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:

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

Rapid tool for the surveillance of cysticercosis

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.

Dengue and Chikungunya infections among febrile children in Busia County Referral Hospital

Dengue and Chikungunya infections among febrile children in Busia County Referral Hospital


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

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

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


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