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Antimicrobial status at the Human-Animal Interface in Kenya


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Antimicrobial status at the Human-Animal Interface in Kenya

John Kagira is a veterinarian at the Jomo Kenyatta University of Agriculture and Technology in Kenya and a grantee of Grand Challenges Africa (GC Africa), which seeks to promote Africa-led scientific innovations to help countries achieve the Sustainable Development Goals by awarding seed and full grants to the continent’s most impressive solutions. GC Africa is implemented through the AESA Platform. Alliance for Accelerating Excellence in Science in Africa (AESA) is a funding, agenda-setting, programme management initiative of the African Academy of Sciences (AAS), the African Union Development Agency (AUDA-NEPAD), founding and funding global partners, and through a resolution of the summit of African Union Heads of Governments. GC Africa is supported by the Bill & Melinda Gates Foundation.


Dr Kagira is leading a collaborative team of scientists from JKUAT and other institutions to investigate the epidemiology and extent of antimicrobial resistance (AMR) in Kenyan livestock farming systems.


As a child, I shepherded my family’s cows and goats, often seeking animal extension officers to treat sick animals. But there were few veterinarians who were often stationed far from farms. Worse, the 1987 Kenyan Structural Adjustment Program reduced the number of veterinary extension service providers. This led to farmers treating sick animals with uncontrolled use of drugs to manage and protect the family’s livelihood without due regard for its effects on human consumption. The dream of becoming a veterinarian was born!

Today, farmers still manage disease on their own. My training in microbiology, parasitology and pathology led to an interest in zoonoses – diseases transmitted between animals and man. Pathogens affecting humans and animals are similar and affect many resource-poor people. “One Health” anticipates that closer collaboration among experts will yield different perspectives to tackle disease at the human-animal interface.  

Milk is an essential and common nutrient. But mastitis, inflammation of the udder due to infection with microorganisms, is common in dairy cows and goats. The consequent reduction in milk production often denies families of milk, particularly affecting young children. Farmers misuse antibiotics to manage mastitis, leading to poor animal disease outcomes and to resistance of bacteria causing mastitis which is transmissible to humans. Veterinarians and human physicians must work together to manage antimicrobial resistance.

A major global and local public health concern

The World Health Organization (WHO) and the Food and Agriculture Organization (FAO) have expressed concern about worldwide emergence and spread of AMR, a challenge in disease management for humans and domestic animals. Globally, annual deaths associated with AMR are estimated at 700,000, and are expected to increase to 10 million with an estimated $100 trillion global economic loss by 2050. Leading threats in developing countries are Methicillin Associated Staphylococcus aureus (MRSA) and Escherichia coli (ESBLs), which have already led to human morbidity, mortality and financial losses. Yet there have been only a few studies on AMR in developing countries.

Current concern

There is widespread use of antibiotics in livestock in Kenya, mainly in ruminants, poultry and pigs and to treat mastitis in cattle and goats. Mastitis is driven by poorly kept animals who become infected by bacteria in the environment and poor hygiene practice during milking leading to spread of mastitis within a herd. The disease causes major losses from reduced milk production and animal death. How does the farmer respond to occurrence of this disease?

In both high- and low-potential livestock production areas in Kenya, most farmers self-treat their animals. This is facilitated by the often easily available antibiotics in local drug and agricultural provision stores, popularly known as AgroVet shops. Veterinarians are few and difficult to reach, especially in an emergency. This has led to increased use of antibiotics without confirmed diagnosis of the disease and lack of awareness of the sensitivity of microorganisms to specific antibiotics. 

Up to 40% of African countries do not have enough data on AMR. My team is investigating the role of livestock in spreading AMR to humans, the association between individual, farm, community, hospital factors and antibiotic resistance patterns in different community settings.

Evidence of AMR

Community-associated AMR is being fuelled by close interaction between man and animal. Our research uses modern molecular biology to generate data on the presence and role in spread of AMR from livestock to humans to inform One Health policy on the control and management of AMR. We believe that bacteria-contaminated milk, especially from animals with sub-clinical mastitis, are the critical entry point of these microorganisms into the food chain. Raw and un-pasteurised milk and associated products such as fermented raw milk, is consumed by 80-100% of pastoral households in this study. But these products as consumed have a high burden of bacteria with a prevalence of sub-clinical mastitis (SCM) of 50-75% in dairy goat and cow milk. SCM causes bacteria such as Staphylococcus aureus, E. coli, Pseudomonas spp and Klebsiella spp to infect both human and domestic animals who cannot be treated by common antibiotics.

 Bacteria isolated from dairy cow and goat milk confirm that a large proportion are resistant to commonly used antibiotics. In one study, S. aureus from dairy goats were resistant to penicillin (100%), tetracycline (20%) and norflaxacin (25%), as well as beta-lactam antibiotics such as cephalexin (63.1%), cefoxitin (34.2%) and cefotaxime (53.0%). Multiple drug resistance was also common. Farmers administer antibiotics to animals uninformed of the danger to human and animal health and without observing withdrawal periods, enabling antibiotic residues and resistant microbes to enter the food chain. If these bacteria are transmitted to humans, they are difficult to treat. Preliminary data from Thika and Kajiado counties in Kenya show that bacteria isolated from nasal cavities and wounds of human beings also have high burden of bacteria resistant to commonly used antibiotics.

We use molecular characterization of bacterial isolates through pulsed field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), spa and SCCmec typing to show spread and evolution of bacteria resistant pathogens, to understand the potential of jumping between species and resultant spread of resistant bacteria from animals to humans.  We hope to provide data that influences policy on the use of antibiotics and management of AMR in Africa.