Antimicrobial Resistance Research Hub - Transmission dynamics

Antimicrobial resistance in the Urban Infant Foodscape project

Ekta Patel — Mon, 02 Nov 2020 11:32:54 +0000

Antimicrobial resistance in the Urban Infant Foodscape project

The aim of the project is to quantify the burden of enteric infection in children aged 6-24 months in low-income communities in Nairobi and assess risk factors across three domains of the food system: the domestic environment, the local marketplace and the production and supply chain.

In addition, the antimicrobial resistance profile in key enteric bacterial pathogens (Escherichia coli, Salmonella and Campylobacter) cultured from children’s food and stool will be described to determine the risk factors for the carriage of antimicrobial resistance in these pathogens along the food value chain.

The data will be used to develop risk assessment models to inform locally appropriate interventions to control these pathogens and reduce foodborne disease.

Starting date

January 1, 2019

Ending data

October 31, 2020

Pillar

Transmission dynamics

Country

Kenya

Region

Africa, Eastern and Southern Africa

Contacts

Donors/Investors

Partners

London School of Hygiene & Tropical Medicine

Understanding microbial diversity at the wildlife–livestock interface in Kapiti, Kenya

Ekta Patel — Mon, 02 Nov 2020 10:59:17 +0000

Understanding microbial diversity at the wildlife–livestock interface in Kapiti, Kenya

The goal of the project is to investigate the occurrence and map the antibiotic-resistance patterns of bacterial species at the wildlife–livestock–ecosystem interface and determine the resistome within animals and the natural environment.

Antimicrobial resistance poses a threat to food security, human health, the natural ecosystem and the global economy. Wildlife carry bacteria, some of which may be resistant to antibiotics. Through horizontal gene transfer, bacteria in a microbial community can transfer antibiotic resistance genes to other microorganisms in the community.

The presence of antimicrobial resistant genes in wildlife could indicate that antimicrobial-resistant bacteria of human or livestock origin are widespread in the environment and that wildlife could be acting as a reservoir for the transfer of antimicrobial resistance genes among people, livestock and the natural environment.

This work is carried out under the One Health Research, Education and Outreach Centre in Africa that is hosted by the International Livestock Research Institute.

Starting date

October 1, 2021

Ending data

October 31, 2022

Pillar

Transmission dynamics

Country

Kenya

Region

Africa, Eastern and Southern Africa

Contacts

Donors/Investors

Public health risks associated with antimicrobial resistance in food crops

admin — Mon, 28 Sep 2020 13:04:26 +0000

Public health risks associated with antimicrobial resistance in food crops

There is growing concern that use of antimicrobials on crops might persist as residues on harvested food. Food crops also risk contamination with resistant microbes previously exposed to human and veterinary antimicrobials that are deposited on plants from agricultural inputs such as manure, irrigation water and soil.

After the crops are harvested, low-dose exposure to antimicrobial residues or to resistant microbes could increase the risk of development of antimicrobial in people.

Using a scoping review of the literature to build a conceptual framework, this project, led by the London School of Hygiene and Tropical Medicine, aims to describe the current state of knowledge and summarize the public health risk factors and transmission pathways of antimicrobial resistance through crop systems, with a focus on low- and middle-income countries.

Pillar

Transmission dynamics

Contacts

Epidemiology of antimicrobial resistant Escherichia coli carriage in sympatric humans and livestock in a rapidly urbanising city

Ekta Patel — Mon, 26 Aug 2019 10:02:08 +0000

Escherichia coli is a harmless gut micro-organism, but some pathogenic strains can cause life-threatening infections and other illnesses like urinary tract infections. It can also cause disease in animals, leading to economic losses due to mortality and morbidity. There are substantial limitations in our understanding of the distribution of antibiotic resistance in humans and livestock in developing countries. This study presents the results of an epidemiological study examining patterns of antimicrobial resistance in Escherichia coli isolates circulating in overlapping geographic human (n = 321) and livestock (n = 633) samples from 99 households across Nairobi, Kenya. E. coli isolates were tested for susceptibility to 13 antimicrobial drugs representing 9 antibiotic classes.

Nairobi is the capital city in Kenya where the population is rapidly growing, and livestock are commonly kept within household compounds bringing them into close contact with people. E. coli is an ideal organism to study the spread of antimicrobial resistance in this complex environment since it is a ubiquitous commensal in both livestock and humans, but with a wide range of resistance phenotypes.

This study focuses on the role of livestock keeping as a potentially high-risk urban interface for antimicrobial resistance transmission between humans and livestock in urban Nairobi. This is the first study to characterize the patterns and epidemiology of antibiotic-resistant E. coli from cohabiting human and livestock populations in a low resource urban setting. At the scale of individual households, we explore the role of livestock as risk factors for antimicrobial resistance carriage in humans, hence providing insight into the pathways of antimicrobial resistance transfer.

Partner institutions

Food and Agriculture Organization of the United Nations
International Livestock Research Institute
Kenya Medical Research Institute
National Museums of Kenya
University of Edinburgh
University of Liverpool
University of Nairobi
University of Oxford
Uppsala University

Funding

Biotechnology and Biological Science Research Council
Economic and Social Research Council
Medical Research Council
Natural Environment Research Council

More information

Muloi, D. et al. 2019. Epidemiology of antimicrobial-resistant Escherichia coli carriage in sympatric humans and livestock in a rapidly urbanizing city. International Journal of Antimicrobial Agents 54(5): 531–537.

Contact

Dishon Muloi (d.muloi@cgiar.org)

Deterministic processes structure bacterial genetic communities across an urban landscape

Ekta Patel — Tue, 25 Jun 2019 16:38:56 +0000

Contact Details

Eric Fèvre (eric.fevre@liverpool.ac.uk). Institute of Infection and Global Health (IGH), University of Liverpool and jointly appointed at the International Livestock Research Institute, Nairobi, Kenya.

Background

How do zoonotic diseases spillover into humans? If we are able to understand the influence of environmental changes on the diversity and distribution of microbial communities in wildlife we may be able to make some progress in improving our understanding.

Project Overview

Wild birds were sampled across 99 wildlife-livestock-human interfaces across Nairobi, Kenya and whole genome sequencing (WGS) was used to generate data that allowed characterization of bacterial genes known to be carried on mobile genetic elements with avian-borne E. coli.

Research Impact

The results of this study show that there are differences in the response to wildlife species to changes in urban land use which could play a part in determining how microbial genetic diversity is related to host community diversity. Evidence suggests that households may act as an interface for the exchange of genes encoding AMR between livestock and wild birds.

Researchers

James Hassel^1,2, Melissa Ward^3,4, Dishon Mulio^2,3,5, Judy Bettridge^1,2, H. Phan^4,6, Timothy Robinson⁷, Allan Ogendo², T. Imboma⁸, John Kiiru⁹, Sam Kariuki⁹, Michael Begon¹⁰, Erastus Kang’ethe¹¹, Mark Woolhouse^3,5, Eric Fèvre^1,2.

Institutions Involved

Institute of Infection and Global Health, University of Liverpool, UK
International Livestock Research Institute, Nairobi, Kenya
Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
Faculty of Medicine, NIHR BRC Southampton, University of Southampton, UK
Food and Agriculture Organization of the United Nations, Rome, Italy
National Museums of Kenya, Nairobi, Kenya
Kenya Medical Research Institute, Nairobi, Kenya
Institute of Integrative Biology, University of Liverpool, UK
University of Nairobi, Kenya.

Funding

Funding was provided by:

UK Medical Research Council, through the Environmental and Social Ecology of Human Infectious Diseases Initiative (ESEI)
A cross-research council initiative supported by the Medical Research Council, Biotechnology and Biological Science Research Council, the Economic and Social Research Council and the Natural
Environment Research Council and in part, by the CGIAR Research Program on Agriculture for Nutrition and Health (A4NH), led by the International Food Policy Research Institute

More information

Full publication available here: https://doi.org/10.1038/s41467-019-10595-1
Zoonoses in Livestock in Kenya (ZooLinK). http://www.zoonotic-diseases.org/project/zoolink-project/

Clinically relevant antimicrobial resistance at the wildlife–livestock–human interface in Nairobi: an epidemiological study

Ekta Patel — Tue, 25 Jun 2019 06:36:33 +0000

Contact Details:

Background

One of the greatest challenges facing global health security is antimicrobial resistance. An understudied key component of the epidemiology of antimicrobial resistance is the role of wildlife, especially wildlife found in urban environments. In this study, scientists investigate the carriage of antimicrobial resistance in peri-domestic wildlife, humans, livestock and their shared environment across the developing city of Nairobi in Kenya. The data generated have been used to examine the role of urban wildlife in the spread of clinically relevant antimicrobial resistance.

Project Overview

Regions within the city were selected on the basis of a socioeconomic stratification. Within these, households (n=99) were randomly selected, ensuring that households with and without domestic livestock were selected. A detailed survey of household characteristics was undertaken, and faecal, environmental and other samples were collected. In all, over 2000 wildlife samples, representing 75 different wildlife species, were collected, together with similar number of livestock and human samples, and samples from the wider environment.

Research Impact

Wildlife from urban environments were found to carry a high burden of clinically relevant antimicrobial-resistant E. coli, exhibiting resistance to drugs considered crucial for human medicine by the World Health Organization. Wildlife that interact closely with humans, livestock, and both human and livestock waste within households, were exposed to more antimicrobial resistant phenotypes, and could therefore act as carriers for the dissemination of clinically relevant antimicrobial resistance to the wider environment. These results provide novel insight into the broader epidemiology of antimicrobial resistance in complex urban environments, characteristic of lower-middle-income countries, and demonstrate the importance of taking an ecological approach to understanding AMR in complex environments.

Researchers

James Hassel^a,b, Melissa Ward^c,e, Dishon Mulio^b,c,d, Judy Bettridge^a,b, Timothy Robinson^f, Sam Kariuki^g, Allan Ogendo^b, John Kiiru^g, Titu Imboma^h, Erastus Kang’etheⁱ, Elin Öghren^j, Nicola Williams^a, Michael Begon^k, Mark Woolhouse^c,d, Eric Fèvre^a,b.

Institutions Involved

Institute of Infection and Global Health, University of Liverpool, UK
International Livestock Research Institute, Nairobi, Kenya
Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
Food and Agriculture Organization of the United Nations, Rome, Italy
Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
National Museums of Kenya, Nairobi, Kenya
University of Nairobi, Nairobi, Kenya
Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
Institute of Integrative Biology, University of Liverpool, UK

Funding

UK Medical Research Council and CGIAR Research Program on Agriculture for Nutrition and Health.

More information

Full publication available here: https://doi.org/10.1016/S2542-5196(19)30083-X
An integrated study of human and animal infectious disease in the Lake Victoria crescent small-holder crop-livestock production system, Kenya.https://doi.org/10.1186/s12879-017-2559-6
Zoonoses in Livestock in Kenya(ZooLink). http://www.zoonotic-diseases.org/project/zoolink-project/

Antimicrobial Resistant Escherichia coli and Staphylococcus aureus Isolates Detected in Raw Milk of Livestock in Pastoral Areas of Northern Kenya

Cevelyn — Sat, 16 Feb 2019 10:21:14 +0000

Contact details:

Bernard Bett (b.bett@cgiark.org). International Livestock Research Institute, Nairobi, Kenya.

Catherine Ngaywa (cheledi@uonbi.ac.ke). International Livestock Research Institute, Nairobi, Kenya /Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, University of Nairobi, Kenya.

Background

In northern Kenya, milk constitutes a major diet for the local people who engage in pastoralism as the main source of livelihoods. Consumption of raw milk is a common practice amongst farmers from these communities as it is perceived as being more nutritive and containing medicinal properties. This practice poses a threat to food safety and ultimately food security, as unpasteurized milk has the potential to carry infectious pathogens, which might also be carrying resistance genes.

Amongst the most important resistant genes identified, resistance to b-lactam antibiotics is considered a critical problem as this family of antibiotics is used as a first-line treatment of many bacterial infections affecting animals and humans. Moreover, genes that confer resistance to b-lactams are encoded in mobile genetic elements that can be transferred and disseminated to other bacteria. Therefore, the identification of AMR genes, especially those encoding Extended-Spectrum Beta-Lactamases (ESBL) and methicillin-resistant Staphylococcus aureus (MRSA), is crucial to minimise the risk posed to people consuming raw milk in Kenyan pastoral communities.

Project overview

The aim of this study was to investigate the prevalence of AMR in household milk for human consumption in Isiolo and Marsabit Counties, Kenya. A total of 603 milk samples were randomly selected from milk-producer households. E. coli and S. aureus were isolated from 42 and 85 samples, respectively and their antimicrobial resistance profiles determined phenotypically and genetically using microbiological and molecular techniques. Additionally, a survey was applied to household members to collect additional information on milk processing practices, consumption patterns and use of antibiotics in livestock. All the households that were used in the study were geo-referenced. The survey also collected information about animal data, and the animal species kept.

Main findings

The study identified multiresistant E. coli and S. aureus isolates in the raw milk that household members from these communities were consuming. Moreover, genes encoding resistance to b-lactams antibiotics were widely present in these isolates, and these genes were able to confer resistance to the third or fourth generation of this antibiotic families. Resistant genes to tetracyclines, aminoglycosides and methicillin among other antibiotics were also identified. Analysis of the questionnaires revealed that pastoralists in the area extensively use antibiotics to treat animal infections and consumed raw milk. Furthermore, communities surveyed were located in remote areas, where sources of cross-contamination with resistant bacteria from other origins were highly unlikely.

Conclusions

The results of the study indicate that pastoralists in Northern Kenya are consuming milk contaminated with multidrug-resistant E. coli and S. aureus. Measures to reduce the burden of resistant bacteria carrying ESBL and MRSA genes need to be taken. Interventions to raise awareness about this issue in these types of communities are necessary to improve the way that antimicrobials are used in animals in this region and minimise the risk of community members contracting food-borne diseases.

Research impact

The study increases our knowledge on the prevalence of antimicrobial resistant bacteria in milk in pastoral and agro-pastoral production systems in Kenya, and supports awareness campaigns amongst pastoralists about the risk of consuming potentially harmful raw milk and how the misuse of antibiotics in animal treatment could be putting pressure on bacteria to develop resistance.

Researchers

C. Ngaywa¹^,³, B. Bett¹, G. O. Aboge²^,³, G. Obiero³, I. Omwenga¹^, 2, M. Wainaina¹, G. Wamwere¹.

Institutions involved

International Livestock Research Institute, Kenya.
Department of Public Health Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Nairobi, Kenya.
Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, University of Nairobi, Kenya.

Research Subject Area(s)

Animal health, Microbiology, Genomics.

Funding

This study was jointly funded by the United States Agency for International Development (USAID) and the CGIAR Research Program Agriculture for Nutrition and Health (A4NH).

More information

Antimicrobial Resistant Escherichia coli isolates detected in raw milk of livestock in pastoral areas of northern Kenya. 2019. Ngaywa, C., Aboge, G.O., Obiero, G., Omwenga, I., Ngwili, N., Wamwere, G., Wainaina, M. and Bett, B. Food Control 102: 173–178. https://hdl.handle.net/10568/100537

Download a pdf version of this project here:

AMR_milk.pdf

Multibacteria species resistance to cephalosporins

Cevelyn — Sat, 16 Feb 2019 10:09:32 +0000

Contact details:

Background

The ability of bacteria of interchanging genes that confer the ability to survive exposure to antibiotic drugs is a global concern, as the dissemination of antimicrobial resistance genes amongst different bacterial species has been reported by a number of studies. This is an evolutive process that occurs as a consequence of putting selective pressure on bacteria from continuous antimicrobial use. Genes encoding resistance mechanisms to different families of antibiotics can be transferred together, between bacteria of the same species or between species of bacteria, if they are present in the same mobile genetic element, especially in plasmids. Multi-drug resistance plasmids are especially important, as these can mediate resistance to different families of antibiotics.

Bacterial species of clinical importance such as Salmonella, Campylobacter, Klebsiella, and Proteus can be found in many food products of animal origin and have the potential to interchange resistance mechanisms. These bacterial species are commonly found as commensals in the microbiome of many animal species bred for human consumption. However, some strains of this bacterial species have pathogenic potential and are the main cause of food-borne bacterial diarrheal disease in humans.

Project overview

The aim of this research is to determine shared drug resistance mechanisms between multiple bacterial species including Salmonella spp, Campylobacter spp, Klebsiella sp and Proteus sp isolated in a hospital clinical environment. In this project, focussed studies on human-derived clinically relevant isolates of a range of bacterial species sharing the same phenotype (cephalosporin resistance) are being sequenced to understand if the resistance mechanisms are shared. This will have important implications for the management of antibiotics in a hospital setting in East Africa.

Research impact

A better understanding of which drug resistance mechanisms are shared between different bacterial species will inform policymakers on which antibiotics have prevalent resistance genes and need to be considered in the implementation of policies oriented towards reducing antimicrobial resistance.

Researchers

Eric Fèvre¹^, 2, Sam Kariuki³, Revathi Gunturu⁴, Katie Hamilton¹.

Institutions involved

University of Liverpool Institute of Infection and Global Health, UK.
International Livestock Research Institute, Kenya.
Kenya Medical Research Institute, Kenya.
Aga Khan University, Kenya.
Wellcome Trust Sanger Institute, UK.

Research Subject Area(s)

Animal health, Microbiology, Genomics

Funding

CGIAR research program on Agriculture for Nutrition and Health (A4NH).
Zoonoses in Emerging Livestock System (ZELS) of UK BBRSC.
Global Challenges Research Fund, UK Medical Research Council (MRC).

More information

Zoonoses in Livestock in Kenya (ZooLink). http://www.zoonotic-diseases.org/project/zoolink-project/

Download a pdf version of this project here:

Multibacteria_species.pdf

Drug resistance patterns of Escherichia coli isolates obtained from cattle in rural western Kenya

Cevelyn — Sat, 16 Feb 2019 09:38:57 +0000

Contact details:

Background

The International Livestock Research Institute (ILRI) works closely with researchers from the University of Liverpool, Kenya Medical Research Institute, University of Nairobi and the Zoonotic Disease Unit of the Government of Kenya to establish a surveillance programme for zoonoses, which includes monitoring antimicrobial resistance in zoonotic bacterial diseases in Kenya, and can be used as a model for developing a National surveillance Programme for zoonoses. Activities within this programme are carried out to understand how changes in agricultural practices and livestock production are affecting trading patterns and transforming previously subsistence farming systems into intensive farming systems, and how these changes may be introducing pressure on local bacterial populations to develop resistance.

Mixed smallholder livestock farming systems are common in western Kenya. These mixed farming systems comprise of cattle, sheep, goats, a small number of pigs and crop production, which is fertilised by the manure produced by these animals. The less than rational use of antibiotics in these types of systems might be introducing selective pressure over local bacterial populations and increasing the likelihood of transmission of resistance genes amongst bacteria colonizing different animal species. Furthermore, the use of manure as crop fertilizer could be further facilitating the dissemination of resistance genes to bacterial species in the soil.

Project overview

The aim of this research is to identify drug resistance patterns in E. coli isolates obtained from cattle bred on mixed smallholder livestock farming systems from western Kenya. The area of study is widely representative of the Lake Victoria Crescent ecosystem which also includes areas of Uganda and Tanzania. Cattle were sampled from around 100 farms and phenotypic and genotypic characterization of E. coli isolates was performed, which included an examination of drug resistance carriage in these bacteria. Qualitative surveys of drug use and access were conducted, as well as structured sampling of animals (faecal samples) and humans on farms.

The results of this study will allow researchers and public policymakers to identify which antibiotics have associated resistance genes present in E. coli isolates and that will need to be targeted in a programme to control antimicrobial usage in animal production.

Research impact

The identification of antimicrobial resistance patterns in bacteria affecting livestock in Kenya will contribute to a better understanding of which antimicrobials commonly used in livestock might no longer be working as a result of the emergence of resistant bacteria. The research will lead towards more rational use of drugs in the agricultural sector.

Researchers

Eric Fèvre^1,2, Nicola Williams¹, Samuel Kariuki³, Steven Kemp¹, Allan Ogendo⁴.

Institutions involved

University of Liverpool Institute of Infection and Global Health, and Centre for Genomic Research, UK.
International Livestock Research Institute, Nairobi, Kenya.
Kenya Medical Research Institute (KEMRI), Kenya.
County Government of Busia, Kenya.

Research Subject Area(s)

Animal health, Microbiology, Genomics.

Funding

This study is funded through the CGIAR research program on Agriculture for Nutrition and Health (A4NH) and the Zoonoses in Emerging Livestock System (ZELS) of UK BBRSC.

More information

An integrated study of human and animal infectious disease in the Lake Victoria crescent small-holder crop-livestock production system, Kenya.https://doi.org/10.1186/s12879-017-2559-6
Zoonoses in Livestock in Kenya(ZooLink). http://www.zoonotic-diseases.org/project/zoolink-project/

Download a pdf version of this project here:

Drug_resistance_patterns.pdf