Modelling Gut Pathogen - Commensal
Interactions
GAMIDI (WP7)/ ER-3/C2/C3
Gerard Fleming
CHEMOSTAT TECHNOLOGY LABORATORY
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Postgraduate Students:
 Paul Mc Cay (completing Ph.D.)
 David Mc Carthy (completing Ph.D.)
 Maurice Martyn (starting part-time M.Sc.)
 Olivia Duignan (Ph.D. with Dr. Carroll)
Post-Doctoral Investigator:
 Dr. Alain A. Ocampo Sosa (joined Nov ’07)
 Deep-Ocean Post Doc – February 08
Strategic Areas of Research
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Microbial Evolution in Continuous Cultures
 Mutation, selection and competition in single-stage
chemostats
 Microbial adaptation to selection pressures
Deep Ocean Microbiology
 Keystone metabolically active microorganisms
 Laboratory culture of obligate piezophiles
Aquaculture/ Bioaerosols
 Method validation: Antimicrobial Susceptibility Testing
 Novel biocides for the aquaculture sector
 Endotoxin levels in bioaerosols
GAMIDI (WP7)
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The Pathogens:
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The Commensals:
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Campylobacter jejuni, Salmonella enterica, and
Listeria monocytogenes
Escherichia coli, Bacteroides spp., Lactic acid
bacteria
Why Continuous Culture ?
 Plug /continuous flow
 Extended period of culture
 Competition exclusion
 Mutation and selection
Mutation / Selection in Practice: P. aeruginosa adaptation to biocide
BKC MIC
250
150
-1
BKC (mg l )
200
100
50
0
0
50
100
Generations elapsed
BKC Conc supplemented in culture
Population MIC (BKC)
146
The Work Package
Population level
 Colonisation / exclusion
rates in single and multistage chemostats +/Matrices
 Efficacy of clinical and
sub-clinical levels of
antibiotics on microbial
persistence
 Influence of growth
conditions on competitive
indices
 Modelling of competition
dynamics
Molecular level
 Adherence / exclusion
influences
 Nature of Intrinsic /
acquired mutations
resulting in enhanced
competitiveness
 Gene regulation with
particular reference to
MDR efflux pumps
Needs/ Collaborations
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Mathematical Modelling Capability
 Dr. Saji Varghese (Physics) and other
collaborators
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Molecular Analysis
 Genetic analysis of mutants and capability to
make “knock-out” mutants
 Microarray analysis up/down regulation of
genes
 Molecular analysis at the protein level
 FISH