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:

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

Freshwater Vector Snails and their Infection with Trematode cercariae in Busia County


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


Letter from the PI: Introducing the ZooLink Suite of Projects

Prof. Eric Fèvre

Prof. Eric Fèvre

It’s a real pleasure to write the first “Letter from the PI” for the Zoonoses in Livestock in Kenya (ZooLinK) project, part of the Zoonoses in Emerging Livestock Systems programme, funded by the UK Research Councils (led by the BBSRC), UK DFID and UK DSTL.

Our project has been underway since 2015, engaged in planning and staffing, followed by refurbishing of our field lab and the commencement of field activities in Kenya.  It’s satisfying, a year and a half in, to now be able to start reporting on how we are doing and what we are up to. While we have been and will continue to share updates through social media on a regular basis, our project newsletters serve to provide slightly more indepth ongoing reporting of our work.  Newsletter articles will also appear on our project website as blog articles – we are active on social media both on the web at and through twitter @ZoonoticDisease, with #zels #zoolink.

Dr. Laura Falzon has been appointed as our postdoctoral epidemiologist, leading activity in our field sites.  Laura is co-ordinating scientific activity at our primary laboratory, based in the town of Busia, on Kenya’s border with Uganda. The lab houses BSL-2 standard biosecurity and is fully spec’ed for basic parasitological diagnostic work, serological assays, PCR and molecular diagnostics and microbiological assays.  Later this year, we’ll have some exciting DNA sequencing capacity there too. Samples are flowing through this laboratory where a number of our project scientists are working, and two Masters theses have already resulted from this ongoing work (projects undertaken by Isaac Ngere and Maurice Omondi on arboviruses and Fasciola spp– see our blog). Dr. hristine Mosoti is our ZooLinK project manager, and is the primary point of contact for any external queries on the project.

While the ZELS programme does not directly fund PhD students, we’ve successfully attracted a real diversity of academic interests to our programme with some innovative co-funding mechanisms.  Ten PhD students are currently active in the programme, some nearing the end of their first year, others just beginning their studies, on topics as wide ranging as within household economics to genetic diversity of parasites – we’ll ensure that the students’ work is highlighted regularly in the student’s section of this newsletter – see Jessica Floyd’s entry in this edition.

We’ve been engaging very successfully with the national veterinary system too, with two seconded members of County Veterinary Staff attached to our project and so far two cohorts of Animal Health Diploma holders coming through on 3 month “One Health” graduate internships.  Elsewhere in Kenya, we’re investing, with our national partners, in the surveillance of several other zoonotic disease issues: we put significant effort into surveillance for Rift Valley Fever during the rainy season early this year and in to understanding the epidemiology of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in camelids and humans.  We’ve also been working on enumerating and vaccinating dogs for rabies in central Kenya.  Much work, and many challenges lie ahead, but our excellent team is already proving that it can face these challenges successfully, and I am very proud of the excellent interdisciplinary work that we are doing.

Human, Food and Environmental data collection

WhatsApp-Image-20160607Human, food and environmental data are among the wide range of data collected within the 99 households. The data are often collected by Clinical Officers. Human sampling involves among others, individual consenting to participate, questionnaire interviews administration, general physical examination and anthropometric measurements, biological data collection and offering feedback and health education on the outcome of the laboratory based investigations. Two sets of structured questionnaires are administered; a general household and individual participant questionnaires. Biological data that is collected includes fecal samples and nasal swabs. Fecal samples are assessed for E. coli and campylobacter bacteria while nasal swabs are assessed for antimicrobial resistance. Collection and transportation of human samples from the field to laboratories involves sterile techniques.

Like human sampling, sterile steps are also observed during food and environmental data collection. Only livestock sourced foods are collected in the study. A sample of meat, milk and a wipe of egg shells if available, are collected. Sterile wipes of kitchen working surfaces such as chopping boards as well as kitchen door knobs are also collected. Environmental samples are collected using sterile boot socks. Normal saline-wet boot socks are worn and environmental samples collected by walking around the area surrounding the household as well as surfaces within livestock pens if available. Whirl pack bags are used in transportation of environmental samples. Water samples from water puddles, boreholes or storage water tanks are also collected as environmental samples. Subsamples of food and environmental samples are marked with a red dot to identify those going for whole genome sequencing and a blue dot on those being analyzed for campylobacter. All collected data are de-identified using barcode numbers to enhance participant and sample anonymity.

On completion of data collection, participants in the household are either given Albendazole or Mebendazole anthelminthic depending on age. Anyone found to be clinically ill is offered a prescription. If they are seriously ill a written referral letter to the nearest and most preferred health facility for further management is offered. Laboratory outcomes are communicated back to individual participants within two to three weeks of data collection. This is accompanied by health education with emphasis on how to maintain proper hygiene as well as interaction with livestock. Like many other community studies, our study is not devoid of challenges. Some of the challenges encountered involve heavy traffic. As investigators, we have to sometimes anticipate early morning starts. Participants which means rescheduling the day to collect data. Others include withdrawal from participation and inability to access household heads especially in high income settings.

Laureen AlumasaFredrick Amanya

 Article by Lorren Alumasa & Amanya Fredrick

This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Update: 99 Households study: wildlife component

Wildlife 2As we approach the final quarter of the 99 household study, it is a pleasure to be asked to reflect on the wildlife sampling component of this study. The wildlife sampling team has come a long way since its inception in September 2015, when we were all relative novices in trapping Nairobi’s diverse array of wildlife species. We have had some long days and sleepless nights, but to their credit, the enthusiasm of those involved has never waivered.

A typical day for the wildlife team starts at 5am, when we embark on bird sampling. To ensure we follow best practice for all of our trapping we collaborate with experts at the National Museums of Kenya, and in the mornings Titus Imboma (an ornithologist from the museums) helps us set up an array of mist nets, aimed at trapping birds as they fly in proximity to the household and livestock-keeping areas of each compound. Once caught, each bird is placed in a paper bag to collect a faecal sample, before a number of other body measurements and biological samples are collected. Such opportunistic sampling is a common philosophy among wildlife Table 1-Taxadisease ecologists, and additional samples provide an important resource for future epidemiological work. We next check the rodent traps – we use live-capture Sherman traps which are set throughout the house, livestock-keeping facilities and the household compound. Any rodents that we catch are transported back to the lab at ILRI, where they are humanely euthanized and subjected to a post-mortem examination (PME). This procedure is used to permit the collection of fresh faeces and organ samples which are stored frozen and in formalin. The latter ensures that tissues from these animals are preserved for histopathological interpretation, should the need arise in the future. As dusk settles over Nairobi, the sampling team heads back to the house to trap bats.

The techniques used to trap bats are vey similar to those for birds; very fine mist nets are suspended between fly-ways where bats seek their food (either insects or fruit depending on the species of bat). Due to their propensity to bite, bats present a challenge to remove from the nets and restrain during sampling, but with the appropriate techniques and equipment (i.e. tough gloves!) they can be safely held to collect measurements and samples. We sacrifice a maximum of two bats each night, which are taken back to the lab at ILRI for PME. The rest are sampled live, and released Wildlife 4unharmed. When we encounter a bird or bat roost, we use tarpaulins spread underneath the roost in order to collect pooled faecal samples representative of the individual animals using the roost.

Something that has become evident as we move from house-to-house, navigating Nairobi’s  maze of leafy suburbs, high-rise apartments and river-side slums, is the shear diversity of wildlife habitat present in this city. This is reflected in the number of species (birds, rodents, bats, primates and carnivores) we have sampled to date (see table 1). All of these species inhabit different ecological niches which likely govern their levels of interaction with humans and livestock; as an example one would expect very different levels of interaction between house rats that scavenge on animal feed and sunbirds that rely on nectar. How this translates to the risk of disease transmission is something we hope to shed light on by studying the genetic diversity of E. coli in these wildlife, and comparing it to those from humans, livestock and the

James Hassell

Article By James Hassell


This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

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