Antimicrobial Resistance

Current work on antimicrobial resistance

Carbapenem Resistant Organisms in Scotland

Carbapenem resistance is an emerging threat worldwide. Although carbapenem resistance remains rare in Scotland, it shows a worrying upward trend. Further work to better understand the epidemiology of carbapenem resistant organisms in both population and molecular levels are needed to curb future emergence and spread of resistance. We aim to evaluate prevalence and outcomes (morbidity and mortality) trends, risk factors for carbapenem resistant organisms (CROs) acquisition among patients, the association between antimicrobial prescription, usage and CROs acquisition by building appropriate statistics models. Also, sequencing data will be used to explore phylogenetic relationships between CROs isolates in Scotland.

Main researcher: Shengyuan Zhao

Global Disease Burden from Antimicrobial Resistance

The WHO report on the global burden of antimicrobial resistance (AMR) in 2014 highlighted the issues relating to AMR surveillance including poor data and lack of standardisation across microbiology laboratories.  Our group have argued that to truly measure the disease burden of AMR information needs to be collected on the number of deaths attributable to the failure of antibiotic therapy due to antibiotic resistance. These kind of estimates currently have only been made from single hospital studies. We have been looking at AMR surveillance methods within local and national microbiology laboratories and within the International Classification of Diseases (ICD) coding system with an aim to improve the recording of disease attributable to AMR.

Main researcher: Meghan Perry

Sequence Based Diagnostics

Continual improvements in DNA sequencing technologies, and the associated reduction in the costs of sequencing has meant that the routine diagnosis of infections by sequence based methods are becoming increasingly viable. Diagnostics of bacterial infections by whole-genome sequencing is particularly promising; giving species and strain identification, virulence determinants, and determining the antimicrobial resistance genes present within a much shorter time-frame than traditional microbiological techniques. Moreover, the degree of resolution provided by sequencing is useful in its own right, showing not only the antibiotic resistance genes present but the mutations associated with them, and where in the bacterial genome they lie – either on the chromosome, or plasmids. This information can inform healthcare surveillance programs, helping to determine the origin and potential spread of particular resistance genes; allowing for more effective action to be taken to curtail their dissemination.

Main researcher: Stefan Rooke

Metagenomics of Hospital Sewage

The microbial communities in sewage are an important reservoir of AMR as they contain pathogenic organisms, human commensal organisms and resistance-carrying environmental organisms.  By directly analysing the resistome of hospital sewage using metagenomics and correlating it with whole genome sequencing of inpatient clinical isolates we hope to provide information on the cycle of antimicrobial resistance between patients and the environment and establish if hospital effluent analysis could be a useful antimicrobial surveillance tool.

Main researcher: Meghan Perry

Global Sewage Project

Metagenomic sequencing of human sewage and quantification of antimicrobial resistance genes and residues combined with epidemiological data is a possible way to determine the occurrence and burden of resistance in defined healthy human populations.
Recent developments in high‐throughput sequencing offer the ability to rapidly identify nucleic acids from various organisms in clinical and environmental samples. Sewage systems are recognized as an important source of human pathogens, especially in crowded settings with poor infrastructure.
The project will serve as proof‐of‐concept for applying metagenomic approaches, which could initiate a global surveillance of human infectious diseases including antimicrobial resistance from sewage collected in major cities around the world to detect, control, prevent and predict human infectious diseases.

Main researcher: Bram van Bunnik

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Global Surveillance of Antimicrobial Resistance

This project follows up on the Global Sewage Project mentioned above and will provide global longitudinal sampling of human sewage for metagenomic sequencing and quantification of antimicrobial resistance genes.

Main researcher: Bram van Bunnik

Selection and Transmission of Antimicrobial Resistance in Complex Systems

Selection and transmission are key determinants for the dissemination of antimicrobial resistance (AMR) across the planet. These determinants of AMR are frequently studied in laboratory settings while in reality they occur in complex systems, e.g. in microbial communities that colonize human and animal guts or in environmental ecosystems. The central aim of STARCS (Selection and Transmission of Antimicrobial Resistance in Complex Systems) is to characterize and quantify the processes of selection and transmission of AMR genes and drug-resistant bacteria in complex (eco)systems from a ‘One Health’ perspective and to integrate these elements into predictive mathematical models, which will be used to inform policy development.

Main researcher: Bram van Bunnik

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99 Households Study

It is often claimed that urbanization makes pathogen emergence more likely, but the underlying mechanisms are poorly understood. What characteristics of urban environments might predispose to an emergence event, and what is the contribution of livestock keeping to this process?
The 99 Household study is a cross sectional survey of households across socio-economic groups in Nairobi to isolate a diverse population of Escherichia coli (E. coli) bacteria from the city.
As part of this project we are working on understanding the quantitative evidence regarding the frequency and direction of the transmission of bacteria and their antimicrobial resistance determinants within and between human and livestock populations in Nairobi, Kenya.

Main researcher: Dishon Muloi

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