Challenges associated with tracking the movements of people and their livestock

Challenges associated with tracking the movements of people and their livestock

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

Do livestock have a role in the emergence of disease in urban cities?

Do livestock have a role in the emergence of disease in urban cities?

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.

Non-typhoidal Salmonella (NTS) in pigs in Busia, Nairobi and Malawi

Non-typhoidal Salmonella (NTS) in pigs in Busia, Nairobi and Malawi

This blog post was authored by Catherine Wilson an MRES Student from the University of Liverpool attached under our #ZooLink project

I am investigating the prevalence of Non-typhoidal Salmonella (NTS) in pigs in both Kenya and Malawi in extensive, low input production systems.  The aim is to determine whether invasive NTS are present in the pig population of three study areas; one rural and one urban area in Kenya and one rural region of Malawi. In sub-Saharan Africa, NTS is a leading cause of human mortality, particularly in the very young, old, malnourished, or those suffering from co-morbidities such as HIV or malaria.

Pig slaughter slab in Bumala

Pig slaughter slab in Bumala

An invasive NTS serovar has been found to be able to cause severe disease in chickens; suspicion is therefore arising that transmission between humans is not the sole route of spread of NTS, and that zoonotic transmission, especially from pigs, may have a role to play in the epidemiology of the disease. Should this invasive strain of bacteria be found in pigs, we will assess whether the same serovar clinically affects humans in the same geographical location, using data already gathered from human hospitals. A correlation between the two would indicate that zoonotic transmission may be occurring.

The final part of this study will assess the presence of drug resistance in the strains of NTS isolated from pigs, and whether this bears any correlation to a similar antimicrobial resistance pattern of NTS to that previously detected in humans in the same area.  Should antimicrobial resistance be detected, other management techniques for the swine, such alterations in husbandry and hygiene, may be trialed.  In the longer-term vaccination development may be a possibility as an important method of preventing zoonotic disease transmission in the study areas, for which research is currently in the very early stages.

For sampling,  both faecal and mesenteric lymph nodes samples were collected post mortem from 256 pigs in Busia and 304 pigs in Nairobi.  The location in which the pigs were reared, as well as details of signalment, any previous antibiotic treatment if known and the method of transport of the pig to the slaughterhouse, were recorded for each individual pig.

Samples were processed at the Busia Field Lab and ILRI laboratories respectively. Culture and serotyping was carried out to confirm the presence of Salmonella followed by antimicrobial susceptibility testing to a range of antibiotics.  Positive isolates have then been stored for transport to the UK, where whole genome sequencing will be undertaken to identify the presence of any antimicrobial resistance genes. Once the results have returned, analysis is planned compare antimicrobial resistance profiles of the pig samples to those of humans in the same geographical location, to assess whether zoonotic transmission may be occurring.

Confronting the rising threat of antibiotic resistance in livestock

Confronting the rising threat of antibiotic resistance in livestock

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

Laboratory capacity to diagnose Mycobacterium bovis in East Africa

Laboratory capacity to diagnose Mycobacterium bovis in East Africa

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.

Pin It on Pinterest