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• genetics, genomics and molecular biology
• infectious disease and the immune system
• bioengineering/medical devices

• Medicine
• Surgery
• Paediatrics
• Pathology
• Public Health

• Cardiac Surgery
• Gastroenterology
• Geriatric Medicine
• Infectious diseases
• Neonatology
• Nephrology
• Respiratory Medicine

Work in my laboratory comprises two main themes. The first involves microbial genomics. We use sequence-based typing to study the epidemiology of infections [1, 2] and the evolution of pathogens [3?4]. We also work on internal bacterial structures whose widespread existence has been revealed by genome sequencing ? bacterial microcompartments. About 30 % of sequenced bacterial genomes contain operons specifying enzyme-packed bacterial microcompartments [5, 6] conferring additional metabolic capacity. We are applying genomics to understand the functional principles of these structures and the advantages they confer on their hosts.

The second theme is a collaboration funded by the Healthcare Infection Society (UK) with Professors John Sodeau and John Wenger of the Centre for Research in Atmospheric Chemistry at UCC and Professor Barry Plant, Director, Adult Cystic Fibrosis Centre, Cork University Hospital to apply a ?smart? particle detector proven to measure bioaerosols in outdoor air [7] to measure indoor air quality and risks of airborne infection in hospitals.

References (PubMed ID)
1. 20637901
2. 26072272
3. 27221796
4. 27618184
5. 27296169
6. 22982517
7. 25987290

Potential Research Project 1

Bacterial microcompartment metabolism in urinary tract infection.

Microcompartment-mediated metabolism of small carbon compounds allows Enterobacterial pathogens (including E.coli) to outcompete commensal bacteria during acute enteric infection. While E. coli is known to change from fucose metabolism and glycolysis in commensal growth in the gut to amino acid catabolism and gluconeogenesis in urinary tract infection, published RNAseq studies suggest the ethanolamine utilisation (Eut) microcompartment operon is induced in both niches. With preliminary funding from the APC Microbiome Institute we confirmed E. coli Eut operon mRNA transcription by RT-PCR in approximately 13% of unselected (i.e. not prescreened as E. coli) infected urine samples. The project will apply a variety of in vivo and in vitro strategies including RNASeq to explore the role of microcompartment-mediated metabolism in urinary tract infection. Host-microbe interaction effects of Eut operon induction (host microRNA and cytokine expression) will be studied in collaboration with Dr John MacSharry, Lecturer in Molecular Microbiology.

Potential Research Project 2

WIBS and Healthcare Infection
The Waveband Integrated Bioaerosol Sensor (WIBS-4) is a portable (13.6 kg) continuous monitoring instrument detecting biological particles by auto-fluorescence, coupled with time-of-flight measurements and spatial light scattering analysis of shape. Preliminary WIBS data we have obtained from different hospitals has shown the expected biological particle gradient decrease from ward to plenum ventilated operating theatre to ultraclean operating theatre and has detected aerosol production from clinical appliances. In this project the student will use WIBS to assess the effect of empirical air cleaning measures, compare WIBS with other similar machines appearing in this rapidly developing field, or exploring non-culture based molecular methods to identify the bacteria and fungi that WIBS is detecting.