Zoonoses in Livestock in Kenya – The Beginnings of Surveillance

By Steven Kemp, PhD student, University of Liverpool

After a period of intense lab work at both KEMRI and the UK, investigating the patterns of antimicrobial resistance in faecal bacteria isolated from slaughterhouse workers in Busia County and the surrounding areas, I have returned to Kenya to begin the next phase of my PhD project.

ZooLinK is a cyclical programme which aims to set up surveillance systems of both human and animal health sectors over a long period of time. Surveillance of disease is particularly important, as the more information we have, the better we can treat diseases in both human and animal sectors. Recent research by colleagues indicates that the incidence of several zoonotic diseases, including E. coli, Salmonella sp. and others are vastly underestimated.

In recent times, we often hear about how we should now look to conform to the ‘One Health’ approach; this is where, in order to combat issues surrounding antimicrobial resistance and associated issues effectively, intersectoral approaches which share the cost and responsibility evenly between environmental, human & veterinary health professionals is required. In theory, this would be a perfect way to help educate and better promote antimicrobial stewardship.

Currently, I have large amounts of data on access to, use of, and perceptions of antimicrobials from a variety of parties, including animal healthcare workers, district veterinary offices, farmers and agrovet shops. Over the last three months, I have added to this repository by investigating the amounts of antibiotic resistance found in E. coli, which have been isolated from the faeces of workers in 142 slaughterhouses which were selected in western Kenya. These included slaughterhouses in Busia County and the surrounding Kakamega and Bungoma counties.

For the next portion of this study, I am attempting to collect four different sets of samples – to complete the ‘picture’. I will attempt to collect both human and animal faecal samples, from farmers and farm animals, water samples (to determine if there are patterns of resistance in animals which share common grazing grounds) and environmental samples (from the inside of homesteads, where animals are allowed to roam). By covering all of these bases, we will be able to eventually determine not only if there is transfer of antimicrobial resistance between animals and humans and the environment, but also which direction it is going in.

Typical small-holder farm in Funyula, Busia. Most farmers manage between 5-25 cattle.

Example of environment which may also be a good idea to sample in the future. If antimicrobial resistance can be found in the envi-ronment, then why not in wild animals such as these Zebra?

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.

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.

Rapid tool for the surveillance of cysticercosis

A blog entry by Kimetrica discusses promising progress in the development of a rapid tool for the surveillance of cysticercosis which will contribute to the global efforts by the World Health Organization in controlling cysticercosis by 2020. The proposed control method is rapid, cheap and requires little resources but which could yield important epidemiological information on community risk.
Read more about these developments on the Kimetrica blog by clicking here.

Tracking the movements of people and their livestock

cattle-with-trackersAs zoonotic diseases can be transported across landscapes by hosts, understanding the complexities of host-mediated pathogen movement is a priority for zoonotic disease research.  For my research, I   have been using surveys and GPS trackers to gather data on the movement patterns of people and their livestock. We will be looking at the differences in movement patterns between the wet and dry seasons: the first part of the study took place in July and we anticipate completion in November 2016.

At each selected household, we interview the adults present and ask them questions about places they regularly go to, how they get there and how long they stay. We also ask questions about places they go to less regularly and their activities involving livestock kept by the household. At the end of the interview, we ask the adult who spends the most time looking after the livestock (if they have any) to wear a GPS tracker on a lanyard around their neck for one week which stores their location once a minute. At the same time, if they keep cattle, goats or sheep then one of these animals (usually a cow) is fitted with an identical device attached to a collar. If the household does not keep any livestock, one person is still asked to wear a tracker, so that we can detect differences in movement patterns between people who do keep livestock and those who don’t. Once the week is up, we return to the household to collect the devices and download the data. The devices are set to record their location once a minute, and the batteries can last up to 10 days.

Nearly all of the people we interviewed have been willing to wear a tracker and all of the trackers given out have been returned without problems. We look forward to sharing some results from this study in the next newsletter! Floyd Jess

Article authored by Jessica Floyd, PhD student, University of Southampton, UK.

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