Project summary

This project investigates how slaughterhouse wastewater contributes to the spread of antimicrobial-resistant bacteria in Kampala’s urban water systems. Focusing on effluent from Kalerwe Abattoir into the Nsooba Channel, the study will use Escherichia coli as a sentinel organism to trace environmental contamination and resistance patterns. Through a combination of microbiological analysis and whole genome sequencing, the research will characterize resistant bacteria in upstream, discharge and downstream water samples.

The resulting genomic data will then be compared with publicly available Ugandan and clinical E. coli datasets to assess potential links between environmental contamination and human health risks. The project aims to generate locally relevant evidence to inform wastewater management, improve antimicrobial resistance surveillance and support public health decision-making in Uganda.

What are this project's goals? How will you achieve them?

This project has two main goals. First, it will determine whether slaughterhouse wastewater contributes to the spread and persistence of antimicrobial-resistant bacteria in Kampala’s urban water systems. Second, it will assess how environmentally derived resistant bacteria relate to clinically relevant strains found in Uganda.

To achieve this, the study will collect water samples from three key points along the Nsooba Channel: upstream of the abattoir, at the point of effluent discharge and downstream. Escherichia coli will be isolated as a sentinel organism and bacterial load will be quantified using the Colony Forming Unit (CFU) method to assess contamination levels across sampling sites. Standard microbiological techniques will be used to determine antimicrobial resistance patterns among isolates. Selected resistant isolates will then undergo whole genome sequencing to identify resistance genes and assess genetic relatedness. Finally, genomic data will be compared with publicly available Ugandan E. coli datasets to evaluate possible overlaps between environmental and clinical strains, providing insight into potential public health risks.

How will this funding be used?

This funding will be used to support the core laboratory and fieldwork activities required to complete the study. It will cover the collection of wastewater samples from Kalerwe Abattoir and along the Nsooba Channel, including transport, sampling materials and field logistics. It will also support laboratory analyses such as bacterial isolation, antimicrobial susceptibility testing, and quantification of Escherichia coli from environmental samples.

In addition, the funds will contribute to molecular work, including DNA extraction and whole genome sequencing of selected isolates, as well as basic bioinformatics analysis to interpret resistance genes and genetic relationships. Where necessary, the funding will also help support data management, access to public genomic databases and software tools required for comparative analysis.

Overall, the support will directly enable generation of high-quality genomic and microbiological data needed to understand the role of abattoir wastewater in spreading antimicrobial resistance in Kampala’s urban environment.

Who is on your team? What's your track record on similar projects?

The work will be supervised by a multidisciplinary team of three experienced scientists. Dr. Emma Doughty, PhD (https://uk.linkedin.com/in/emmadoughty) is a molecular microbiologist in London, United Kingdom with strong expertise in microbial genomics and pathogen evolution. Prof. Jesca Nakavuma, PhD (https://ug.linkedin.com/in/jesca-nakavuma-1b7352157) is an Associate Professor at Makerere University with extensive experience in bacterial drug resistance, food safety microbiology and applied veterinary and public health microbiology. Dr. Eric Katagirya (https://ug.linkedin.com/in/eric-katagirya-65a81623) is a clinical microbiologist and genomics researcher at Makerere University with strong expertise in pathogen genomics, host–pathogen interactions and whole genome sequencing applications in infectious disease research. Together, this supervisory team provides strong technical and clinical expertise that directly supports the project’s goals.

My current training has equipped me with hands-on experience in core microbiological techniques. For instance: For instance, I volunteer at the Microbiology and Molecular laboratories at Makerere University where I have interacted with a number of similar wastewater samples, generating expertise on bacterial culture, isolation and antimicrobial susceptibility testing, which are directly relevant to this project. I have also been exposed to molecular biology workflows such as DNA extraction and preparation for downstream genomic analysis. Consequently, I have worked on similar projects like Using CRISPR-Cas to detect infectious disease in wastewater, and the other being Identification of resistome and virulence profiles from sewage in Kampala-Uganda.

In addition to laboratory skills, I have developed experience in research design, data interpretation and scientific writing through my academic coursework and ongoing research work on AMR in wastewater systems in Kampala. I am actively building capacity in bioinformatics and genome-based analysis to support comparative studies of bacterial isolates.

While this will be my first fully funded independent project of this scale, it builds directly on my academic training and current research direction. I am well-prepared to execute it with rigor and support from my academic team.

What are the most likely causes and outcomes if this project fails?

The most likely risks to this project include challenges related to environmental sampling conditions, such as contamination issues and inconsistent recovery of Escherichia coli from some sampling points. In addition, delays in laboratory workflows and potential limited sequencing capacity could slow down genomic analysis. Bioinformatics capacity and data processing requirements may also present challenges if computational resources or technical support are constrained.

If these challenges occur and the project cannot be completed as planned, the primary outcome would be incomplete datasets that limit the ability to fully compare contamination patterns across all sampling sites or to complete full genomic comparisons with publicly available datasets. This would reduce the strength of conclusions regarding the link between abattoir effluent and antimicrobial resistance dissemination in urban waterways. This would constrain evidence-based information required be utilised locally by the Kampala Capital City Authority and the national AMR stewardship programs.

However, even in a partial outcome scenario, the project would still generate valuable preliminary data on E. coli presence and antimicrobial resistance patterns in Kampala’s wastewater systems. These findings would provide a foundation for future, larger-scale studies and help refine sampling and analytical approaches for environmental AMR surveillance in Uganda.

How much money have you raised in the last 12 months, and from where?

In the last 12 months, I have self-raised approximately USD 800 from personal savings and academic assistance to support the initial phase of this project. This contribution will specifically cover basic analysis of approximately six whole genome sequences of Escherichia coli isolates. This initial investment has allowed me to begin generating foundational genomic data and demonstrate feasibility for the study.

Beyond personal contributions, I have not yet received formal external research grants for this project. I am now seeking additional funding to expand sample coverage, increase the number of sequenced isolates and complete comprehensive environmental and comparative genomic analyses needed to strengthen the study’s public health relevance in Kampala, Uganda.