of the Urban Zoo project is to quantify and understand microbial diversity in an urban setting and to try and link that to urban livestock keeping. In so doing we aim to elucidate the possible role of livestock as a risk factor in the emergence of disease in cities.

To give us a handle on microbial diversity we have chosen commensal Escherichia coli as an indicator species, which we have isolated from samples taken from a diversity of sources across the city of Nairobi. These comprise people and their living spaces, including the food they eat; their immediate environments, including water sources, waste and wildlife; and the livestock that they keep either for their own consumption or for sale. From these samples we isolate and culture E. coli, extract their DNA, and perform whole genome sequencing, enabling us to compare isolates from different compartments and to determine how closely related they are, and thus how microorganisms might pass from one to another.

The collection of these samples has been guided by a highly structured sampling frame, which I described in Urban Zoo newsletter number 7. Essentially, we have selected 33 sub-locations in Nairobi representing a range of social strata and, within each, have chosen 3 households to sample: one with no livestock; one with only monogastric species (pigs or chickens); and one with ruminant livestock (sheep, goats or cattle); You can view the spatial maps at our earlier post by clicking here .

The collection of such comprehensive data from these 99 households was an enormous undertaking and has been a considerable logistical feat of coordination between the field and the laboratory. The good news is that the sampling is now complete, thanks to the heroic efforts of the field team, led by Judy Bettridge and James Akoko, and of our colleagues in the laboratories.

Overall, 2,351 samples have been collected and we managed to culture E. coli from 80% of these (1,850). Once the last few have been done this will give us 1,809 whole genome sequences to analyse. 327 of these are from people; 58 from the places where they prepare food; 64 from animal source foods (milk meat and eggs); 644 from 12 different species of livestock; 239 from the environment around the home-stead including water sources; and 477 from a wide diversity of wildlife in the vicinity of the household.

But it is not over yet. We will very soon have finalised the sequencing and now comes the equally challenging task of deciphering all of this genetic data to unveil the pattern of microbial diversity across Nairobi. Over to you Melissa!

On that note, I would like once again to congratulate the field and laboratory teams, and to wish everyone a great year ahead, 2017.

This article was authored by Dr. Timothy Robinson who is a co-principal investigator in the Urban Zoo project and also a principal scientist with ILRI’s Livestock Systems and Environment research group.

This blogpost was authored by Tim Robinson a co-principal investigator in two of our projects (#UrbanZoo and #ZooLink) and originally appeared on Cambribge Core Blog available at: http://blog.journals.cambridge.org/2017/01/24/confronting-the-rising-threat-of-antibiotic-resistance-in-livestock/

Resistance to antimicrobials is developing faster than ever before due to decades of abusing these important drugs. A ‘post-antibiotic’ world looms as a result, the consequences of which would be many people and farm animals sickening and dying of what, until now, have been preventable or treatable infections.

The good news is that the world is taking notice. On 21 September 2016, the United Nations General Assembly addressed this global challenge. At the UN headquarters in New York, member states reaffirmed their commitment to develop national action plans to stem and reduce the continuing rise in antimicrobial resistance (AMR). These action plans will be based on a Global Action Plan on Antimicrobial Resistance developed in 2015 by the World Health Organisation (WHO) together with the Food and Agriculture Organization (FAO) and the World Organisation for Animal Health (OIE)—the so called ‘Tripartite’. The aims of the Tripartite are first, to ensure that antimicrobial agents continue to be effective and useful to cure diseases in humans and animals; second, to promote prudent and responsible use of antimicrobial agents; and last, to ensure global access to medicines of good quality. Countries will be required to report on their progress in September 2018.

Addressing the rising threat of antimicrobial resistance requires a holistic and multisectoral ‘One Health’ approach, because of the interconnected roles played by animals, people and the environment in the evolution and spread of AMR. The potential role of the livestock sector in mitigating AMR in pathogens of medical as well as veterinary importance is critical. Livestock consume at least half of all antibiotics produced globally and there is a substantial and growing body of evidence linking antibiotic use in livestock production to the development of antibiotic resistance in disease-causing bacteria that pose major threats to public health.

It is widely held that the use of antibiotics in livestock production—in particular, to promote livestock growth and prevent disease, but also to treat disease—could be reduced considerably through improved production practices and other interventions. Robinson and colleagues propose interventions that can be made directly on farms; those that can help create enabling environments; and others that can raise awareness of the problem and ways to solve it.

The potential to reduce use of antibiotic drugs is particularly large in low- and middle-income countries where the use of antibiotics in livestock production is already high and is predicted to grow massively—if mitigation measures are not taken—in line with projected livestock sector growth. It is critical that this unique window of opportunity, with heightened public awareness and across-the-board political will so recently expressed, is harnessed to guide research and policy in AMR, and so to exploit fully the potential of livestock sector development to mitigate antibiotic resistance. The lives, health and well-being of people and livestock depend on our conserving these precious drugs as part of our arsenal against microbial infections.

The open access Opinion paper is published in animal: Antibiotic resistance: mitigation opportunities in livestock sector development
Authors: T. P. Robinson, D. P. Bu, J. Carrique-Mas, E. M. Fèvre, M. Gilbert, D. Grace, S. I. Hay, J. Jiwakanon, M. Kakkar, S. Kariuki, R. Laxminarayan, J. Lubroth, U. Magnusson, P. Thi Ngoc, T. P. Van Boeckel, M. E. J. Woolhouse

The full report can be accessed at this link: http://www.rr-africa.oie.int/docspdf/en/2016/CHEROTICH1.pdf

A report by Dr. Chepkwony submitted to the OIE- Regional Representation for Africa explores the diagnostic capacities at different scales for both human and animal national tuberculosis reference laboratories in Kenya, Uganda and Tanzania to diagnose Mycobacterium bovis. One recommendation put forward is that national governments should invest in new and more accurate diagnostic technologies for detecting zoonotic tuberculosis. Moreover, it is important to utilize regional and international partnerships and carefully determine how to link these new tests and incorporate them within a country’s national diagnostic algorithm.

Recruitment and venous blood sampling of children in the study

Infections leading to fever are the largest causes of child morbidity and mortality in Africa. Dengue and Chikungunya infections are among viral diseases that cause fever even in traditionally malaria endemic areas. We set out to determine the prevalence and risk factors of Dengue and Chikungunya infections and estimate coinfection with malaria among children aged between 1 and 12 years presenting with fever at Busia County Referral Hospital in Western Kenya.

We sampled a cross section of children presenting with fever. We interviewed the parents/guardians of these children and collected blood samples and tested by microscopy for malaria and by conventional PCR for dengue and chikungunya. We found that chikungunya was prevalent among febrile children and infection was more likely among children presenting with vomiting and children with positive blood slide for malaria. None of the children screened was found to have dengue.

Our results suggest that mainly chikungunya virus appears to be actively circulating in western Kenya even in the absence of a declared outbreak. We recommend the establishment of prevention measures and routine laboratory testing of febrile cases for chikungunya in western Kenya.

Article by Isaac Ngere– Resident, Kenya FELTP

Capturing snails

In this study, we  sought to identify snail species infected with Trematode cercariae and environmental factors that correlate with their presence.  This was undertaken to better understand the underlying biology of these species to better understand the risk of transmission of livestock- and human-infectious trematodes.

We found that lymnaeid snails were widely distributed in all the agro-ecological zones (AEZs) we studied, and were the majority snail

at low altitudes. Biomphalariae, Bulinus, Oncomelaniae and Melanoides were present in some but not all of the zones. The study found that snails were more abundant in streams originating from springs and swamps near the shores of Lake Victoria. Biomphalariae and Lymnaeid species were found to be infected with trematode cercariae. The B. sudanica species found in the swamps near the lakeshore were infected with both Fasciola gigantica and Schistosoma mansoni pointing to a co-existence of Schistosoma and Fasciola infection at the site. The relative abundance of vector snails was found to be influenced by water pH, water temperature, ambient temperature and vegetation cover.

Identification/Isolation of cercariae

The presence of vector snails and cercariae in all of the zones points to the presence of possible transmission foci for Schistosomiasis, Fascioliasis and other foodborne trematodiases. People and animals using water and pasture from these sites in western Kenya are at a risk of contracting these parasitic infections.

Control of foodborne trematode infection should be targeted in all the AEZ’s with emphasis placed on the areas that border the lake and those with streams flowing from springs.

Article by Maurice Omondi Owiny, Resident, Kenya FELTP. Resident, Kenya Field Epidemiology and Laboratory Training Programme based at the International Livestock Research Institute

The Epidemiology Ecology and Social-Economics of Disease emergence in Nairobi (ESEI) project has hosted a variety of studies each with different study designs since its conception. MSc students, Mercy Gichuyia, James Macharia and I had the opportunity to work within an aspect of this wider project which involved a cross-sectional study among livestock keeping house-holds in Korogocho and Viwandani informal settlements of Nairobi. We sampled blood and faeces from humans and different livestock species kept in the area and from the faecal samples, identified the prevalence and antimicrobial susceptibility patterns of Salmonella, Campylobacter and E.coli. This article will focus on the interaction with the different team members and partners during our field sample collection. The science we undertook is currently being prepared for publication.

MSc Students, James Macharia Mercy Gichuyia and Maurine Chepkwony

I had the opportunity to work with a large and robust multi-institutional team that was well coordinated and that gave me the best introduction anyone could hope for in how a collaborative project functions. Our typical field day began at 6am where we would be picked from the University of Nairobi, College of Agriculture and Veterinary Sciences by Fredrick Amanya, Lorren Alumasa or James Akoko (all from ILRI).  Our voyage would get us to the heart of the informal settlements where we would meet with a team from the African Population and Health Research Centre (APHRC): Sophie and Jacky, as well as three residents from each area who acted as our security guides and who are known to the chief, elders and the APHRC. These two groups of people were crucial in creating rapport with the households as well as locating the randomly selected households and also acted as guides while navigating the otherwise complex neighbour-hoods.

Lorren and Amanya (both Clinical officers based at ILRI) would give clinical feedback to household members whose laboratory findings required some form of clinical feedback. This acted as community feedback, one of the many community benefits from the project. After a morning of questionnaire administration, collecting human feacal samples (with the help of Fredrick and Lorren) and livestock sampling with the help of Akoko (project field coordinator), we (Mercy, Macharia and I) would then head to the University of Nairobi (UoN) for laboratory isolation and analysis of the livestock samples  while the human samples were transported to the KEMRI-CMR laboratory.

The fatigue from the morning physical work notwithstanding, laboratory work was very exciting owing to the very dedicated and motivating University of Nairobi Laboratory team led by Mr. Nduhiu Gitahi and comprising of Mr. Masinde, Mrs. Mungai, Ms. Wandia, Mrs. Gateri, Mr. Wambaru among others who offered us a lot of guidance and encouragement. The KEMRI –CMR laboratory team was also a huge part of our work and from my standing, a great resource to my work. I learnt several skills from this team particularly antimicrobial susceptibility testing using the agar dilution method from Mr. Ngetich and how to run a PCR as well as analysing of sequence data from Mr. Samuel Njoroge. The two institutional laboratories have very distinct tasks in the project, but the linkages of these activities and support from the Labora-tory coordinator, Dr. John Kiiru, gave me an excellent opportunity to accomplish different aspects of my project as a student since I was able to work in both laboratories with a lot of ease. The contribution of Dr. John Kiiru from KEMRI cannot be overstated especially in the facilitation of this inter-laboratory collaboration ob-served.

Now I understand that it takes a village to make a successful project. Even with the above mentioned activities, a lot went on in the background. The whole urban zoo team was very efficient in the coordinating of activities including field work, and laboratory equipment and reagent acquisitions.  Dr. Victoria Kyallo and Mr. James Akoko were very effective, including Maurice Karani and Patrick Muinde (research technicians based at ILRI) were also instrumental in the project implementation. We were lucky to have supervisors: Prof. Kang’ethe (UoN) and Prof. Fevre (University of Liverpool/ILRI) who were always available and ready to support and guide us whenever we needed assistance in solving problems. I also interacted with Dr. Gemma Wattret from the University of Liverpool who was of great assistance in my Campylobacter research and especially so, in the molecular analysis and Laura Made of University of Liverpool in the study design. I cannot forget Dr. Annie Cook who taught us the ropes of rodent trapping and handling.

Although  this article reports on a successful multi institutional interaction during my experience in the urban zoo project, it is actually an acknowledgement from Mercy, Macharia and myself to the project and, institutions and all the individuals mentioned and not mentioned in this article that were involved in making our Master of Science research projects a success. Working with the urban zoo team was without a doubt a very exciting experience as well as an opportunity for growth both personally and profession-ally. We are very grateful for all your input.

This article has been written by  Maurine  Chepkwony (An MSc student under the Urban Zoo Project, based jointly between University of Nairobi  and International Livestock Research Institute (ILRI) in Kenya).